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<s>[INST]<<SYS>>
Your task is to determine the relationship between a chemical CAA and a gene or protein cathepsin B in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Bind', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a chemical leads to higher gene expression, or higher gene expression increases sensitivity to the chemical, or a gene variant exacerbates the chemical's side effects, or a gene causes an over-response to the chemical, or there is a positive interaction between two genes in any manner.
'Negative_Correlation' indicates that a chemical leads to reduced gene expression, or higher gene expression results in decreased sensitivity or resistance to the chemical, or a gene variant offers protection against the chemical's adverse effects, or a gene contributes to resistance against the chemical, or there exists a negative interaction between two genes in any form.
'Bind' means that a chemical either connects to a gene's promoter region or a protein acts as a receptor for that chemical.
'Association' is used to describe relation that don't clearly fall under categories like positive correlation, negative correlation and bind , or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[CAA,ChemicalEntity]' and '[cathepsin B,GeneOrGeneProduct]'.
- Title of the Paper: Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy.
- Abstract of the Paper: [Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients.]
Identify how '[CAA,ChemicalEntity]' and '[cathepsin B,GeneOrGeneProduct]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Bind', 'Association']. [/INST]Negative_Correlation</s> | Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy. | Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients. | {
"name": "CAA",
"type": "ChemicalEntity"
} | {
"name": "cathepsin B",
"type": "GeneOrGeneProduct"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Bind",
"Association"
] | Negative_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a chemical CAA and a gene or protein caspase-8 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Bind', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a chemical leads to higher gene expression, or higher gene expression increases sensitivity to the chemical, or a gene variant exacerbates the chemical's side effects, or a gene causes an over-response to the chemical, or there is a positive interaction between two genes in any manner.
'Negative_Correlation' indicates that a chemical leads to reduced gene expression, or higher gene expression results in decreased sensitivity or resistance to the chemical, or a gene variant offers protection against the chemical's adverse effects, or a gene contributes to resistance against the chemical, or there exists a negative interaction between two genes in any form.
'Bind' means that a chemical either connects to a gene's promoter region or a protein acts as a receptor for that chemical.
'Association' is used to describe relation that don't clearly fall under categories like positive correlation, negative correlation and bind , or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[CAA,ChemicalEntity]' and '[caspase-8,GeneOrGeneProduct]'.
- Title of the Paper: Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy.
- Abstract of the Paper: [Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients.]
Identify how '[CAA,ChemicalEntity]' and '[caspase-8,GeneOrGeneProduct]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Bind', 'Association']. [/INST]Negative_Correlation</s> | Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy. | Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients. | {
"name": "CAA",
"type": "ChemicalEntity"
} | {
"name": "caspase-8",
"type": "GeneOrGeneProduct"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Bind",
"Association"
] | Negative_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a chemical CAA and a gene or protein caspase-3 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Bind', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a chemical leads to higher gene expression, or higher gene expression increases sensitivity to the chemical, or a gene variant exacerbates the chemical's side effects, or a gene causes an over-response to the chemical, or there is a positive interaction between two genes in any manner.
'Negative_Correlation' indicates that a chemical leads to reduced gene expression, or higher gene expression results in decreased sensitivity or resistance to the chemical, or a gene variant offers protection against the chemical's adverse effects, or a gene contributes to resistance against the chemical, or there exists a negative interaction between two genes in any form.
'Bind' means that a chemical either connects to a gene's promoter region or a protein acts as a receptor for that chemical.
'Association' is used to describe relation that don't clearly fall under categories like positive correlation, negative correlation and bind , or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[CAA,ChemicalEntity]' and '[caspase-3,GeneOrGeneProduct]'.
- Title of the Paper: Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy.
- Abstract of the Paper: [Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients.]
Identify how '[CAA,ChemicalEntity]' and '[caspase-3,GeneOrGeneProduct]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Bind', 'Association']. [/INST]Negative_Correlation</s> | Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy. | Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients. | {
"name": "CAA",
"type": "ChemicalEntity"
} | {
"name": "caspase-3",
"type": "GeneOrGeneProduct"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Bind",
"Association"
] | Negative_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a chemical CAA and a disease necrosis in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means there's a direct link between a chemical and a disease. This includes cases where the chemical causes the disease, higher doses of the chemical increase disease risk, the disease raises the chemical's level in the body, there's a direct positive link between the chemical's level and disease risk, or exposure to the chemical during development affects disease susceptibility later on.
'Negative_Correlation' means there's an inverse relation between a chemical substance and a disease. This includes situations where the chemical or drug is used to treat the disease, the presence of the disease lowers the level of the chemical in the body, or the chemical or drug reduces the likelihood of the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[CAA,ChemicalEntity]' and '[necrosis,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy.
- Abstract of the Paper: [Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients.]
Identify how '[CAA,ChemicalEntity]' and '[necrosis,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy. | Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients. | {
"name": "CAA",
"type": "ChemicalEntity"
} | {
"name": "necrosis",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a chemical CAA and a chemical thiols in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Drug_Interaction', 'Cotreatment', 'Conversion', 'Comparison', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' indicates that Chemical A increases the effectiveness of Chemical B. This includes making Chemical B more sensitive, enhancing its ability to treat or induce a disease, or boosting its role in gene activation.
'Negative_Correlation' means that Chemical A reduces the effectiveness and impact of Chemical B. This includes decreasing Chemical B's sensitivity, reducing its ability to treat or induce a disease, diminishing its side effects, and lowering the gene activation it causes.
'Drug_Interaction' is when two different drugs or chemicals affect each other's action in the body, happening when they are used at the same time.
'Cotreatment' means that two different drugs or chemicals are used in combination therapy.
'Conversion' means that one chemical changes into another chemical.
'Comparison' means that two different drugs or chemicals have some differences and similarities in their effects.
'Association' refers to the relation between two chemicals that do not fit into any specific, predefined categories of relations.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[CAA,ChemicalEntity]' and '[thiols,ChemicalEntity]'.
- Title of the Paper: Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy.
- Abstract of the Paper: [Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients.]
Identify how '[CAA,ChemicalEntity]' and '[thiols,ChemicalEntity]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Drug_Interaction', 'Cotreatment', 'Conversion', 'Comparison', 'Association']. [/INST]Negative_Correlation</s> | Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy. | Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients. | {
"name": "CAA",
"type": "ChemicalEntity"
} | {
"name": "thiols",
"type": "ChemicalEntity"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Drug_Interaction",
"Cotreatment",
"Conversion",
"Comparison",
"Association"
] | Negative_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a chemical Chloroacetaldehyde and a disease nephropathy in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means there's a direct link between a chemical and a disease. This includes cases where the chemical causes the disease, higher doses of the chemical increase disease risk, the disease raises the chemical's level in the body, there's a direct positive link between the chemical's level and disease risk, or exposure to the chemical during development affects disease susceptibility later on.
'Negative_Correlation' means there's an inverse relation between a chemical substance and a disease. This includes situations where the chemical or drug is used to treat the disease, the presence of the disease lowers the level of the chemical in the body, or the chemical or drug reduces the likelihood of the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[Chloroacetaldehyde,ChemicalEntity]' and '[nephropathy,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy.
- Abstract of the Paper: [Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients.]
Identify how '[Chloroacetaldehyde,ChemicalEntity]' and '[nephropathy,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy. | Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients. | {
"name": "Chloroacetaldehyde",
"type": "ChemicalEntity"
} | {
"name": "nephropathy",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease nephropathy and a chemical ifosfamide in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means there's a direct link between a chemical and a disease. This includes cases where the chemical causes the disease, higher doses of the chemical increase disease risk, the disease raises the chemical's level in the body, there's a direct positive link between the chemical's level and disease risk, or exposure to the chemical during development affects disease susceptibility later on.
'Negative_Correlation' means there's an inverse relation between a chemical substance and a disease. This includes situations where the chemical or drug is used to treat the disease, the presence of the disease lowers the level of the chemical in the body, or the chemical or drug reduces the likelihood of the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[nephropathy,DiseaseOrPhenotypicFeature]' and '[ifosfamide,ChemicalEntity]'.
- Title of the Paper: Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy.
- Abstract of the Paper: [Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients.]
Identify how '[nephropathy,DiseaseOrPhenotypicFeature]' and '[ifosfamide,ChemicalEntity]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy. | Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients. | {
"name": "nephropathy",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "ifosfamide",
"type": "ChemicalEntity"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease tumor and a chemical IFO in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means there's a direct link between a chemical and a disease. This includes cases where the chemical causes the disease, higher doses of the chemical increase disease risk, the disease raises the chemical's level in the body, there's a direct positive link between the chemical's level and disease risk, or exposure to the chemical during development affects disease susceptibility later on.
'Negative_Correlation' means there's an inverse relation between a chemical substance and a disease. This includes situations where the chemical or drug is used to treat the disease, the presence of the disease lowers the level of the chemical in the body, or the chemical or drug reduces the likelihood of the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[tumor,DiseaseOrPhenotypicFeature]' and '[IFO,ChemicalEntity]'.
- Title of the Paper: Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy.
- Abstract of the Paper: [Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients.]
Identify how '[tumor,DiseaseOrPhenotypicFeature]' and '[IFO,ChemicalEntity]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Negative_Correlation</s> | Chloroacetaldehyde as a sulfhydryl reagent: the role of critical thiol groups in ifosfamide nephropathy. | Chloroacetaldehyde (CAA) is a metabolite of the alkylating agent ifosfamide (IFO) and putatively responsible for renal damage following anti-tumor therapy with IFO. Depletion of sulfhydryl (SH) groups has been reported from cell culture, animal and clinical studies. In this work the effect of CAA on human proximal tubule cells in primary culture (hRPTEC) was investigated. Toxicity of CAA was determined by protein content, cell number, LDH release, trypan blue exclusion assay and caspase-3 activity. Free thiols were measured by the method of Ellman. CAA reduced hRPTEC cell number and protein, induced a loss in free intracellular thiols and an increase in necrosis markers. CAA but not acrolein inhibited the cysteine proteases caspase-3, caspase-8 and cathepsin B. Caspase activation by cisplatin was inhibited by CAA. In cells stained with fluorescent dyes targeting lysosomes, CAA induced an increase in lysosomal size and lysosomal leakage. The effects of CAA on cysteine protease activities and thiols could be reproduced in cell lysate. Acidification, which slowed the reaction of CAA with thiol donors, could also attenuate effects of CAA on necrosis markers, thiol depletion and cysteine protease inhibition in living cells. Thus, CAA directly reacts with cellular protein and non-protein thiols, mediating its toxicity on hRPTEC. This effect can be reduced by acidification. Therefore, urinary acidification could be an option to prevent IFO nephropathy in patients. | {
"name": "tumor",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "IFO",
"type": "ChemicalEntity"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Negative_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a chemical phenylephrine and a disease hypertensive in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means there's a direct link between a chemical and a disease. This includes cases where the chemical causes the disease, higher doses of the chemical increase disease risk, the disease raises the chemical's level in the body, there's a direct positive link between the chemical's level and disease risk, or exposure to the chemical during development affects disease susceptibility later on.
'Negative_Correlation' means there's an inverse relation between a chemical substance and a disease. This includes situations where the chemical or drug is used to treat the disease, the presence of the disease lowers the level of the chemical in the body, or the chemical or drug reduces the likelihood of the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[phenylephrine,ChemicalEntity]' and '[hypertensive,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Delayed institution of hypertension during focal cerebral ischemia: effect on brain edema.
- Abstract of the Paper: [The effect of induced hypertension instituted after a 2-h delay following middle cerebral artery occlusion (MCAO) on brain edema formation and histochemical injury was studied. Under isoflurane anesthesia, the MCA of 14 spontaneously hypertensive rats was occluded. In the control group (n = 7), the mean arterial pressure (MAP) was not manipulated. In the hypertensive group (n = 7), the MAP was elevated by 25-30 mm Hg beginning 2 h after MCAO. Four hours after MCAO, the rats were killed and the brains harvested. The brains were sectioned along coronal planes spanning the distribution of ischemia produced by MCAO. Specific gravity (SG) was determined in the subcortex and in two sites in the cortex (core and periphery of the ischemic territory). The extent of neuronal injury was determined by 2,3,5-triphenyltetrazolium staining. In the ischemic core, there was no difference in SG in the subcortex and cortex in the two groups. In the periphery of the ischemic territory, SG in the cortex was greater (less edema accumulation) in the hypertensive group (1.041 +/- 0.001 vs 1.039 +/- 0.001, P less than 0.05). The area of histochemical injury (as a percent of the cross-sectional area of the hemisphere) was less in the hypertensive group (33 +/- 3% vs 21 +/- 2%, P less than 0.05). The data indicate that phenylephrine-induced hypertension instituted 2 h after MCAO does not aggravate edema in the ischemic core, that it improves edema in the periphery of the ischemic territory, and that it reduces the area of histochemical neuronal dysfunction.]
Identify how '[phenylephrine,ChemicalEntity]' and '[hypertensive,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Delayed institution of hypertension during focal cerebral ischemia: effect on brain edema. | The effect of induced hypertension instituted after a 2-h delay following middle cerebral artery occlusion (MCAO) on brain edema formation and histochemical injury was studied. Under isoflurane anesthesia, the MCA of 14 spontaneously hypertensive rats was occluded. In the control group (n = 7), the mean arterial pressure (MAP) was not manipulated. In the hypertensive group (n = 7), the MAP was elevated by 25-30 mm Hg beginning 2 h after MCAO. Four hours after MCAO, the rats were killed and the brains harvested. The brains were sectioned along coronal planes spanning the distribution of ischemia produced by MCAO. Specific gravity (SG) was determined in the subcortex and in two sites in the cortex (core and periphery of the ischemic territory). The extent of neuronal injury was determined by 2,3,5-triphenyltetrazolium staining. In the ischemic core, there was no difference in SG in the subcortex and cortex in the two groups. In the periphery of the ischemic territory, SG in the cortex was greater (less edema accumulation) in the hypertensive group (1.041 +/- 0.001 vs 1.039 +/- 0.001, P less than 0.05). The area of histochemical injury (as a percent of the cross-sectional area of the hemisphere) was less in the hypertensive group (33 +/- 3% vs 21 +/- 2%, P less than 0.05). The data indicate that phenylephrine-induced hypertension instituted 2 h after MCAO does not aggravate edema in the ischemic core, that it improves edema in the periphery of the ischemic territory, and that it reduces the area of histochemical neuronal dysfunction. | {
"name": "phenylephrine",
"type": "ChemicalEntity"
} | {
"name": "hypertensive",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein PEMT and a disease NASH in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[PEMT,GeneOrGeneProduct]' and '[NASH,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: The phosphatidylethanolamine N-methyltransferase gene V175M single nucleotide polymorphism confers the susceptibility to NASH in Japanese population.
- Abstract of the Paper: [BACKGROUND/AIMS: The genetic predisposition on the development of nonalcoholic steatohepatitis (NASH) has been poorly understood. A functional polymorphism Val175Met was reported in phosphatidylethanolamine N-methyltransferase (PEMT) that catalyzes the conversion of phosphatidylethanolamine to phosphatidylcholine. The aim of this study was to investigate whether the carriers of Val175Met variant impaired in PEMT activity are more susceptible to NASH. METHODS: Blood samples of 107 patients with biopsy-proven NASH and of 150 healthy volunteers were analyzed by the polymerase chain reaction (PCR) and restriction fragment length polymorphism. RESULTS: Val175Met variant allele of the PEMT gene was significantly more frequent in NASH patients than in healthy volunteers (p<0.001), and carriers of Val175Met variant were significantly more frequent in NASH patients than in healthy volunteers (p<0.01). Among NASH patients, body mass index was significantly lower (p<0.05), and non-obese patients were significantly more frequent (p<0.001) in carriers of Val175Met variant than in homozygotes of wild type PEMT. CONCLUSIONS: Val175Met variant of PEMT could be a candidate molecule that determines the susceptibility to NASH, because it is more frequently observed in NASH patients and non-obese persons with Val175Met variant of PEMT are facilitated to develop NASH.]
Identify how '[PEMT,GeneOrGeneProduct]' and '[NASH,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | The phosphatidylethanolamine N-methyltransferase gene V175M single nucleotide polymorphism confers the susceptibility to NASH in Japanese population. | BACKGROUND/AIMS: The genetic predisposition on the development of nonalcoholic steatohepatitis (NASH) has been poorly understood. A functional polymorphism Val175Met was reported in phosphatidylethanolamine N-methyltransferase (PEMT) that catalyzes the conversion of phosphatidylethanolamine to phosphatidylcholine. The aim of this study was to investigate whether the carriers of Val175Met variant impaired in PEMT activity are more susceptible to NASH. METHODS: Blood samples of 107 patients with biopsy-proven NASH and of 150 healthy volunteers were analyzed by the polymerase chain reaction (PCR) and restriction fragment length polymorphism. RESULTS: Val175Met variant allele of the PEMT gene was significantly more frequent in NASH patients than in healthy volunteers (p<0.001), and carriers of Val175Met variant were significantly more frequent in NASH patients than in healthy volunteers (p<0.01). Among NASH patients, body mass index was significantly lower (p<0.05), and non-obese patients were significantly more frequent (p<0.001) in carriers of Val175Met variant than in homozygotes of wild type PEMT. CONCLUSIONS: Val175Met variant of PEMT could be a candidate molecule that determines the susceptibility to NASH, because it is more frequently observed in NASH patients and non-obese persons with Val175Met variant of PEMT are facilitated to develop NASH. | {
"name": "PEMT",
"type": "GeneOrGeneProduct"
} | {
"name": "NASH",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a chemical phosphatidylethanolamine and a chemical phosphatidylcholine in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Drug_Interaction', 'Cotreatment', 'Conversion', 'Comparison', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' indicates that Chemical A increases the effectiveness of Chemical B. This includes making Chemical B more sensitive, enhancing its ability to treat or induce a disease, or boosting its role in gene activation.
'Negative_Correlation' means that Chemical A reduces the effectiveness and impact of Chemical B. This includes decreasing Chemical B's sensitivity, reducing its ability to treat or induce a disease, diminishing its side effects, and lowering the gene activation it causes.
'Drug_Interaction' is when two different drugs or chemicals affect each other's action in the body, happening when they are used at the same time.
'Cotreatment' means that two different drugs or chemicals are used in combination therapy.
'Conversion' means that one chemical changes into another chemical.
'Comparison' means that two different drugs or chemicals have some differences and similarities in their effects.
'Association' refers to the relation between two chemicals that do not fit into any specific, predefined categories of relations.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[phosphatidylethanolamine,ChemicalEntity]' and '[phosphatidylcholine,ChemicalEntity]'.
- Title of the Paper: The phosphatidylethanolamine N-methyltransferase gene V175M single nucleotide polymorphism confers the susceptibility to NASH in Japanese population.
- Abstract of the Paper: [BACKGROUND/AIMS: The genetic predisposition on the development of nonalcoholic steatohepatitis (NASH) has been poorly understood. A functional polymorphism Val175Met was reported in phosphatidylethanolamine N-methyltransferase (PEMT) that catalyzes the conversion of phosphatidylethanolamine to phosphatidylcholine. The aim of this study was to investigate whether the carriers of Val175Met variant impaired in PEMT activity are more susceptible to NASH. METHODS: Blood samples of 107 patients with biopsy-proven NASH and of 150 healthy volunteers were analyzed by the polymerase chain reaction (PCR) and restriction fragment length polymorphism. RESULTS: Val175Met variant allele of the PEMT gene was significantly more frequent in NASH patients than in healthy volunteers (p<0.001), and carriers of Val175Met variant were significantly more frequent in NASH patients than in healthy volunteers (p<0.01). Among NASH patients, body mass index was significantly lower (p<0.05), and non-obese patients were significantly more frequent (p<0.001) in carriers of Val175Met variant than in homozygotes of wild type PEMT. CONCLUSIONS: Val175Met variant of PEMT could be a candidate molecule that determines the susceptibility to NASH, because it is more frequently observed in NASH patients and non-obese persons with Val175Met variant of PEMT are facilitated to develop NASH.]
Identify how '[phosphatidylethanolamine,ChemicalEntity]' and '[phosphatidylcholine,ChemicalEntity]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Drug_Interaction', 'Cotreatment', 'Conversion', 'Comparison', 'Association']. [/INST]Conversion</s> | The phosphatidylethanolamine N-methyltransferase gene V175M single nucleotide polymorphism confers the susceptibility to NASH in Japanese population. | BACKGROUND/AIMS: The genetic predisposition on the development of nonalcoholic steatohepatitis (NASH) has been poorly understood. A functional polymorphism Val175Met was reported in phosphatidylethanolamine N-methyltransferase (PEMT) that catalyzes the conversion of phosphatidylethanolamine to phosphatidylcholine. The aim of this study was to investigate whether the carriers of Val175Met variant impaired in PEMT activity are more susceptible to NASH. METHODS: Blood samples of 107 patients with biopsy-proven NASH and of 150 healthy volunteers were analyzed by the polymerase chain reaction (PCR) and restriction fragment length polymorphism. RESULTS: Val175Met variant allele of the PEMT gene was significantly more frequent in NASH patients than in healthy volunteers (p<0.001), and carriers of Val175Met variant were significantly more frequent in NASH patients than in healthy volunteers (p<0.01). Among NASH patients, body mass index was significantly lower (p<0.05), and non-obese patients were significantly more frequent (p<0.001) in carriers of Val175Met variant than in homozygotes of wild type PEMT. CONCLUSIONS: Val175Met variant of PEMT could be a candidate molecule that determines the susceptibility to NASH, because it is more frequently observed in NASH patients and non-obese persons with Val175Met variant of PEMT are facilitated to develop NASH. | {
"name": "phosphatidylethanolamine",
"type": "ChemicalEntity"
} | {
"name": "phosphatidylcholine",
"type": "ChemicalEntity"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Drug_Interaction",
"Cotreatment",
"Conversion",
"Comparison",
"Association"
] | Conversion |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant Val175Met and a chemical phosphatidylcholine in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' suggests a mutual reinforcement between genetic variations and chemicals. This includes the chemical causing increased gene expression because of the variant, the variant increasing the body's sensitivity to the chemical, the variant causing a stronger reaction to the chemical, or any other type of positive relation between the variant and the chemical.
'Negative_Correlation' means a gene variant weakens the effect of a chemical. Thisinclude when the variant causes less gene activity due to the chemical, makes the body less responsive to the chemical, creates resistance to the chemical, or shows any decrease in interaction between the gene and the chemical.
'Association' indicates that the relation between a chemical and gene variations cannot be clearly defined as either positive or negative correlation.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[Val175Met,SequenceVariant]' and '[phosphatidylcholine,ChemicalEntity]'.
- Title of the Paper: The phosphatidylethanolamine N-methyltransferase gene V175M single nucleotide polymorphism confers the susceptibility to NASH in Japanese population.
- Abstract of the Paper: [BACKGROUND/AIMS: The genetic predisposition on the development of nonalcoholic steatohepatitis (NASH) has been poorly understood. A functional polymorphism Val175Met was reported in phosphatidylethanolamine N-methyltransferase (PEMT) that catalyzes the conversion of phosphatidylethanolamine to phosphatidylcholine. The aim of this study was to investigate whether the carriers of Val175Met variant impaired in PEMT activity are more susceptible to NASH. METHODS: Blood samples of 107 patients with biopsy-proven NASH and of 150 healthy volunteers were analyzed by the polymerase chain reaction (PCR) and restriction fragment length polymorphism. RESULTS: Val175Met variant allele of the PEMT gene was significantly more frequent in NASH patients than in healthy volunteers (p<0.001), and carriers of Val175Met variant were significantly more frequent in NASH patients than in healthy volunteers (p<0.01). Among NASH patients, body mass index was significantly lower (p<0.05), and non-obese patients were significantly more frequent (p<0.001) in carriers of Val175Met variant than in homozygotes of wild type PEMT. CONCLUSIONS: Val175Met variant of PEMT could be a candidate molecule that determines the susceptibility to NASH, because it is more frequently observed in NASH patients and non-obese persons with Val175Met variant of PEMT are facilitated to develop NASH.]
Identify how '[Val175Met,SequenceVariant]' and '[phosphatidylcholine,ChemicalEntity]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | The phosphatidylethanolamine N-methyltransferase gene V175M single nucleotide polymorphism confers the susceptibility to NASH in Japanese population. | BACKGROUND/AIMS: The genetic predisposition on the development of nonalcoholic steatohepatitis (NASH) has been poorly understood. A functional polymorphism Val175Met was reported in phosphatidylethanolamine N-methyltransferase (PEMT) that catalyzes the conversion of phosphatidylethanolamine to phosphatidylcholine. The aim of this study was to investigate whether the carriers of Val175Met variant impaired in PEMT activity are more susceptible to NASH. METHODS: Blood samples of 107 patients with biopsy-proven NASH and of 150 healthy volunteers were analyzed by the polymerase chain reaction (PCR) and restriction fragment length polymorphism. RESULTS: Val175Met variant allele of the PEMT gene was significantly more frequent in NASH patients than in healthy volunteers (p<0.001), and carriers of Val175Met variant were significantly more frequent in NASH patients than in healthy volunteers (p<0.01). Among NASH patients, body mass index was significantly lower (p<0.05), and non-obese patients were significantly more frequent (p<0.001) in carriers of Val175Met variant than in homozygotes of wild type PEMT. CONCLUSIONS: Val175Met variant of PEMT could be a candidate molecule that determines the susceptibility to NASH, because it is more frequently observed in NASH patients and non-obese persons with Val175Met variant of PEMT are facilitated to develop NASH. | {
"name": "Val175Met",
"type": "SequenceVariant"
} | {
"name": "phosphatidylcholine",
"type": "ChemicalEntity"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant Val175Met and a chemical phosphatidylethanolamine in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' suggests a mutual reinforcement between genetic variations and chemicals. This includes the chemical causing increased gene expression because of the variant, the variant increasing the body's sensitivity to the chemical, the variant causing a stronger reaction to the chemical, or any other type of positive relation between the variant and the chemical.
'Negative_Correlation' means a gene variant weakens the effect of a chemical. Thisinclude when the variant causes less gene activity due to the chemical, makes the body less responsive to the chemical, creates resistance to the chemical, or shows any decrease in interaction between the gene and the chemical.
'Association' indicates that the relation between a chemical and gene variations cannot be clearly defined as either positive or negative correlation.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[Val175Met,SequenceVariant]' and '[phosphatidylethanolamine,ChemicalEntity]'.
- Title of the Paper: The phosphatidylethanolamine N-methyltransferase gene V175M single nucleotide polymorphism confers the susceptibility to NASH in Japanese population.
- Abstract of the Paper: [BACKGROUND/AIMS: The genetic predisposition on the development of nonalcoholic steatohepatitis (NASH) has been poorly understood. A functional polymorphism Val175Met was reported in phosphatidylethanolamine N-methyltransferase (PEMT) that catalyzes the conversion of phosphatidylethanolamine to phosphatidylcholine. The aim of this study was to investigate whether the carriers of Val175Met variant impaired in PEMT activity are more susceptible to NASH. METHODS: Blood samples of 107 patients with biopsy-proven NASH and of 150 healthy volunteers were analyzed by the polymerase chain reaction (PCR) and restriction fragment length polymorphism. RESULTS: Val175Met variant allele of the PEMT gene was significantly more frequent in NASH patients than in healthy volunteers (p<0.001), and carriers of Val175Met variant were significantly more frequent in NASH patients than in healthy volunteers (p<0.01). Among NASH patients, body mass index was significantly lower (p<0.05), and non-obese patients were significantly more frequent (p<0.001) in carriers of Val175Met variant than in homozygotes of wild type PEMT. CONCLUSIONS: Val175Met variant of PEMT could be a candidate molecule that determines the susceptibility to NASH, because it is more frequently observed in NASH patients and non-obese persons with Val175Met variant of PEMT are facilitated to develop NASH.]
Identify how '[Val175Met,SequenceVariant]' and '[phosphatidylethanolamine,ChemicalEntity]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | The phosphatidylethanolamine N-methyltransferase gene V175M single nucleotide polymorphism confers the susceptibility to NASH in Japanese population. | BACKGROUND/AIMS: The genetic predisposition on the development of nonalcoholic steatohepatitis (NASH) has been poorly understood. A functional polymorphism Val175Met was reported in phosphatidylethanolamine N-methyltransferase (PEMT) that catalyzes the conversion of phosphatidylethanolamine to phosphatidylcholine. The aim of this study was to investigate whether the carriers of Val175Met variant impaired in PEMT activity are more susceptible to NASH. METHODS: Blood samples of 107 patients with biopsy-proven NASH and of 150 healthy volunteers were analyzed by the polymerase chain reaction (PCR) and restriction fragment length polymorphism. RESULTS: Val175Met variant allele of the PEMT gene was significantly more frequent in NASH patients than in healthy volunteers (p<0.001), and carriers of Val175Met variant were significantly more frequent in NASH patients than in healthy volunteers (p<0.01). Among NASH patients, body mass index was significantly lower (p<0.05), and non-obese patients were significantly more frequent (p<0.001) in carriers of Val175Met variant than in homozygotes of wild type PEMT. CONCLUSIONS: Val175Met variant of PEMT could be a candidate molecule that determines the susceptibility to NASH, because it is more frequently observed in NASH patients and non-obese persons with Val175Met variant of PEMT are facilitated to develop NASH. | {
"name": "Val175Met",
"type": "SequenceVariant"
} | {
"name": "phosphatidylethanolamine",
"type": "ChemicalEntity"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant V175M and a disease NASH in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[V175M,SequenceVariant]' and '[NASH,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: The phosphatidylethanolamine N-methyltransferase gene V175M single nucleotide polymorphism confers the susceptibility to NASH in Japanese population.
- Abstract of the Paper: [BACKGROUND/AIMS: The genetic predisposition on the development of nonalcoholic steatohepatitis (NASH) has been poorly understood. A functional polymorphism Val175Met was reported in phosphatidylethanolamine N-methyltransferase (PEMT) that catalyzes the conversion of phosphatidylethanolamine to phosphatidylcholine. The aim of this study was to investigate whether the carriers of Val175Met variant impaired in PEMT activity are more susceptible to NASH. METHODS: Blood samples of 107 patients with biopsy-proven NASH and of 150 healthy volunteers were analyzed by the polymerase chain reaction (PCR) and restriction fragment length polymorphism. RESULTS: Val175Met variant allele of the PEMT gene was significantly more frequent in NASH patients than in healthy volunteers (p<0.001), and carriers of Val175Met variant were significantly more frequent in NASH patients than in healthy volunteers (p<0.01). Among NASH patients, body mass index was significantly lower (p<0.05), and non-obese patients were significantly more frequent (p<0.001) in carriers of Val175Met variant than in homozygotes of wild type PEMT. CONCLUSIONS: Val175Met variant of PEMT could be a candidate molecule that determines the susceptibility to NASH, because it is more frequently observed in NASH patients and non-obese persons with Val175Met variant of PEMT are facilitated to develop NASH.]
Identify how '[V175M,SequenceVariant]' and '[NASH,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | The phosphatidylethanolamine N-methyltransferase gene V175M single nucleotide polymorphism confers the susceptibility to NASH in Japanese population. | BACKGROUND/AIMS: The genetic predisposition on the development of nonalcoholic steatohepatitis (NASH) has been poorly understood. A functional polymorphism Val175Met was reported in phosphatidylethanolamine N-methyltransferase (PEMT) that catalyzes the conversion of phosphatidylethanolamine to phosphatidylcholine. The aim of this study was to investigate whether the carriers of Val175Met variant impaired in PEMT activity are more susceptible to NASH. METHODS: Blood samples of 107 patients with biopsy-proven NASH and of 150 healthy volunteers were analyzed by the polymerase chain reaction (PCR) and restriction fragment length polymorphism. RESULTS: Val175Met variant allele of the PEMT gene was significantly more frequent in NASH patients than in healthy volunteers (p<0.001), and carriers of Val175Met variant were significantly more frequent in NASH patients than in healthy volunteers (p<0.01). Among NASH patients, body mass index was significantly lower (p<0.05), and non-obese patients were significantly more frequent (p<0.001) in carriers of Val175Met variant than in homozygotes of wild type PEMT. CONCLUSIONS: Val175Met variant of PEMT could be a candidate molecule that determines the susceptibility to NASH, because it is more frequently observed in NASH patients and non-obese persons with Val175Met variant of PEMT are facilitated to develop NASH. | {
"name": "V175M",
"type": "SequenceVariant"
} | {
"name": "NASH",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant rs1155974 and a disease adiposity in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[rs1155974,SequenceVariant]' and '[adiposity,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[rs1155974,SequenceVariant]' and '[adiposity,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "rs1155974",
"type": "SequenceVariant"
} | {
"name": "adiposity",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant rs2073162 and a disease T2D in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[rs2073162,SequenceVariant]' and '[T2D,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[rs2073162,SequenceVariant]' and '[T2D,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "rs2073162",
"type": "SequenceVariant"
} | {
"name": "T2D",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant rs2073162 and a disease adiposity in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[rs2073162,SequenceVariant]' and '[adiposity,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[rs2073162,SequenceVariant]' and '[adiposity,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "rs2073162",
"type": "SequenceVariant"
} | {
"name": "adiposity",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant rs1155794 and a disease T2D in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[rs1155794,SequenceVariant]' and '[T2D,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[rs1155794,SequenceVariant]' and '[T2D,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "rs1155794",
"type": "SequenceVariant"
} | {
"name": "T2D",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease T2D and a variant rs1155974 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[T2D,DiseaseOrPhenotypicFeature]' and '[rs1155974,SequenceVariant]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[T2D,DiseaseOrPhenotypicFeature]' and '[rs1155974,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "T2D",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "rs1155974",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease type 2 diabetes and a chemical glucose in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means there's a direct link between a chemical and a disease. This includes cases where the chemical causes the disease, higher doses of the chemical increase disease risk, the disease raises the chemical's level in the body, there's a direct positive link between the chemical's level and disease risk, or exposure to the chemical during development affects disease susceptibility later on.
'Negative_Correlation' means there's an inverse relation between a chemical substance and a disease. This includes situations where the chemical or drug is used to treat the disease, the presence of the disease lowers the level of the chemical in the body, or the chemical or drug reduces the likelihood of the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[type 2 diabetes,DiseaseOrPhenotypicFeature]' and '[glucose,ChemicalEntity]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[type 2 diabetes,DiseaseOrPhenotypicFeature]' and '[glucose,ChemicalEntity]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "type 2 diabetes",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "glucose",
"type": "ChemicalEntity"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant rs2073163 and a disease T2D in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[rs2073163,SequenceVariant]' and '[T2D,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[rs2073163,SequenceVariant]' and '[T2D,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "rs2073163",
"type": "SequenceVariant"
} | {
"name": "T2D",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant rs2073163 and a disease adiposity in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[rs2073163,SequenceVariant]' and '[adiposity,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[rs2073163,SequenceVariant]' and '[adiposity,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "rs2073163",
"type": "SequenceVariant"
} | {
"name": "adiposity",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a chemical glucose and a variant rs1155794 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' suggests a mutual reinforcement between genetic variations and chemicals. This includes the chemical causing increased gene expression because of the variant, the variant increasing the body's sensitivity to the chemical, the variant causing a stronger reaction to the chemical, or any other type of positive relation between the variant and the chemical.
'Negative_Correlation' means a gene variant weakens the effect of a chemical. Thisinclude when the variant causes less gene activity due to the chemical, makes the body less responsive to the chemical, creates resistance to the chemical, or shows any decrease in interaction between the gene and the chemical.
'Association' indicates that the relation between a chemical and gene variations cannot be clearly defined as either positive or negative correlation.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[glucose,ChemicalEntity]' and '[rs1155794,SequenceVariant]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[glucose,ChemicalEntity]' and '[rs1155794,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "glucose",
"type": "ChemicalEntity"
} | {
"name": "rs1155794",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a chemical glucose and a variant rs2073163 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' suggests a mutual reinforcement between genetic variations and chemicals. This includes the chemical causing increased gene expression because of the variant, the variant increasing the body's sensitivity to the chemical, the variant causing a stronger reaction to the chemical, or any other type of positive relation between the variant and the chemical.
'Negative_Correlation' means a gene variant weakens the effect of a chemical. Thisinclude when the variant causes less gene activity due to the chemical, makes the body less responsive to the chemical, creates resistance to the chemical, or shows any decrease in interaction between the gene and the chemical.
'Association' indicates that the relation between a chemical and gene variations cannot be clearly defined as either positive or negative correlation.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[glucose,ChemicalEntity]' and '[rs2073163,SequenceVariant]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[glucose,ChemicalEntity]' and '[rs2073163,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "glucose",
"type": "ChemicalEntity"
} | {
"name": "rs2073163",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease adiposity and a variant rs11798018 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[adiposity,DiseaseOrPhenotypicFeature]' and '[rs11798018,SequenceVariant]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[adiposity,DiseaseOrPhenotypicFeature]' and '[rs11798018,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "adiposity",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "rs11798018",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease adiposity and a variant rs4828037 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[adiposity,DiseaseOrPhenotypicFeature]' and '[rs4828037,SequenceVariant]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[adiposity,DiseaseOrPhenotypicFeature]' and '[rs4828037,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "adiposity",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "rs4828037",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease adiposity and a variant rs5966709 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[adiposity,DiseaseOrPhenotypicFeature]' and '[rs5966709,SequenceVariant]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[adiposity,DiseaseOrPhenotypicFeature]' and '[rs5966709,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "adiposity",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "rs5966709",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein TNMD and a disease type 2 diabetes in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[TNMD,GeneOrGeneProduct]' and '[type 2 diabetes,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[TNMD,GeneOrGeneProduct]' and '[type 2 diabetes,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "TNMD",
"type": "GeneOrGeneProduct"
} | {
"name": "type 2 diabetes",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein TNMD and a chemical glucose in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Bind', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a chemical leads to higher gene expression, or higher gene expression increases sensitivity to the chemical, or a gene variant exacerbates the chemical's side effects, or a gene causes an over-response to the chemical, or there is a positive interaction between two genes in any manner.
'Negative_Correlation' indicates that a chemical leads to reduced gene expression, or higher gene expression results in decreased sensitivity or resistance to the chemical, or a gene variant offers protection against the chemical's adverse effects, or a gene contributes to resistance against the chemical, or there exists a negative interaction between two genes in any form.
'Bind' means that a chemical either connects to a gene's promoter region or a protein acts as a receptor for that chemical.
'Association' is used to describe relation that don't clearly fall under categories like positive correlation, negative correlation and bind , or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[TNMD,GeneOrGeneProduct]' and '[glucose,ChemicalEntity]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[TNMD,GeneOrGeneProduct]' and '[glucose,ChemicalEntity]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Bind', 'Association']. [/INST]Association</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "TNMD",
"type": "GeneOrGeneProduct"
} | {
"name": "glucose",
"type": "ChemicalEntity"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Bind",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein Tenomodulin and a disease diabetes in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[Tenomodulin,GeneOrGeneProduct]' and '[diabetes,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[Tenomodulin,GeneOrGeneProduct]' and '[diabetes,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "Tenomodulin",
"type": "GeneOrGeneProduct"
} | {
"name": "diabetes",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein Tenomodulin and a disease obesity in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[Tenomodulin,GeneOrGeneProduct]' and '[obesity,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study.
- Abstract of the Paper: [We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.]
Identify how '[Tenomodulin,GeneOrGeneProduct]' and '[obesity,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Tenomodulin is associated with obesity and diabetes risk: the Finnish diabetes prevention study. | We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men. | {
"name": "Tenomodulin",
"type": "GeneOrGeneProduct"
} | {
"name": "obesity",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein TLR2 and a disease inflammatory bowel disease in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[TLR2,GeneOrGeneProduct]' and '[inflammatory bowel disease,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease.
- Abstract of the Paper: [BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD.]
Identify how '[TLR2,GeneOrGeneProduct]' and '[inflammatory bowel disease,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease. | BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD. | {
"name": "TLR2",
"type": "GeneOrGeneProduct"
} | {
"name": "inflammatory bowel disease",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein TLR4 and a disease IBD in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[TLR4,GeneOrGeneProduct]' and '[IBD,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease.
- Abstract of the Paper: [BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD.]
Identify how '[TLR4,GeneOrGeneProduct]' and '[IBD,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease. | BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD. | {
"name": "TLR4",
"type": "GeneOrGeneProduct"
} | {
"name": "IBD",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant P631H and a disease IBD in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[P631H,SequenceVariant]' and '[IBD,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease.
- Abstract of the Paper: [BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD.]
Identify how '[P631H,SequenceVariant]' and '[IBD,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Negative_Correlation</s> | Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease. | BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD. | {
"name": "P631H",
"type": "SequenceVariant"
} | {
"name": "IBD",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Negative_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant D299G and a disease IBD in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[D299G,SequenceVariant]' and '[IBD,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease.
- Abstract of the Paper: [BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD.]
Identify how '[D299G,SequenceVariant]' and '[IBD,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Negative_Correlation</s> | Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease. | BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD. | {
"name": "D299G",
"type": "SequenceVariant"
} | {
"name": "IBD",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Negative_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein CARD15 and a disease IBD in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[CARD15,GeneOrGeneProduct]' and '[IBD,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease.
- Abstract of the Paper: [BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD.]
Identify how '[CARD15,GeneOrGeneProduct]' and '[IBD,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease. | BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD. | {
"name": "CARD15",
"type": "GeneOrGeneProduct"
} | {
"name": "IBD",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease Crohn's disease and a gene or protein CARD15 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a protein or gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or drug) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[Crohn's disease,DiseaseOrPhenotypicFeature]' and '[CARD15,GeneOrGeneProduct]'.
- Title of the Paper: Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease.
- Abstract of the Paper: [BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD.]
Identify how '[Crohn's disease,DiseaseOrPhenotypicFeature]' and '[CARD15,GeneOrGeneProduct]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease. | BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD. | {
"name": "Crohn's disease",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "CARD15",
"type": "GeneOrGeneProduct"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease Crohn's disease and a gene or protein NOD1 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a protein or gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or drug) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[Crohn's disease,DiseaseOrPhenotypicFeature]' and '[NOD1,GeneOrGeneProduct]'.
- Title of the Paper: Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease.
- Abstract of the Paper: [BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD.]
Identify how '[Crohn's disease,DiseaseOrPhenotypicFeature]' and '[NOD1,GeneOrGeneProduct]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Mutations in pattern recognition receptor genes modulate seroreactivity to microbial antigens in patients with inflammatory bowel disease. | BACKGROUND AND AIMS: A number of antibodies against microbial epitopes or self-antigens have been associated with Crohn's disease. The development of antibodies reflects a loss of tolerance to intestinal bacteria that underlies Crohn's disease, resulting in an exaggerated adaptive immune response to these bacteria. It was hypothesised that the development of antimicrobial antibodies is influenced by the presence of genetic variants in pattern recognition receptor genes. The aim of this study was therefore to investigate the influence of mutations in these innate immune receptor genes (nucleotide oligomerisation domain (NOD) 2/caspase recruitment domain (CARD) 15, NOD1/CARD4, TUCAN/CARDINAL/CARD8, Toll-like receptor (TLR) 4, TLR2, TLR1 and TLR6) on the development of antimicrobial and antiglycan antibodies in inflammatory bowel disease (IBD). Materials and METHODS: A cohort of 1163 unrelated patients with IBD (874 Crohn's disease, 259 ulcerative colitis, 30 indeterminate colitis) and 312 controls were analysed for anti-Saccharomyces cerevisiae antibodies (gASCA) IgG, anti-laminaribioside antibodies (ALCA) IgG, anti-chitobioside antibodies (ACCA) IgA, anti-mannobioside antibodies (AMCA) IgG and outer membrane porin (Omp) IgA and were genotyped for variants in NOD2/CARD15, TUCAN/CARDINAL/CARD8, NOD1/CARD4, TLR4, TLR1, TLR2 and TLR6. RESULTS: When compared with Crohn's disease patients without CARD15 mutations, the presence of at least one CARD15 variant in Crohn's disease patients more frequently led to gASCA positivity (66.1% versus 51.5%, p < 0.0001) and ALCA positivity (43.3% versus 34.9%, p = 0.018) and higher gASCA titers (85.7 versus 51.8 ELISA units, p < 0.0001), independent of ileal involvement. A gene dosage effect, with increasing gASCA and ALCA positivity for patients carrying none, one and two CARD15 variants, respectively, was seen for both markers. Similarly, Crohn's disease patients carrying NOD1/CARD4 indel had a higher prevalence of gASCA antibodies than wild-type patients (63.8% versus 55.2%, p = 0.014), also with a gene dosage effect. An opposite effect was observed for the TLR4 D299G and TLR2 P631H variants, with a lower prevalence of ACCA antibodies (23.4% versus 35%, p = 0.013) and Omp antibodies (20.5% versus 34.6%, p = 0.009), respectively. CONCLUSION: Variants in innate immune receptor genes were found to influence antibody formation against microbial epitopes. In this respect, it is intriguing that an opposite effect of CARD15 and TLR4 variants was observed. These findings may contribute to an understanding of the aetiology of the seroreactivity observed in IBD. | {
"name": "Crohn's disease",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "NOD1",
"type": "GeneOrGeneProduct"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein FGFR3 and a disease achondroplasia in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[FGFR3,GeneOrGeneProduct]' and '[achondroplasia,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: An improved tetra-primer PCR approach for the detection of the FGFR3 G380R mutation responsible for achondroplasia.
- Abstract of the Paper: [Achondroplasia is the most common form of dwarfism and has an incidence of approximately 1/7500. In more than 98% of cases, the disease is associated with a G to A or G to C substitution at nucleotide position 1138 (p.G380R) of the fibroblast growth factor receptor 3 (FGFR3) gene. We have developed a sensitive single tube tetra-primer PCR assay to detect both the c.1138G>A and c.1138G>C mutations and can successfully distinguish DNA samples that are homozygous and heterozygous for the c.1138G>A mutation. Titration studies showed that the assay could reliably detect one copy of the mutant allele in a mix of 100 wild-type alleles. The assay has been tested in 50 healthy controls, 3 known patients with achondroplasia, and 5 amniotic fluids suspected of having achondroplasia and for whom we had previously determined the genotypes for the c.1138G>A mutation by PCR-RFLP. We have observed complete concordance between methods. Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for FGFR3 p.G380R genotyping, which could be used even in "low-tech" laboratories.]
Identify how '[FGFR3,GeneOrGeneProduct]' and '[achondroplasia,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | An improved tetra-primer PCR approach for the detection of the FGFR3 G380R mutation responsible for achondroplasia. | Achondroplasia is the most common form of dwarfism and has an incidence of approximately 1/7500. In more than 98% of cases, the disease is associated with a G to A or G to C substitution at nucleotide position 1138 (p.G380R) of the fibroblast growth factor receptor 3 (FGFR3) gene. We have developed a sensitive single tube tetra-primer PCR assay to detect both the c.1138G>A and c.1138G>C mutations and can successfully distinguish DNA samples that are homozygous and heterozygous for the c.1138G>A mutation. Titration studies showed that the assay could reliably detect one copy of the mutant allele in a mix of 100 wild-type alleles. The assay has been tested in 50 healthy controls, 3 known patients with achondroplasia, and 5 amniotic fluids suspected of having achondroplasia and for whom we had previously determined the genotypes for the c.1138G>A mutation by PCR-RFLP. We have observed complete concordance between methods. Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for FGFR3 p.G380R genotyping, which could be used even in "low-tech" laboratories. | {
"name": "FGFR3",
"type": "GeneOrGeneProduct"
} | {
"name": "achondroplasia",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant G380R and a disease achondroplasia in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[G380R,SequenceVariant]' and '[achondroplasia,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: An improved tetra-primer PCR approach for the detection of the FGFR3 G380R mutation responsible for achondroplasia.
- Abstract of the Paper: [Achondroplasia is the most common form of dwarfism and has an incidence of approximately 1/7500. In more than 98% of cases, the disease is associated with a G to A or G to C substitution at nucleotide position 1138 (p.G380R) of the fibroblast growth factor receptor 3 (FGFR3) gene. We have developed a sensitive single tube tetra-primer PCR assay to detect both the c.1138G>A and c.1138G>C mutations and can successfully distinguish DNA samples that are homozygous and heterozygous for the c.1138G>A mutation. Titration studies showed that the assay could reliably detect one copy of the mutant allele in a mix of 100 wild-type alleles. The assay has been tested in 50 healthy controls, 3 known patients with achondroplasia, and 5 amniotic fluids suspected of having achondroplasia and for whom we had previously determined the genotypes for the c.1138G>A mutation by PCR-RFLP. We have observed complete concordance between methods. Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for FGFR3 p.G380R genotyping, which could be used even in "low-tech" laboratories.]
Identify how '[G380R,SequenceVariant]' and '[achondroplasia,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | An improved tetra-primer PCR approach for the detection of the FGFR3 G380R mutation responsible for achondroplasia. | Achondroplasia is the most common form of dwarfism and has an incidence of approximately 1/7500. In more than 98% of cases, the disease is associated with a G to A or G to C substitution at nucleotide position 1138 (p.G380R) of the fibroblast growth factor receptor 3 (FGFR3) gene. We have developed a sensitive single tube tetra-primer PCR assay to detect both the c.1138G>A and c.1138G>C mutations and can successfully distinguish DNA samples that are homozygous and heterozygous for the c.1138G>A mutation. Titration studies showed that the assay could reliably detect one copy of the mutant allele in a mix of 100 wild-type alleles. The assay has been tested in 50 healthy controls, 3 known patients with achondroplasia, and 5 amniotic fluids suspected of having achondroplasia and for whom we had previously determined the genotypes for the c.1138G>A mutation by PCR-RFLP. We have observed complete concordance between methods. Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for FGFR3 p.G380R genotyping, which could be used even in "low-tech" laboratories. | {
"name": "G380R",
"type": "SequenceVariant"
} | {
"name": "achondroplasia",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein DMC1 and a disease infertility in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[DMC1,GeneOrGeneProduct]' and '[infertility,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Genetic investigation of four meiotic genes in women with premature ovarian failure.
- Abstract of the Paper: [OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon.]
Identify how '[DMC1,GeneOrGeneProduct]' and '[infertility,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Genetic investigation of four meiotic genes in women with premature ovarian failure. | OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon. | {
"name": "DMC1",
"type": "GeneOrGeneProduct"
} | {
"name": "infertility",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein DMC1 and a disease premature ovarian failure in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[DMC1,GeneOrGeneProduct]' and '[premature ovarian failure,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Genetic investigation of four meiotic genes in women with premature ovarian failure.
- Abstract of the Paper: [OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon.]
Identify how '[DMC1,GeneOrGeneProduct]' and '[premature ovarian failure,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Genetic investigation of four meiotic genes in women with premature ovarian failure. | OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon. | {
"name": "DMC1",
"type": "GeneOrGeneProduct"
} | {
"name": "premature ovarian failure",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein MSH5 and a disease POF in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[MSH5,GeneOrGeneProduct]' and '[POF,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Genetic investigation of four meiotic genes in women with premature ovarian failure.
- Abstract of the Paper: [OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon.]
Identify how '[MSH5,GeneOrGeneProduct]' and '[POF,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Genetic investigation of four meiotic genes in women with premature ovarian failure. | OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon. | {
"name": "MSH5",
"type": "GeneOrGeneProduct"
} | {
"name": "POF",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease infertility and a gene or protein MSH5 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a protein or gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or drug) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[infertility,DiseaseOrPhenotypicFeature]' and '[MSH5,GeneOrGeneProduct]'.
- Title of the Paper: Genetic investigation of four meiotic genes in women with premature ovarian failure.
- Abstract of the Paper: [OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon.]
Identify how '[infertility,DiseaseOrPhenotypicFeature]' and '[MSH5,GeneOrGeneProduct]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Genetic investigation of four meiotic genes in women with premature ovarian failure. | OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon. | {
"name": "infertility",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "MSH5",
"type": "GeneOrGeneProduct"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease infertility and a variant M200V in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[infertility,DiseaseOrPhenotypicFeature]' and '[M200V,SequenceVariant]'.
- Title of the Paper: Genetic investigation of four meiotic genes in women with premature ovarian failure.
- Abstract of the Paper: [OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon.]
Identify how '[infertility,DiseaseOrPhenotypicFeature]' and '[M200V,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Genetic investigation of four meiotic genes in women with premature ovarian failure. | OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon. | {
"name": "infertility",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "M200V",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease infertility and a variant P29S in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[infertility,DiseaseOrPhenotypicFeature]' and '[P29S,SequenceVariant]'.
- Title of the Paper: Genetic investigation of four meiotic genes in women with premature ovarian failure.
- Abstract of the Paper: [OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon.]
Identify how '[infertility,DiseaseOrPhenotypicFeature]' and '[P29S,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Genetic investigation of four meiotic genes in women with premature ovarian failure. | OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon. | {
"name": "infertility",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "P29S",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant M200V and a disease POF in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[M200V,SequenceVariant]' and '[POF,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Genetic investigation of four meiotic genes in women with premature ovarian failure.
- Abstract of the Paper: [OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon.]
Identify how '[M200V,SequenceVariant]' and '[POF,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Genetic investigation of four meiotic genes in women with premature ovarian failure. | OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon. | {
"name": "M200V",
"type": "SequenceVariant"
} | {
"name": "POF",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease POF and a variant (proline) with a polar amino acid (serine) at position 29 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[POF,DiseaseOrPhenotypicFeature]' and '[(proline) with a polar amino acid (serine) at position 29,SequenceVariant]'.
- Title of the Paper: Genetic investigation of four meiotic genes in women with premature ovarian failure.
- Abstract of the Paper: [OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon.]
Identify how '[POF,DiseaseOrPhenotypicFeature]' and '[(proline) with a polar amino acid (serine) at position 29,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Genetic investigation of four meiotic genes in women with premature ovarian failure. | OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon. | {
"name": "POF",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "(proline) with a polar amino acid (serine) at position 29",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein IRF5 and a disease systemic lupus erythaematosus in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[IRF5,GeneOrGeneProduct]' and '[systemic lupus erythaematosus,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: A single nucleotide polymorphism in the IRF5 promoter region is associated with susceptibility to rheumatoid arthritis in the Japanese population.
- Abstract of the Paper: [OBJECTIVES: Interferon regulatory factor 5 (IRF5) is a member of the IRF family of transcription factors, which regulate the production of proinflammatory cytokines. Polymorphisms in the IRF5 gene have been associated with susceptibility to systemic lupus erythaematosus (SLE) in Caucasian and Asian populations, but their involvement in other autoimmune diseases is still uncertain. Here, we assessed the genetic role of IRF5 in susceptibility to rheumatoid arthritis (RA) in Japanese subjects. METHODS: We selected 13 single nucleotide polymorphisms (SNPs) and a CGGGG insertion-deletion polymorphism in the IRF5 gene. We performed 2 sets of case-control comparisons using Japanese subjects (first set: 830 patients with RA and 658 controls; second set: 1112 patients with RA and 940 controls), and then performed a stratified analysis using human leukocyte antigen (HLA)-DRB1 shared epitope (SE) status. We genotyped the SNPs using TaqMan assays. RESULTS: A significant association of the rs729302 A allele with RA susceptibility was found in both sets (odds ratio (OR) 1.22, 95% CI 1.09 to 1.35, p<0.001 in the combined analysis). When the patients were stratified by the SE, the rs729302 A allele was found to confer increased risk to RA in patients that were SE negative (OR 1.50, 95% CI 1.17 to 1.92, p = 0.001) as compared with patients carrying the SE (OR 1.11, 95% CI 0.93 to 1.33, p = 0.24). In both sets, no genotyped polymorphisms were significantly associated with RA susceptibility, but rs729302 was significantly associated. CONCLUSIONS: These findings indicate that the promoter polymorphism of IRF5 is a genetic factor conferring predisposition to RA, and that it contributes considerably to disease pathogenesis in patients that were SE negative.]
Identify how '[IRF5,GeneOrGeneProduct]' and '[systemic lupus erythaematosus,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | A single nucleotide polymorphism in the IRF5 promoter region is associated with susceptibility to rheumatoid arthritis in the Japanese population. | OBJECTIVES: Interferon regulatory factor 5 (IRF5) is a member of the IRF family of transcription factors, which regulate the production of proinflammatory cytokines. Polymorphisms in the IRF5 gene have been associated with susceptibility to systemic lupus erythaematosus (SLE) in Caucasian and Asian populations, but their involvement in other autoimmune diseases is still uncertain. Here, we assessed the genetic role of IRF5 in susceptibility to rheumatoid arthritis (RA) in Japanese subjects. METHODS: We selected 13 single nucleotide polymorphisms (SNPs) and a CGGGG insertion-deletion polymorphism in the IRF5 gene. We performed 2 sets of case-control comparisons using Japanese subjects (first set: 830 patients with RA and 658 controls; second set: 1112 patients with RA and 940 controls), and then performed a stratified analysis using human leukocyte antigen (HLA)-DRB1 shared epitope (SE) status. We genotyped the SNPs using TaqMan assays. RESULTS: A significant association of the rs729302 A allele with RA susceptibility was found in both sets (odds ratio (OR) 1.22, 95% CI 1.09 to 1.35, p<0.001 in the combined analysis). When the patients were stratified by the SE, the rs729302 A allele was found to confer increased risk to RA in patients that were SE negative (OR 1.50, 95% CI 1.17 to 1.92, p = 0.001) as compared with patients carrying the SE (OR 1.11, 95% CI 0.93 to 1.33, p = 0.24). In both sets, no genotyped polymorphisms were significantly associated with RA susceptibility, but rs729302 was significantly associated. CONCLUSIONS: These findings indicate that the promoter polymorphism of IRF5 is a genetic factor conferring predisposition to RA, and that it contributes considerably to disease pathogenesis in patients that were SE negative. | {
"name": "IRF5",
"type": "GeneOrGeneProduct"
} | {
"name": "systemic lupus erythaematosus",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein IRF5 and a disease rheumatoid arthritis in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[IRF5,GeneOrGeneProduct]' and '[rheumatoid arthritis,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: A single nucleotide polymorphism in the IRF5 promoter region is associated with susceptibility to rheumatoid arthritis in the Japanese population.
- Abstract of the Paper: [OBJECTIVES: Interferon regulatory factor 5 (IRF5) is a member of the IRF family of transcription factors, which regulate the production of proinflammatory cytokines. Polymorphisms in the IRF5 gene have been associated with susceptibility to systemic lupus erythaematosus (SLE) in Caucasian and Asian populations, but their involvement in other autoimmune diseases is still uncertain. Here, we assessed the genetic role of IRF5 in susceptibility to rheumatoid arthritis (RA) in Japanese subjects. METHODS: We selected 13 single nucleotide polymorphisms (SNPs) and a CGGGG insertion-deletion polymorphism in the IRF5 gene. We performed 2 sets of case-control comparisons using Japanese subjects (first set: 830 patients with RA and 658 controls; second set: 1112 patients with RA and 940 controls), and then performed a stratified analysis using human leukocyte antigen (HLA)-DRB1 shared epitope (SE) status. We genotyped the SNPs using TaqMan assays. RESULTS: A significant association of the rs729302 A allele with RA susceptibility was found in both sets (odds ratio (OR) 1.22, 95% CI 1.09 to 1.35, p<0.001 in the combined analysis). When the patients were stratified by the SE, the rs729302 A allele was found to confer increased risk to RA in patients that were SE negative (OR 1.50, 95% CI 1.17 to 1.92, p = 0.001) as compared with patients carrying the SE (OR 1.11, 95% CI 0.93 to 1.33, p = 0.24). In both sets, no genotyped polymorphisms were significantly associated with RA susceptibility, but rs729302 was significantly associated. CONCLUSIONS: These findings indicate that the promoter polymorphism of IRF5 is a genetic factor conferring predisposition to RA, and that it contributes considerably to disease pathogenesis in patients that were SE negative.]
Identify how '[IRF5,GeneOrGeneProduct]' and '[rheumatoid arthritis,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | A single nucleotide polymorphism in the IRF5 promoter region is associated with susceptibility to rheumatoid arthritis in the Japanese population. | OBJECTIVES: Interferon regulatory factor 5 (IRF5) is a member of the IRF family of transcription factors, which regulate the production of proinflammatory cytokines. Polymorphisms in the IRF5 gene have been associated with susceptibility to systemic lupus erythaematosus (SLE) in Caucasian and Asian populations, but their involvement in other autoimmune diseases is still uncertain. Here, we assessed the genetic role of IRF5 in susceptibility to rheumatoid arthritis (RA) in Japanese subjects. METHODS: We selected 13 single nucleotide polymorphisms (SNPs) and a CGGGG insertion-deletion polymorphism in the IRF5 gene. We performed 2 sets of case-control comparisons using Japanese subjects (first set: 830 patients with RA and 658 controls; second set: 1112 patients with RA and 940 controls), and then performed a stratified analysis using human leukocyte antigen (HLA)-DRB1 shared epitope (SE) status. We genotyped the SNPs using TaqMan assays. RESULTS: A significant association of the rs729302 A allele with RA susceptibility was found in both sets (odds ratio (OR) 1.22, 95% CI 1.09 to 1.35, p<0.001 in the combined analysis). When the patients were stratified by the SE, the rs729302 A allele was found to confer increased risk to RA in patients that were SE negative (OR 1.50, 95% CI 1.17 to 1.92, p = 0.001) as compared with patients carrying the SE (OR 1.11, 95% CI 0.93 to 1.33, p = 0.24). In both sets, no genotyped polymorphisms were significantly associated with RA susceptibility, but rs729302 was significantly associated. CONCLUSIONS: These findings indicate that the promoter polymorphism of IRF5 is a genetic factor conferring predisposition to RA, and that it contributes considerably to disease pathogenesis in patients that were SE negative. | {
"name": "IRF5",
"type": "GeneOrGeneProduct"
} | {
"name": "rheumatoid arthritis",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant rs729302 and a disease RA in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[rs729302,SequenceVariant]' and '[RA,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: A single nucleotide polymorphism in the IRF5 promoter region is associated with susceptibility to rheumatoid arthritis in the Japanese population.
- Abstract of the Paper: [OBJECTIVES: Interferon regulatory factor 5 (IRF5) is a member of the IRF family of transcription factors, which regulate the production of proinflammatory cytokines. Polymorphisms in the IRF5 gene have been associated with susceptibility to systemic lupus erythaematosus (SLE) in Caucasian and Asian populations, but their involvement in other autoimmune diseases is still uncertain. Here, we assessed the genetic role of IRF5 in susceptibility to rheumatoid arthritis (RA) in Japanese subjects. METHODS: We selected 13 single nucleotide polymorphisms (SNPs) and a CGGGG insertion-deletion polymorphism in the IRF5 gene. We performed 2 sets of case-control comparisons using Japanese subjects (first set: 830 patients with RA and 658 controls; second set: 1112 patients with RA and 940 controls), and then performed a stratified analysis using human leukocyte antigen (HLA)-DRB1 shared epitope (SE) status. We genotyped the SNPs using TaqMan assays. RESULTS: A significant association of the rs729302 A allele with RA susceptibility was found in both sets (odds ratio (OR) 1.22, 95% CI 1.09 to 1.35, p<0.001 in the combined analysis). When the patients were stratified by the SE, the rs729302 A allele was found to confer increased risk to RA in patients that were SE negative (OR 1.50, 95% CI 1.17 to 1.92, p = 0.001) as compared with patients carrying the SE (OR 1.11, 95% CI 0.93 to 1.33, p = 0.24). In both sets, no genotyped polymorphisms were significantly associated with RA susceptibility, but rs729302 was significantly associated. CONCLUSIONS: These findings indicate that the promoter polymorphism of IRF5 is a genetic factor conferring predisposition to RA, and that it contributes considerably to disease pathogenesis in patients that were SE negative.]
Identify how '[rs729302,SequenceVariant]' and '[RA,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | A single nucleotide polymorphism in the IRF5 promoter region is associated with susceptibility to rheumatoid arthritis in the Japanese population. | OBJECTIVES: Interferon regulatory factor 5 (IRF5) is a member of the IRF family of transcription factors, which regulate the production of proinflammatory cytokines. Polymorphisms in the IRF5 gene have been associated with susceptibility to systemic lupus erythaematosus (SLE) in Caucasian and Asian populations, but their involvement in other autoimmune diseases is still uncertain. Here, we assessed the genetic role of IRF5 in susceptibility to rheumatoid arthritis (RA) in Japanese subjects. METHODS: We selected 13 single nucleotide polymorphisms (SNPs) and a CGGGG insertion-deletion polymorphism in the IRF5 gene. We performed 2 sets of case-control comparisons using Japanese subjects (first set: 830 patients with RA and 658 controls; second set: 1112 patients with RA and 940 controls), and then performed a stratified analysis using human leukocyte antigen (HLA)-DRB1 shared epitope (SE) status. We genotyped the SNPs using TaqMan assays. RESULTS: A significant association of the rs729302 A allele with RA susceptibility was found in both sets (odds ratio (OR) 1.22, 95% CI 1.09 to 1.35, p<0.001 in the combined analysis). When the patients were stratified by the SE, the rs729302 A allele was found to confer increased risk to RA in patients that were SE negative (OR 1.50, 95% CI 1.17 to 1.92, p = 0.001) as compared with patients carrying the SE (OR 1.11, 95% CI 0.93 to 1.33, p = 0.24). In both sets, no genotyped polymorphisms were significantly associated with RA susceptibility, but rs729302 was significantly associated. CONCLUSIONS: These findings indicate that the promoter polymorphism of IRF5 is a genetic factor conferring predisposition to RA, and that it contributes considerably to disease pathogenesis in patients that were SE negative. | {
"name": "rs729302",
"type": "SequenceVariant"
} | {
"name": "RA",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant guanine insertion/deletion (G/D), the -1607 promoter polymorphism and a disease lumbar disc disease in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[guanine insertion/deletion (G/D), the -1607 promoter polymorphism,SequenceVariant]' and '[lumbar disc disease,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Association between promoter -1607 polymorphism of MMP1 and lumbar disc disease in Southern Chinese.
- Abstract of the Paper: [BACKGROUND: Matrix metalloproteinases (MMPs) are involved in the degradation of the extracellular matrix of the intervertebral disc. A SNP for guanine insertion/deletion (G/D), the -1607 promoter polymorphism, of the MMP1 gene was found significantly affecting promoter activity and corresponding transcription level. Hence it is a good candidate for genetic studies in DDD. METHODS: Southern Chinese volunteers between 18 and 55 years were recruited from the population. DDD in the lumbar spine was defined by MRI using Schneiderman's classification. Genomic DNA was isolated from the leukocytes and genotyping was performed using the Sequenom platform. Association and Hardy-Weinberg equilibrium checking were assessed by Chi-square test and Mann-Whitney U test. RESULTS: Our results showed substantial evidence of association between -1607 promoter polymorphism of MMP1 and DDD in the Southern Chinese subjects. D allelic was significantly associated with DDD (p value = 0.027, odds ratio = 1.41 with 95% CI = 1.04-1.90) while Genotypic association on the presence of D allele was also significantly associated with DDD (p value = 0.046, odds ratio = 1.50 with 95% CI = 1.01-2.24). Further age stratification showed significant genotypic as well as allelic association in the group of over 40 years (genotypic: p value = 0.035, odds ratio = 1.617 with 95% CI = 1.033-2.529; allelic: p value = 0.033, odds ratio = 1.445 with 95% CI = 1.029-2.029). Disc bulge, annular tears and the Schmorl's nodes were not associated with the D allele. CONCLUSION: We demonstrated that individuals with the presence of D allele for the -1607 promoter polymorphism of MMP1 are about 1.5 times more susceptible to develop DDD when compared with those having G allele only. Further association was identified in individuals over 40 years of age. Disc bulge, annular tear as well as Schmorl's nodes were not associated with this polymorphism.]
Identify how '[guanine insertion/deletion (G/D), the -1607 promoter polymorphism,SequenceVariant]' and '[lumbar disc disease,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Association between promoter -1607 polymorphism of MMP1 and lumbar disc disease in Southern Chinese. | BACKGROUND: Matrix metalloproteinases (MMPs) are involved in the degradation of the extracellular matrix of the intervertebral disc. A SNP for guanine insertion/deletion (G/D), the -1607 promoter polymorphism, of the MMP1 gene was found significantly affecting promoter activity and corresponding transcription level. Hence it is a good candidate for genetic studies in DDD. METHODS: Southern Chinese volunteers between 18 and 55 years were recruited from the population. DDD in the lumbar spine was defined by MRI using Schneiderman's classification. Genomic DNA was isolated from the leukocytes and genotyping was performed using the Sequenom platform. Association and Hardy-Weinberg equilibrium checking were assessed by Chi-square test and Mann-Whitney U test. RESULTS: Our results showed substantial evidence of association between -1607 promoter polymorphism of MMP1 and DDD in the Southern Chinese subjects. D allelic was significantly associated with DDD (p value = 0.027, odds ratio = 1.41 with 95% CI = 1.04-1.90) while Genotypic association on the presence of D allele was also significantly associated with DDD (p value = 0.046, odds ratio = 1.50 with 95% CI = 1.01-2.24). Further age stratification showed significant genotypic as well as allelic association in the group of over 40 years (genotypic: p value = 0.035, odds ratio = 1.617 with 95% CI = 1.033-2.529; allelic: p value = 0.033, odds ratio = 1.445 with 95% CI = 1.029-2.029). Disc bulge, annular tears and the Schmorl's nodes were not associated with the D allele. CONCLUSION: We demonstrated that individuals with the presence of D allele for the -1607 promoter polymorphism of MMP1 are about 1.5 times more susceptible to develop DDD when compared with those having G allele only. Further association was identified in individuals over 40 years of age. Disc bulge, annular tear as well as Schmorl's nodes were not associated with this polymorphism. | {
"name": "guanine insertion/deletion (G/D), the -1607 promoter polymorphism",
"type": "SequenceVariant"
} | {
"name": "lumbar disc disease",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease DDD and a variant guanine insertion/deletion (G/D), the -1607 promoter polymorphism in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[DDD,DiseaseOrPhenotypicFeature]' and '[guanine insertion/deletion (G/D), the -1607 promoter polymorphism,SequenceVariant]'.
- Title of the Paper: Association between promoter -1607 polymorphism of MMP1 and lumbar disc disease in Southern Chinese.
- Abstract of the Paper: [BACKGROUND: Matrix metalloproteinases (MMPs) are involved in the degradation of the extracellular matrix of the intervertebral disc. A SNP for guanine insertion/deletion (G/D), the -1607 promoter polymorphism, of the MMP1 gene was found significantly affecting promoter activity and corresponding transcription level. Hence it is a good candidate for genetic studies in DDD. METHODS: Southern Chinese volunteers between 18 and 55 years were recruited from the population. DDD in the lumbar spine was defined by MRI using Schneiderman's classification. Genomic DNA was isolated from the leukocytes and genotyping was performed using the Sequenom platform. Association and Hardy-Weinberg equilibrium checking were assessed by Chi-square test and Mann-Whitney U test. RESULTS: Our results showed substantial evidence of association between -1607 promoter polymorphism of MMP1 and DDD in the Southern Chinese subjects. D allelic was significantly associated with DDD (p value = 0.027, odds ratio = 1.41 with 95% CI = 1.04-1.90) while Genotypic association on the presence of D allele was also significantly associated with DDD (p value = 0.046, odds ratio = 1.50 with 95% CI = 1.01-2.24). Further age stratification showed significant genotypic as well as allelic association in the group of over 40 years (genotypic: p value = 0.035, odds ratio = 1.617 with 95% CI = 1.033-2.529; allelic: p value = 0.033, odds ratio = 1.445 with 95% CI = 1.029-2.029). Disc bulge, annular tears and the Schmorl's nodes were not associated with the D allele. CONCLUSION: We demonstrated that individuals with the presence of D allele for the -1607 promoter polymorphism of MMP1 are about 1.5 times more susceptible to develop DDD when compared with those having G allele only. Further association was identified in individuals over 40 years of age. Disc bulge, annular tear as well as Schmorl's nodes were not associated with this polymorphism.]
Identify how '[DDD,DiseaseOrPhenotypicFeature]' and '[guanine insertion/deletion (G/D), the -1607 promoter polymorphism,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Association between promoter -1607 polymorphism of MMP1 and lumbar disc disease in Southern Chinese. | BACKGROUND: Matrix metalloproteinases (MMPs) are involved in the degradation of the extracellular matrix of the intervertebral disc. A SNP for guanine insertion/deletion (G/D), the -1607 promoter polymorphism, of the MMP1 gene was found significantly affecting promoter activity and corresponding transcription level. Hence it is a good candidate for genetic studies in DDD. METHODS: Southern Chinese volunteers between 18 and 55 years were recruited from the population. DDD in the lumbar spine was defined by MRI using Schneiderman's classification. Genomic DNA was isolated from the leukocytes and genotyping was performed using the Sequenom platform. Association and Hardy-Weinberg equilibrium checking were assessed by Chi-square test and Mann-Whitney U test. RESULTS: Our results showed substantial evidence of association between -1607 promoter polymorphism of MMP1 and DDD in the Southern Chinese subjects. D allelic was significantly associated with DDD (p value = 0.027, odds ratio = 1.41 with 95% CI = 1.04-1.90) while Genotypic association on the presence of D allele was also significantly associated with DDD (p value = 0.046, odds ratio = 1.50 with 95% CI = 1.01-2.24). Further age stratification showed significant genotypic as well as allelic association in the group of over 40 years (genotypic: p value = 0.035, odds ratio = 1.617 with 95% CI = 1.033-2.529; allelic: p value = 0.033, odds ratio = 1.445 with 95% CI = 1.029-2.029). Disc bulge, annular tears and the Schmorl's nodes were not associated with the D allele. CONCLUSION: We demonstrated that individuals with the presence of D allele for the -1607 promoter polymorphism of MMP1 are about 1.5 times more susceptible to develop DDD when compared with those having G allele only. Further association was identified in individuals over 40 years of age. Disc bulge, annular tear as well as Schmorl's nodes were not associated with this polymorphism. | {
"name": "DDD",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "guanine insertion/deletion (G/D), the -1607 promoter polymorphism",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant D allele for the -1607 and a disease DDD in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[D allele for the -1607,SequenceVariant]' and '[DDD,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Association between promoter -1607 polymorphism of MMP1 and lumbar disc disease in Southern Chinese.
- Abstract of the Paper: [BACKGROUND: Matrix metalloproteinases (MMPs) are involved in the degradation of the extracellular matrix of the intervertebral disc. A SNP for guanine insertion/deletion (G/D), the -1607 promoter polymorphism, of the MMP1 gene was found significantly affecting promoter activity and corresponding transcription level. Hence it is a good candidate for genetic studies in DDD. METHODS: Southern Chinese volunteers between 18 and 55 years were recruited from the population. DDD in the lumbar spine was defined by MRI using Schneiderman's classification. Genomic DNA was isolated from the leukocytes and genotyping was performed using the Sequenom platform. Association and Hardy-Weinberg equilibrium checking were assessed by Chi-square test and Mann-Whitney U test. RESULTS: Our results showed substantial evidence of association between -1607 promoter polymorphism of MMP1 and DDD in the Southern Chinese subjects. D allelic was significantly associated with DDD (p value = 0.027, odds ratio = 1.41 with 95% CI = 1.04-1.90) while Genotypic association on the presence of D allele was also significantly associated with DDD (p value = 0.046, odds ratio = 1.50 with 95% CI = 1.01-2.24). Further age stratification showed significant genotypic as well as allelic association in the group of over 40 years (genotypic: p value = 0.035, odds ratio = 1.617 with 95% CI = 1.033-2.529; allelic: p value = 0.033, odds ratio = 1.445 with 95% CI = 1.029-2.029). Disc bulge, annular tears and the Schmorl's nodes were not associated with the D allele. CONCLUSION: We demonstrated that individuals with the presence of D allele for the -1607 promoter polymorphism of MMP1 are about 1.5 times more susceptible to develop DDD when compared with those having G allele only. Further association was identified in individuals over 40 years of age. Disc bulge, annular tear as well as Schmorl's nodes were not associated with this polymorphism.]
Identify how '[D allele for the -1607,SequenceVariant]' and '[DDD,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Association between promoter -1607 polymorphism of MMP1 and lumbar disc disease in Southern Chinese. | BACKGROUND: Matrix metalloproteinases (MMPs) are involved in the degradation of the extracellular matrix of the intervertebral disc. A SNP for guanine insertion/deletion (G/D), the -1607 promoter polymorphism, of the MMP1 gene was found significantly affecting promoter activity and corresponding transcription level. Hence it is a good candidate for genetic studies in DDD. METHODS: Southern Chinese volunteers between 18 and 55 years were recruited from the population. DDD in the lumbar spine was defined by MRI using Schneiderman's classification. Genomic DNA was isolated from the leukocytes and genotyping was performed using the Sequenom platform. Association and Hardy-Weinberg equilibrium checking were assessed by Chi-square test and Mann-Whitney U test. RESULTS: Our results showed substantial evidence of association between -1607 promoter polymorphism of MMP1 and DDD in the Southern Chinese subjects. D allelic was significantly associated with DDD (p value = 0.027, odds ratio = 1.41 with 95% CI = 1.04-1.90) while Genotypic association on the presence of D allele was also significantly associated with DDD (p value = 0.046, odds ratio = 1.50 with 95% CI = 1.01-2.24). Further age stratification showed significant genotypic as well as allelic association in the group of over 40 years (genotypic: p value = 0.035, odds ratio = 1.617 with 95% CI = 1.033-2.529; allelic: p value = 0.033, odds ratio = 1.445 with 95% CI = 1.029-2.029). Disc bulge, annular tears and the Schmorl's nodes were not associated with the D allele. CONCLUSION: We demonstrated that individuals with the presence of D allele for the -1607 promoter polymorphism of MMP1 are about 1.5 times more susceptible to develop DDD when compared with those having G allele only. Further association was identified in individuals over 40 years of age. Disc bulge, annular tear as well as Schmorl's nodes were not associated with this polymorphism. | {
"name": "D allele for the -1607",
"type": "SequenceVariant"
} | {
"name": "DDD",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein MMP1 and a disease DDD in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[MMP1,GeneOrGeneProduct]' and '[DDD,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Association between promoter -1607 polymorphism of MMP1 and lumbar disc disease in Southern Chinese.
- Abstract of the Paper: [BACKGROUND: Matrix metalloproteinases (MMPs) are involved in the degradation of the extracellular matrix of the intervertebral disc. A SNP for guanine insertion/deletion (G/D), the -1607 promoter polymorphism, of the MMP1 gene was found significantly affecting promoter activity and corresponding transcription level. Hence it is a good candidate for genetic studies in DDD. METHODS: Southern Chinese volunteers between 18 and 55 years were recruited from the population. DDD in the lumbar spine was defined by MRI using Schneiderman's classification. Genomic DNA was isolated from the leukocytes and genotyping was performed using the Sequenom platform. Association and Hardy-Weinberg equilibrium checking were assessed by Chi-square test and Mann-Whitney U test. RESULTS: Our results showed substantial evidence of association between -1607 promoter polymorphism of MMP1 and DDD in the Southern Chinese subjects. D allelic was significantly associated with DDD (p value = 0.027, odds ratio = 1.41 with 95% CI = 1.04-1.90) while Genotypic association on the presence of D allele was also significantly associated with DDD (p value = 0.046, odds ratio = 1.50 with 95% CI = 1.01-2.24). Further age stratification showed significant genotypic as well as allelic association in the group of over 40 years (genotypic: p value = 0.035, odds ratio = 1.617 with 95% CI = 1.033-2.529; allelic: p value = 0.033, odds ratio = 1.445 with 95% CI = 1.029-2.029). Disc bulge, annular tears and the Schmorl's nodes were not associated with the D allele. CONCLUSION: We demonstrated that individuals with the presence of D allele for the -1607 promoter polymorphism of MMP1 are about 1.5 times more susceptible to develop DDD when compared with those having G allele only. Further association was identified in individuals over 40 years of age. Disc bulge, annular tear as well as Schmorl's nodes were not associated with this polymorphism.]
Identify how '[MMP1,GeneOrGeneProduct]' and '[DDD,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Association between promoter -1607 polymorphism of MMP1 and lumbar disc disease in Southern Chinese. | BACKGROUND: Matrix metalloproteinases (MMPs) are involved in the degradation of the extracellular matrix of the intervertebral disc. A SNP for guanine insertion/deletion (G/D), the -1607 promoter polymorphism, of the MMP1 gene was found significantly affecting promoter activity and corresponding transcription level. Hence it is a good candidate for genetic studies in DDD. METHODS: Southern Chinese volunteers between 18 and 55 years were recruited from the population. DDD in the lumbar spine was defined by MRI using Schneiderman's classification. Genomic DNA was isolated from the leukocytes and genotyping was performed using the Sequenom platform. Association and Hardy-Weinberg equilibrium checking were assessed by Chi-square test and Mann-Whitney U test. RESULTS: Our results showed substantial evidence of association between -1607 promoter polymorphism of MMP1 and DDD in the Southern Chinese subjects. D allelic was significantly associated with DDD (p value = 0.027, odds ratio = 1.41 with 95% CI = 1.04-1.90) while Genotypic association on the presence of D allele was also significantly associated with DDD (p value = 0.046, odds ratio = 1.50 with 95% CI = 1.01-2.24). Further age stratification showed significant genotypic as well as allelic association in the group of over 40 years (genotypic: p value = 0.035, odds ratio = 1.617 with 95% CI = 1.033-2.529; allelic: p value = 0.033, odds ratio = 1.445 with 95% CI = 1.029-2.029). Disc bulge, annular tears and the Schmorl's nodes were not associated with the D allele. CONCLUSION: We demonstrated that individuals with the presence of D allele for the -1607 promoter polymorphism of MMP1 are about 1.5 times more susceptible to develop DDD when compared with those having G allele only. Further association was identified in individuals over 40 years of age. Disc bulge, annular tear as well as Schmorl's nodes were not associated with this polymorphism. | {
"name": "MMP1",
"type": "GeneOrGeneProduct"
} | {
"name": "DDD",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease lumbar disc disease and a gene or protein MMP1 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a protein or gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or drug) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[lumbar disc disease,DiseaseOrPhenotypicFeature]' and '[MMP1,GeneOrGeneProduct]'.
- Title of the Paper: Association between promoter -1607 polymorphism of MMP1 and lumbar disc disease in Southern Chinese.
- Abstract of the Paper: [BACKGROUND: Matrix metalloproteinases (MMPs) are involved in the degradation of the extracellular matrix of the intervertebral disc. A SNP for guanine insertion/deletion (G/D), the -1607 promoter polymorphism, of the MMP1 gene was found significantly affecting promoter activity and corresponding transcription level. Hence it is a good candidate for genetic studies in DDD. METHODS: Southern Chinese volunteers between 18 and 55 years were recruited from the population. DDD in the lumbar spine was defined by MRI using Schneiderman's classification. Genomic DNA was isolated from the leukocytes and genotyping was performed using the Sequenom platform. Association and Hardy-Weinberg equilibrium checking were assessed by Chi-square test and Mann-Whitney U test. RESULTS: Our results showed substantial evidence of association between -1607 promoter polymorphism of MMP1 and DDD in the Southern Chinese subjects. D allelic was significantly associated with DDD (p value = 0.027, odds ratio = 1.41 with 95% CI = 1.04-1.90) while Genotypic association on the presence of D allele was also significantly associated with DDD (p value = 0.046, odds ratio = 1.50 with 95% CI = 1.01-2.24). Further age stratification showed significant genotypic as well as allelic association in the group of over 40 years (genotypic: p value = 0.035, odds ratio = 1.617 with 95% CI = 1.033-2.529; allelic: p value = 0.033, odds ratio = 1.445 with 95% CI = 1.029-2.029). Disc bulge, annular tears and the Schmorl's nodes were not associated with the D allele. CONCLUSION: We demonstrated that individuals with the presence of D allele for the -1607 promoter polymorphism of MMP1 are about 1.5 times more susceptible to develop DDD when compared with those having G allele only. Further association was identified in individuals over 40 years of age. Disc bulge, annular tear as well as Schmorl's nodes were not associated with this polymorphism.]
Identify how '[lumbar disc disease,DiseaseOrPhenotypicFeature]' and '[MMP1,GeneOrGeneProduct]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Association between promoter -1607 polymorphism of MMP1 and lumbar disc disease in Southern Chinese. | BACKGROUND: Matrix metalloproteinases (MMPs) are involved in the degradation of the extracellular matrix of the intervertebral disc. A SNP for guanine insertion/deletion (G/D), the -1607 promoter polymorphism, of the MMP1 gene was found significantly affecting promoter activity and corresponding transcription level. Hence it is a good candidate for genetic studies in DDD. METHODS: Southern Chinese volunteers between 18 and 55 years were recruited from the population. DDD in the lumbar spine was defined by MRI using Schneiderman's classification. Genomic DNA was isolated from the leukocytes and genotyping was performed using the Sequenom platform. Association and Hardy-Weinberg equilibrium checking were assessed by Chi-square test and Mann-Whitney U test. RESULTS: Our results showed substantial evidence of association between -1607 promoter polymorphism of MMP1 and DDD in the Southern Chinese subjects. D allelic was significantly associated with DDD (p value = 0.027, odds ratio = 1.41 with 95% CI = 1.04-1.90) while Genotypic association on the presence of D allele was also significantly associated with DDD (p value = 0.046, odds ratio = 1.50 with 95% CI = 1.01-2.24). Further age stratification showed significant genotypic as well as allelic association in the group of over 40 years (genotypic: p value = 0.035, odds ratio = 1.617 with 95% CI = 1.033-2.529; allelic: p value = 0.033, odds ratio = 1.445 with 95% CI = 1.029-2.029). Disc bulge, annular tears and the Schmorl's nodes were not associated with the D allele. CONCLUSION: We demonstrated that individuals with the presence of D allele for the -1607 promoter polymorphism of MMP1 are about 1.5 times more susceptible to develop DDD when compared with those having G allele only. Further association was identified in individuals over 40 years of age. Disc bulge, annular tear as well as Schmorl's nodes were not associated with this polymorphism. | {
"name": "lumbar disc disease",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "MMP1",
"type": "GeneOrGeneProduct"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease epileptic and a chemical penicillin-G potassium in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means there's a direct link between a chemical and a disease. This includes cases where the chemical causes the disease, higher doses of the chemical increase disease risk, the disease raises the chemical's level in the body, there's a direct positive link between the chemical's level and disease risk, or exposure to the chemical during development affects disease susceptibility later on.
'Negative_Correlation' means there's an inverse relation between a chemical substance and a disease. This includes situations where the chemical or drug is used to treat the disease, the presence of the disease lowers the level of the chemical in the body, or the chemical or drug reduces the likelihood of the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[epileptic,DiseaseOrPhenotypicFeature]' and '[penicillin-G potassium,ChemicalEntity]'.
- Title of the Paper: Detailed spectral profile analysis of penicillin-induced epileptiform activity in anesthetized rats.
- Abstract of the Paper: [Penicillin model is a widely used experimental model for epilepsy research. In the present study we aimed to portray a detailed spectral analysis of penicillin-induced epileptiform activity in comparison with basal brain activity in anesthetized Wistar rats. Male Wistar rats were anesthetized with i.p. urethane and connected to an electrocorticogram setup. After a short period of basal activity recording, epileptic focus was induced by injecting 400IU/2 microl penicillin-G potassium into the left lateral ventricle while the cortical activity was continuously recorded. Basal activity, latent period and the penicillin-induced epileptiform activity periods were then analyzed using both conventional methods and spectral analysis. Spectral analyses were conducted by dividing the whole spectrum into different frequency bands including delta, theta (slow and fast), alpha-sigma, beta (1 and 2) and gamma (1 and 2) bands. Our results show that the most affected frequency bands were delta, theta, beta-2 and gamma-2 bands during the epileptiform activity and there were marked differences in terms of spectral densities between three investigated episodes (basal activity, latent period and epileptiform activity). Our results may help to analyze novel data obtained using similar experimental models and the simple analysis method described here can be used in similar studies to investigate the basic neuronal mechanism of this or other types of experimental epilepsies.]
Identify how '[epileptic,DiseaseOrPhenotypicFeature]' and '[penicillin-G potassium,ChemicalEntity]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Detailed spectral profile analysis of penicillin-induced epileptiform activity in anesthetized rats. | Penicillin model is a widely used experimental model for epilepsy research. In the present study we aimed to portray a detailed spectral analysis of penicillin-induced epileptiform activity in comparison with basal brain activity in anesthetized Wistar rats. Male Wistar rats were anesthetized with i.p. urethane and connected to an electrocorticogram setup. After a short period of basal activity recording, epileptic focus was induced by injecting 400IU/2 microl penicillin-G potassium into the left lateral ventricle while the cortical activity was continuously recorded. Basal activity, latent period and the penicillin-induced epileptiform activity periods were then analyzed using both conventional methods and spectral analysis. Spectral analyses were conducted by dividing the whole spectrum into different frequency bands including delta, theta (slow and fast), alpha-sigma, beta (1 and 2) and gamma (1 and 2) bands. Our results show that the most affected frequency bands were delta, theta, beta-2 and gamma-2 bands during the epileptiform activity and there were marked differences in terms of spectral densities between three investigated episodes (basal activity, latent period and epileptiform activity). Our results may help to analyze novel data obtained using similar experimental models and the simple analysis method described here can be used in similar studies to investigate the basic neuronal mechanism of this or other types of experimental epilepsies. | {
"name": "epileptic",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "penicillin-G potassium",
"type": "ChemicalEntity"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a chemical penicillin and a disease epileptiform activity in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means there's a direct link between a chemical and a disease. This includes cases where the chemical causes the disease, higher doses of the chemical increase disease risk, the disease raises the chemical's level in the body, there's a direct positive link between the chemical's level and disease risk, or exposure to the chemical during development affects disease susceptibility later on.
'Negative_Correlation' means there's an inverse relation between a chemical substance and a disease. This includes situations where the chemical or drug is used to treat the disease, the presence of the disease lowers the level of the chemical in the body, or the chemical or drug reduces the likelihood of the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[penicillin,ChemicalEntity]' and '[epileptiform activity,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Detailed spectral profile analysis of penicillin-induced epileptiform activity in anesthetized rats.
- Abstract of the Paper: [Penicillin model is a widely used experimental model for epilepsy research. In the present study we aimed to portray a detailed spectral analysis of penicillin-induced epileptiform activity in comparison with basal brain activity in anesthetized Wistar rats. Male Wistar rats were anesthetized with i.p. urethane and connected to an electrocorticogram setup. After a short period of basal activity recording, epileptic focus was induced by injecting 400IU/2 microl penicillin-G potassium into the left lateral ventricle while the cortical activity was continuously recorded. Basal activity, latent period and the penicillin-induced epileptiform activity periods were then analyzed using both conventional methods and spectral analysis. Spectral analyses were conducted by dividing the whole spectrum into different frequency bands including delta, theta (slow and fast), alpha-sigma, beta (1 and 2) and gamma (1 and 2) bands. Our results show that the most affected frequency bands were delta, theta, beta-2 and gamma-2 bands during the epileptiform activity and there were marked differences in terms of spectral densities between three investigated episodes (basal activity, latent period and epileptiform activity). Our results may help to analyze novel data obtained using similar experimental models and the simple analysis method described here can be used in similar studies to investigate the basic neuronal mechanism of this or other types of experimental epilepsies.]
Identify how '[penicillin,ChemicalEntity]' and '[epileptiform activity,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Detailed spectral profile analysis of penicillin-induced epileptiform activity in anesthetized rats. | Penicillin model is a widely used experimental model for epilepsy research. In the present study we aimed to portray a detailed spectral analysis of penicillin-induced epileptiform activity in comparison with basal brain activity in anesthetized Wistar rats. Male Wistar rats were anesthetized with i.p. urethane and connected to an electrocorticogram setup. After a short period of basal activity recording, epileptic focus was induced by injecting 400IU/2 microl penicillin-G potassium into the left lateral ventricle while the cortical activity was continuously recorded. Basal activity, latent period and the penicillin-induced epileptiform activity periods were then analyzed using both conventional methods and spectral analysis. Spectral analyses were conducted by dividing the whole spectrum into different frequency bands including delta, theta (slow and fast), alpha-sigma, beta (1 and 2) and gamma (1 and 2) bands. Our results show that the most affected frequency bands were delta, theta, beta-2 and gamma-2 bands during the epileptiform activity and there were marked differences in terms of spectral densities between three investigated episodes (basal activity, latent period and epileptiform activity). Our results may help to analyze novel data obtained using similar experimental models and the simple analysis method described here can be used in similar studies to investigate the basic neuronal mechanism of this or other types of experimental epilepsies. | {
"name": "penicillin",
"type": "ChemicalEntity"
} | {
"name": "epileptiform activity",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease ventriculomegaly and a variant p.M453T in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[ventriculomegaly,DiseaseOrPhenotypicFeature]' and '[p.M453T,SequenceVariant]'.
- Title of the Paper: Expanding clinical spectrum of non-autoimmune hyperthyroidism due to an activating germline mutation, p.M453T, in the thyrotropin receptor gene.
- Abstract of the Paper: [OBJECTIVE: To describe clinical and genetic features of a Thai family with non-autoimmune hyperthyroidism (NAH) caused by an activating germline mutation in the thyrotropin receptor (TSHR) gene. PATIENTS: Three affected individuals from the same family (a father and his two children) were studied. Clinical and imaging findings were reviewed and compared. GENETIC ANALYSIS: Genomic DNA was extracted from peripheral blood leukocytes and mutation analysis of the entire coding sequence of the TSHR gene was performed in both children and their parents by direct DNA sequencing. RESULTS: A heterozygous germline T to C transition in exon 10 of the TSHR gene (c.1358T-->C) resulting in the substitution of methionine (ATG) by threonine (ACG) at codon 453 (p.M453T) was identified in the father and his two children. They presented with different clinical severity and variable age of onset. In addition to hyperthyroidism, ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers were consistently found in all affected individuals. CONCLUSIONS: Ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers might be characteristic features of NAH because of an activating TSHR germline mutation. In addition, the shortening of the middle phalanges of the fifth fingers has never been previously described, expanding the phenotypic spectrum of the disease.]
Identify how '[ventriculomegaly,DiseaseOrPhenotypicFeature]' and '[p.M453T,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Expanding clinical spectrum of non-autoimmune hyperthyroidism due to an activating germline mutation, p.M453T, in the thyrotropin receptor gene. | OBJECTIVE: To describe clinical and genetic features of a Thai family with non-autoimmune hyperthyroidism (NAH) caused by an activating germline mutation in the thyrotropin receptor (TSHR) gene. PATIENTS: Three affected individuals from the same family (a father and his two children) were studied. Clinical and imaging findings were reviewed and compared. GENETIC ANALYSIS: Genomic DNA was extracted from peripheral blood leukocytes and mutation analysis of the entire coding sequence of the TSHR gene was performed in both children and their parents by direct DNA sequencing. RESULTS: A heterozygous germline T to C transition in exon 10 of the TSHR gene (c.1358T-->C) resulting in the substitution of methionine (ATG) by threonine (ACG) at codon 453 (p.M453T) was identified in the father and his two children. They presented with different clinical severity and variable age of onset. In addition to hyperthyroidism, ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers were consistently found in all affected individuals. CONCLUSIONS: Ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers might be characteristic features of NAH because of an activating TSHR germline mutation. In addition, the shortening of the middle phalanges of the fifth fingers has never been previously described, expanding the phenotypic spectrum of the disease. | {
"name": "ventriculomegaly",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "p.M453T",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease hyperthyroidism and a variant p.M453T in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[hyperthyroidism,DiseaseOrPhenotypicFeature]' and '[p.M453T,SequenceVariant]'.
- Title of the Paper: Expanding clinical spectrum of non-autoimmune hyperthyroidism due to an activating germline mutation, p.M453T, in the thyrotropin receptor gene.
- Abstract of the Paper: [OBJECTIVE: To describe clinical and genetic features of a Thai family with non-autoimmune hyperthyroidism (NAH) caused by an activating germline mutation in the thyrotropin receptor (TSHR) gene. PATIENTS: Three affected individuals from the same family (a father and his two children) were studied. Clinical and imaging findings were reviewed and compared. GENETIC ANALYSIS: Genomic DNA was extracted from peripheral blood leukocytes and mutation analysis of the entire coding sequence of the TSHR gene was performed in both children and their parents by direct DNA sequencing. RESULTS: A heterozygous germline T to C transition in exon 10 of the TSHR gene (c.1358T-->C) resulting in the substitution of methionine (ATG) by threonine (ACG) at codon 453 (p.M453T) was identified in the father and his two children. They presented with different clinical severity and variable age of onset. In addition to hyperthyroidism, ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers were consistently found in all affected individuals. CONCLUSIONS: Ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers might be characteristic features of NAH because of an activating TSHR germline mutation. In addition, the shortening of the middle phalanges of the fifth fingers has never been previously described, expanding the phenotypic spectrum of the disease.]
Identify how '[hyperthyroidism,DiseaseOrPhenotypicFeature]' and '[p.M453T,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Expanding clinical spectrum of non-autoimmune hyperthyroidism due to an activating germline mutation, p.M453T, in the thyrotropin receptor gene. | OBJECTIVE: To describe clinical and genetic features of a Thai family with non-autoimmune hyperthyroidism (NAH) caused by an activating germline mutation in the thyrotropin receptor (TSHR) gene. PATIENTS: Three affected individuals from the same family (a father and his two children) were studied. Clinical and imaging findings were reviewed and compared. GENETIC ANALYSIS: Genomic DNA was extracted from peripheral blood leukocytes and mutation analysis of the entire coding sequence of the TSHR gene was performed in both children and their parents by direct DNA sequencing. RESULTS: A heterozygous germline T to C transition in exon 10 of the TSHR gene (c.1358T-->C) resulting in the substitution of methionine (ATG) by threonine (ACG) at codon 453 (p.M453T) was identified in the father and his two children. They presented with different clinical severity and variable age of onset. In addition to hyperthyroidism, ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers were consistently found in all affected individuals. CONCLUSIONS: Ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers might be characteristic features of NAH because of an activating TSHR germline mutation. In addition, the shortening of the middle phalanges of the fifth fingers has never been previously described, expanding the phenotypic spectrum of the disease. | {
"name": "hyperthyroidism",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "p.M453T",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein TSHR and a disease Ventriculomegaly in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[TSHR,GeneOrGeneProduct]' and '[Ventriculomegaly,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Expanding clinical spectrum of non-autoimmune hyperthyroidism due to an activating germline mutation, p.M453T, in the thyrotropin receptor gene.
- Abstract of the Paper: [OBJECTIVE: To describe clinical and genetic features of a Thai family with non-autoimmune hyperthyroidism (NAH) caused by an activating germline mutation in the thyrotropin receptor (TSHR) gene. PATIENTS: Three affected individuals from the same family (a father and his two children) were studied. Clinical and imaging findings were reviewed and compared. GENETIC ANALYSIS: Genomic DNA was extracted from peripheral blood leukocytes and mutation analysis of the entire coding sequence of the TSHR gene was performed in both children and their parents by direct DNA sequencing. RESULTS: A heterozygous germline T to C transition in exon 10 of the TSHR gene (c.1358T-->C) resulting in the substitution of methionine (ATG) by threonine (ACG) at codon 453 (p.M453T) was identified in the father and his two children. They presented with different clinical severity and variable age of onset. In addition to hyperthyroidism, ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers were consistently found in all affected individuals. CONCLUSIONS: Ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers might be characteristic features of NAH because of an activating TSHR germline mutation. In addition, the shortening of the middle phalanges of the fifth fingers has never been previously described, expanding the phenotypic spectrum of the disease.]
Identify how '[TSHR,GeneOrGeneProduct]' and '[Ventriculomegaly,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Expanding clinical spectrum of non-autoimmune hyperthyroidism due to an activating germline mutation, p.M453T, in the thyrotropin receptor gene. | OBJECTIVE: To describe clinical and genetic features of a Thai family with non-autoimmune hyperthyroidism (NAH) caused by an activating germline mutation in the thyrotropin receptor (TSHR) gene. PATIENTS: Three affected individuals from the same family (a father and his two children) were studied. Clinical and imaging findings were reviewed and compared. GENETIC ANALYSIS: Genomic DNA was extracted from peripheral blood leukocytes and mutation analysis of the entire coding sequence of the TSHR gene was performed in both children and their parents by direct DNA sequencing. RESULTS: A heterozygous germline T to C transition in exon 10 of the TSHR gene (c.1358T-->C) resulting in the substitution of methionine (ATG) by threonine (ACG) at codon 453 (p.M453T) was identified in the father and his two children. They presented with different clinical severity and variable age of onset. In addition to hyperthyroidism, ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers were consistently found in all affected individuals. CONCLUSIONS: Ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers might be characteristic features of NAH because of an activating TSHR germline mutation. In addition, the shortening of the middle phalanges of the fifth fingers has never been previously described, expanding the phenotypic spectrum of the disease. | {
"name": "TSHR",
"type": "GeneOrGeneProduct"
} | {
"name": "Ventriculomegaly",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein TSHR and a disease hyperthyroidism in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[TSHR,GeneOrGeneProduct]' and '[hyperthyroidism,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Expanding clinical spectrum of non-autoimmune hyperthyroidism due to an activating germline mutation, p.M453T, in the thyrotropin receptor gene.
- Abstract of the Paper: [OBJECTIVE: To describe clinical and genetic features of a Thai family with non-autoimmune hyperthyroidism (NAH) caused by an activating germline mutation in the thyrotropin receptor (TSHR) gene. PATIENTS: Three affected individuals from the same family (a father and his two children) were studied. Clinical and imaging findings were reviewed and compared. GENETIC ANALYSIS: Genomic DNA was extracted from peripheral blood leukocytes and mutation analysis of the entire coding sequence of the TSHR gene was performed in both children and their parents by direct DNA sequencing. RESULTS: A heterozygous germline T to C transition in exon 10 of the TSHR gene (c.1358T-->C) resulting in the substitution of methionine (ATG) by threonine (ACG) at codon 453 (p.M453T) was identified in the father and his two children. They presented with different clinical severity and variable age of onset. In addition to hyperthyroidism, ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers were consistently found in all affected individuals. CONCLUSIONS: Ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers might be characteristic features of NAH because of an activating TSHR germline mutation. In addition, the shortening of the middle phalanges of the fifth fingers has never been previously described, expanding the phenotypic spectrum of the disease.]
Identify how '[TSHR,GeneOrGeneProduct]' and '[hyperthyroidism,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Expanding clinical spectrum of non-autoimmune hyperthyroidism due to an activating germline mutation, p.M453T, in the thyrotropin receptor gene. | OBJECTIVE: To describe clinical and genetic features of a Thai family with non-autoimmune hyperthyroidism (NAH) caused by an activating germline mutation in the thyrotropin receptor (TSHR) gene. PATIENTS: Three affected individuals from the same family (a father and his two children) were studied. Clinical and imaging findings were reviewed and compared. GENETIC ANALYSIS: Genomic DNA was extracted from peripheral blood leukocytes and mutation analysis of the entire coding sequence of the TSHR gene was performed in both children and their parents by direct DNA sequencing. RESULTS: A heterozygous germline T to C transition in exon 10 of the TSHR gene (c.1358T-->C) resulting in the substitution of methionine (ATG) by threonine (ACG) at codon 453 (p.M453T) was identified in the father and his two children. They presented with different clinical severity and variable age of onset. In addition to hyperthyroidism, ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers were consistently found in all affected individuals. CONCLUSIONS: Ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers might be characteristic features of NAH because of an activating TSHR germline mutation. In addition, the shortening of the middle phalanges of the fifth fingers has never been previously described, expanding the phenotypic spectrum of the disease. | {
"name": "TSHR",
"type": "GeneOrGeneProduct"
} | {
"name": "hyperthyroidism",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease non-autoimmune hyperthyroidism and a gene or protein thyrotropin receptor in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a protein or gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or drug) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[non-autoimmune hyperthyroidism,DiseaseOrPhenotypicFeature]' and '[thyrotropin receptor,GeneOrGeneProduct]'.
- Title of the Paper: Expanding clinical spectrum of non-autoimmune hyperthyroidism due to an activating germline mutation, p.M453T, in the thyrotropin receptor gene.
- Abstract of the Paper: [OBJECTIVE: To describe clinical and genetic features of a Thai family with non-autoimmune hyperthyroidism (NAH) caused by an activating germline mutation in the thyrotropin receptor (TSHR) gene. PATIENTS: Three affected individuals from the same family (a father and his two children) were studied. Clinical and imaging findings were reviewed and compared. GENETIC ANALYSIS: Genomic DNA was extracted from peripheral blood leukocytes and mutation analysis of the entire coding sequence of the TSHR gene was performed in both children and their parents by direct DNA sequencing. RESULTS: A heterozygous germline T to C transition in exon 10 of the TSHR gene (c.1358T-->C) resulting in the substitution of methionine (ATG) by threonine (ACG) at codon 453 (p.M453T) was identified in the father and his two children. They presented with different clinical severity and variable age of onset. In addition to hyperthyroidism, ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers were consistently found in all affected individuals. CONCLUSIONS: Ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers might be characteristic features of NAH because of an activating TSHR germline mutation. In addition, the shortening of the middle phalanges of the fifth fingers has never been previously described, expanding the phenotypic spectrum of the disease.]
Identify how '[non-autoimmune hyperthyroidism,DiseaseOrPhenotypicFeature]' and '[thyrotropin receptor,GeneOrGeneProduct]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Expanding clinical spectrum of non-autoimmune hyperthyroidism due to an activating germline mutation, p.M453T, in the thyrotropin receptor gene. | OBJECTIVE: To describe clinical and genetic features of a Thai family with non-autoimmune hyperthyroidism (NAH) caused by an activating germline mutation in the thyrotropin receptor (TSHR) gene. PATIENTS: Three affected individuals from the same family (a father and his two children) were studied. Clinical and imaging findings were reviewed and compared. GENETIC ANALYSIS: Genomic DNA was extracted from peripheral blood leukocytes and mutation analysis of the entire coding sequence of the TSHR gene was performed in both children and their parents by direct DNA sequencing. RESULTS: A heterozygous germline T to C transition in exon 10 of the TSHR gene (c.1358T-->C) resulting in the substitution of methionine (ATG) by threonine (ACG) at codon 453 (p.M453T) was identified in the father and his two children. They presented with different clinical severity and variable age of onset. In addition to hyperthyroidism, ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers were consistently found in all affected individuals. CONCLUSIONS: Ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers might be characteristic features of NAH because of an activating TSHR germline mutation. In addition, the shortening of the middle phalanges of the fifth fingers has never been previously described, expanding the phenotypic spectrum of the disease. | {
"name": "non-autoimmune hyperthyroidism",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "thyrotropin receptor",
"type": "GeneOrGeneProduct"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease non-autoimmune hyperthyroidism and a variant p.M453T in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[non-autoimmune hyperthyroidism,DiseaseOrPhenotypicFeature]' and '[p.M453T,SequenceVariant]'.
- Title of the Paper: Expanding clinical spectrum of non-autoimmune hyperthyroidism due to an activating germline mutation, p.M453T, in the thyrotropin receptor gene.
- Abstract of the Paper: [OBJECTIVE: To describe clinical and genetic features of a Thai family with non-autoimmune hyperthyroidism (NAH) caused by an activating germline mutation in the thyrotropin receptor (TSHR) gene. PATIENTS: Three affected individuals from the same family (a father and his two children) were studied. Clinical and imaging findings were reviewed and compared. GENETIC ANALYSIS: Genomic DNA was extracted from peripheral blood leukocytes and mutation analysis of the entire coding sequence of the TSHR gene was performed in both children and their parents by direct DNA sequencing. RESULTS: A heterozygous germline T to C transition in exon 10 of the TSHR gene (c.1358T-->C) resulting in the substitution of methionine (ATG) by threonine (ACG) at codon 453 (p.M453T) was identified in the father and his two children. They presented with different clinical severity and variable age of onset. In addition to hyperthyroidism, ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers were consistently found in all affected individuals. CONCLUSIONS: Ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers might be characteristic features of NAH because of an activating TSHR germline mutation. In addition, the shortening of the middle phalanges of the fifth fingers has never been previously described, expanding the phenotypic spectrum of the disease.]
Identify how '[non-autoimmune hyperthyroidism,DiseaseOrPhenotypicFeature]' and '[p.M453T,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Expanding clinical spectrum of non-autoimmune hyperthyroidism due to an activating germline mutation, p.M453T, in the thyrotropin receptor gene. | OBJECTIVE: To describe clinical and genetic features of a Thai family with non-autoimmune hyperthyroidism (NAH) caused by an activating germline mutation in the thyrotropin receptor (TSHR) gene. PATIENTS: Three affected individuals from the same family (a father and his two children) were studied. Clinical and imaging findings were reviewed and compared. GENETIC ANALYSIS: Genomic DNA was extracted from peripheral blood leukocytes and mutation analysis of the entire coding sequence of the TSHR gene was performed in both children and their parents by direct DNA sequencing. RESULTS: A heterozygous germline T to C transition in exon 10 of the TSHR gene (c.1358T-->C) resulting in the substitution of methionine (ATG) by threonine (ACG) at codon 453 (p.M453T) was identified in the father and his two children. They presented with different clinical severity and variable age of onset. In addition to hyperthyroidism, ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers were consistently found in all affected individuals. CONCLUSIONS: Ventriculomegaly and bilateral shortening of the fifth metacarpal bones and the middle phalanges of the fifth fingers might be characteristic features of NAH because of an activating TSHR germline mutation. In addition, the shortening of the middle phalanges of the fifth fingers has never been previously described, expanding the phenotypic spectrum of the disease. | {
"name": "non-autoimmune hyperthyroidism",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "p.M453T",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein ATR1 and a disease vasovagal syncope in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[ATR1,GeneOrGeneProduct]' and '[vasovagal syncope,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hemodynamic parameters and heart rate variability during a tilt test in relation to gene polymorphism of renin-angiotensin and serotonin system.
- Abstract of the Paper: [PURPOSE: The aim of the study was to evaluate the renin-angiotensin system and serotonin transporter gene polymorphisms in relation to hemodynamic parameters and heart rate variability during a head-up tilt test (HUT) in patients with vasovagal syncope. METHODS: DNA was collected from 191 patients (mean age 44+/-18 years, 61 men, 130 women). The following gene polymorphisms were determined in genomic DNA: angiotensin-converting enzyme insertion/deletion polymorphism (I/D ACE), angiotensinogen gene polymorphism (M 235), angiotensin II receptor type 1 (ATR1) polymorphism (A 11666C), and polymorphism of serotonin transporter gene (5HTTLPR).Heart rate variability during HUT was assessed in 5-minute intervals by low frequency, high frequency, standard deviation of the normal-to-normal (SDNN), and root mean square successive difference parameters. RESULTS: AA genotype of A 1166C polymorphism was associated with lower minimal systolic blood pressure (SBP) and diastolic blood pressure (DBP) during HUT compared with other genotypes (minimal SBP: AA 59.6+/-21,8, AC 79.9+/-22.7, CC 65.4+/-22.7 mmHg, P=0.007), (minimal DBP: AA 36.4+/-22.7, AC 52.3+/-22.9, CC 45.4+/-19.5 mmHg, P=0.007).AA genotype was also associated with higher SDNN compared to other genotypes in the early phase of HUT (SDNN in 5 minutes of tilt: AA 59.7+/-24.6, AC 50.6+/-20.6, CC 46.0+/-13.2, P=0.01) and at syncope occurrence (SDNN: AA 71.0+/-20.9, AC 58.2+/-17.9, CC 58+/-10, P=0.04) CONCLUSION: AA genotype of A 1166C polymorphism in the ATR1 gene may be associated with hypotension and decline in sympathetic tone during HUT. Its role in genetic predisposition to vasovagal syncope cannot be excluded.]
Identify how '[ATR1,GeneOrGeneProduct]' and '[vasovagal syncope,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Hemodynamic parameters and heart rate variability during a tilt test in relation to gene polymorphism of renin-angiotensin and serotonin system. | PURPOSE: The aim of the study was to evaluate the renin-angiotensin system and serotonin transporter gene polymorphisms in relation to hemodynamic parameters and heart rate variability during a head-up tilt test (HUT) in patients with vasovagal syncope. METHODS: DNA was collected from 191 patients (mean age 44+/-18 years, 61 men, 130 women). The following gene polymorphisms were determined in genomic DNA: angiotensin-converting enzyme insertion/deletion polymorphism (I/D ACE), angiotensinogen gene polymorphism (M 235), angiotensin II receptor type 1 (ATR1) polymorphism (A 11666C), and polymorphism of serotonin transporter gene (5HTTLPR).Heart rate variability during HUT was assessed in 5-minute intervals by low frequency, high frequency, standard deviation of the normal-to-normal (SDNN), and root mean square successive difference parameters. RESULTS: AA genotype of A 1166C polymorphism was associated with lower minimal systolic blood pressure (SBP) and diastolic blood pressure (DBP) during HUT compared with other genotypes (minimal SBP: AA 59.6+/-21,8, AC 79.9+/-22.7, CC 65.4+/-22.7 mmHg, P=0.007), (minimal DBP: AA 36.4+/-22.7, AC 52.3+/-22.9, CC 45.4+/-19.5 mmHg, P=0.007).AA genotype was also associated with higher SDNN compared to other genotypes in the early phase of HUT (SDNN in 5 minutes of tilt: AA 59.7+/-24.6, AC 50.6+/-20.6, CC 46.0+/-13.2, P=0.01) and at syncope occurrence (SDNN: AA 71.0+/-20.9, AC 58.2+/-17.9, CC 58+/-10, P=0.04) CONCLUSION: AA genotype of A 1166C polymorphism in the ATR1 gene may be associated with hypotension and decline in sympathetic tone during HUT. Its role in genetic predisposition to vasovagal syncope cannot be excluded. | {
"name": "ATR1",
"type": "GeneOrGeneProduct"
} | {
"name": "vasovagal syncope",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein ATR1 and a disease hypotension in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[ATR1,GeneOrGeneProduct]' and '[hypotension,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hemodynamic parameters and heart rate variability during a tilt test in relation to gene polymorphism of renin-angiotensin and serotonin system.
- Abstract of the Paper: [PURPOSE: The aim of the study was to evaluate the renin-angiotensin system and serotonin transporter gene polymorphisms in relation to hemodynamic parameters and heart rate variability during a head-up tilt test (HUT) in patients with vasovagal syncope. METHODS: DNA was collected from 191 patients (mean age 44+/-18 years, 61 men, 130 women). The following gene polymorphisms were determined in genomic DNA: angiotensin-converting enzyme insertion/deletion polymorphism (I/D ACE), angiotensinogen gene polymorphism (M 235), angiotensin II receptor type 1 (ATR1) polymorphism (A 11666C), and polymorphism of serotonin transporter gene (5HTTLPR).Heart rate variability during HUT was assessed in 5-minute intervals by low frequency, high frequency, standard deviation of the normal-to-normal (SDNN), and root mean square successive difference parameters. RESULTS: AA genotype of A 1166C polymorphism was associated with lower minimal systolic blood pressure (SBP) and diastolic blood pressure (DBP) during HUT compared with other genotypes (minimal SBP: AA 59.6+/-21,8, AC 79.9+/-22.7, CC 65.4+/-22.7 mmHg, P=0.007), (minimal DBP: AA 36.4+/-22.7, AC 52.3+/-22.9, CC 45.4+/-19.5 mmHg, P=0.007).AA genotype was also associated with higher SDNN compared to other genotypes in the early phase of HUT (SDNN in 5 minutes of tilt: AA 59.7+/-24.6, AC 50.6+/-20.6, CC 46.0+/-13.2, P=0.01) and at syncope occurrence (SDNN: AA 71.0+/-20.9, AC 58.2+/-17.9, CC 58+/-10, P=0.04) CONCLUSION: AA genotype of A 1166C polymorphism in the ATR1 gene may be associated with hypotension and decline in sympathetic tone during HUT. Its role in genetic predisposition to vasovagal syncope cannot be excluded.]
Identify how '[ATR1,GeneOrGeneProduct]' and '[hypotension,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Hemodynamic parameters and heart rate variability during a tilt test in relation to gene polymorphism of renin-angiotensin and serotonin system. | PURPOSE: The aim of the study was to evaluate the renin-angiotensin system and serotonin transporter gene polymorphisms in relation to hemodynamic parameters and heart rate variability during a head-up tilt test (HUT) in patients with vasovagal syncope. METHODS: DNA was collected from 191 patients (mean age 44+/-18 years, 61 men, 130 women). The following gene polymorphisms were determined in genomic DNA: angiotensin-converting enzyme insertion/deletion polymorphism (I/D ACE), angiotensinogen gene polymorphism (M 235), angiotensin II receptor type 1 (ATR1) polymorphism (A 11666C), and polymorphism of serotonin transporter gene (5HTTLPR).Heart rate variability during HUT was assessed in 5-minute intervals by low frequency, high frequency, standard deviation of the normal-to-normal (SDNN), and root mean square successive difference parameters. RESULTS: AA genotype of A 1166C polymorphism was associated with lower minimal systolic blood pressure (SBP) and diastolic blood pressure (DBP) during HUT compared with other genotypes (minimal SBP: AA 59.6+/-21,8, AC 79.9+/-22.7, CC 65.4+/-22.7 mmHg, P=0.007), (minimal DBP: AA 36.4+/-22.7, AC 52.3+/-22.9, CC 45.4+/-19.5 mmHg, P=0.007).AA genotype was also associated with higher SDNN compared to other genotypes in the early phase of HUT (SDNN in 5 minutes of tilt: AA 59.7+/-24.6, AC 50.6+/-20.6, CC 46.0+/-13.2, P=0.01) and at syncope occurrence (SDNN: AA 71.0+/-20.9, AC 58.2+/-17.9, CC 58+/-10, P=0.04) CONCLUSION: AA genotype of A 1166C polymorphism in the ATR1 gene may be associated with hypotension and decline in sympathetic tone during HUT. Its role in genetic predisposition to vasovagal syncope cannot be excluded. | {
"name": "ATR1",
"type": "GeneOrGeneProduct"
} | {
"name": "hypotension",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease syncope and a gene or protein ATR1 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a protein or gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or drug) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[syncope,DiseaseOrPhenotypicFeature]' and '[ATR1,GeneOrGeneProduct]'.
- Title of the Paper: Hemodynamic parameters and heart rate variability during a tilt test in relation to gene polymorphism of renin-angiotensin and serotonin system.
- Abstract of the Paper: [PURPOSE: The aim of the study was to evaluate the renin-angiotensin system and serotonin transporter gene polymorphisms in relation to hemodynamic parameters and heart rate variability during a head-up tilt test (HUT) in patients with vasovagal syncope. METHODS: DNA was collected from 191 patients (mean age 44+/-18 years, 61 men, 130 women). The following gene polymorphisms were determined in genomic DNA: angiotensin-converting enzyme insertion/deletion polymorphism (I/D ACE), angiotensinogen gene polymorphism (M 235), angiotensin II receptor type 1 (ATR1) polymorphism (A 11666C), and polymorphism of serotonin transporter gene (5HTTLPR).Heart rate variability during HUT was assessed in 5-minute intervals by low frequency, high frequency, standard deviation of the normal-to-normal (SDNN), and root mean square successive difference parameters. RESULTS: AA genotype of A 1166C polymorphism was associated with lower minimal systolic blood pressure (SBP) and diastolic blood pressure (DBP) during HUT compared with other genotypes (minimal SBP: AA 59.6+/-21,8, AC 79.9+/-22.7, CC 65.4+/-22.7 mmHg, P=0.007), (minimal DBP: AA 36.4+/-22.7, AC 52.3+/-22.9, CC 45.4+/-19.5 mmHg, P=0.007).AA genotype was also associated with higher SDNN compared to other genotypes in the early phase of HUT (SDNN in 5 minutes of tilt: AA 59.7+/-24.6, AC 50.6+/-20.6, CC 46.0+/-13.2, P=0.01) and at syncope occurrence (SDNN: AA 71.0+/-20.9, AC 58.2+/-17.9, CC 58+/-10, P=0.04) CONCLUSION: AA genotype of A 1166C polymorphism in the ATR1 gene may be associated with hypotension and decline in sympathetic tone during HUT. Its role in genetic predisposition to vasovagal syncope cannot be excluded.]
Identify how '[syncope,DiseaseOrPhenotypicFeature]' and '[ATR1,GeneOrGeneProduct]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Hemodynamic parameters and heart rate variability during a tilt test in relation to gene polymorphism of renin-angiotensin and serotonin system. | PURPOSE: The aim of the study was to evaluate the renin-angiotensin system and serotonin transporter gene polymorphisms in relation to hemodynamic parameters and heart rate variability during a head-up tilt test (HUT) in patients with vasovagal syncope. METHODS: DNA was collected from 191 patients (mean age 44+/-18 years, 61 men, 130 women). The following gene polymorphisms were determined in genomic DNA: angiotensin-converting enzyme insertion/deletion polymorphism (I/D ACE), angiotensinogen gene polymorphism (M 235), angiotensin II receptor type 1 (ATR1) polymorphism (A 11666C), and polymorphism of serotonin transporter gene (5HTTLPR).Heart rate variability during HUT was assessed in 5-minute intervals by low frequency, high frequency, standard deviation of the normal-to-normal (SDNN), and root mean square successive difference parameters. RESULTS: AA genotype of A 1166C polymorphism was associated with lower minimal systolic blood pressure (SBP) and diastolic blood pressure (DBP) during HUT compared with other genotypes (minimal SBP: AA 59.6+/-21,8, AC 79.9+/-22.7, CC 65.4+/-22.7 mmHg, P=0.007), (minimal DBP: AA 36.4+/-22.7, AC 52.3+/-22.9, CC 45.4+/-19.5 mmHg, P=0.007).AA genotype was also associated with higher SDNN compared to other genotypes in the early phase of HUT (SDNN in 5 minutes of tilt: AA 59.7+/-24.6, AC 50.6+/-20.6, CC 46.0+/-13.2, P=0.01) and at syncope occurrence (SDNN: AA 71.0+/-20.9, AC 58.2+/-17.9, CC 58+/-10, P=0.04) CONCLUSION: AA genotype of A 1166C polymorphism in the ATR1 gene may be associated with hypotension and decline in sympathetic tone during HUT. Its role in genetic predisposition to vasovagal syncope cannot be excluded. | {
"name": "syncope",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "ATR1",
"type": "GeneOrGeneProduct"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease syncope and a variant A 1166C in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[syncope,DiseaseOrPhenotypicFeature]' and '[A 1166C,SequenceVariant]'.
- Title of the Paper: Hemodynamic parameters and heart rate variability during a tilt test in relation to gene polymorphism of renin-angiotensin and serotonin system.
- Abstract of the Paper: [PURPOSE: The aim of the study was to evaluate the renin-angiotensin system and serotonin transporter gene polymorphisms in relation to hemodynamic parameters and heart rate variability during a head-up tilt test (HUT) in patients with vasovagal syncope. METHODS: DNA was collected from 191 patients (mean age 44+/-18 years, 61 men, 130 women). The following gene polymorphisms were determined in genomic DNA: angiotensin-converting enzyme insertion/deletion polymorphism (I/D ACE), angiotensinogen gene polymorphism (M 235), angiotensin II receptor type 1 (ATR1) polymorphism (A 11666C), and polymorphism of serotonin transporter gene (5HTTLPR).Heart rate variability during HUT was assessed in 5-minute intervals by low frequency, high frequency, standard deviation of the normal-to-normal (SDNN), and root mean square successive difference parameters. RESULTS: AA genotype of A 1166C polymorphism was associated with lower minimal systolic blood pressure (SBP) and diastolic blood pressure (DBP) during HUT compared with other genotypes (minimal SBP: AA 59.6+/-21,8, AC 79.9+/-22.7, CC 65.4+/-22.7 mmHg, P=0.007), (minimal DBP: AA 36.4+/-22.7, AC 52.3+/-22.9, CC 45.4+/-19.5 mmHg, P=0.007).AA genotype was also associated with higher SDNN compared to other genotypes in the early phase of HUT (SDNN in 5 minutes of tilt: AA 59.7+/-24.6, AC 50.6+/-20.6, CC 46.0+/-13.2, P=0.01) and at syncope occurrence (SDNN: AA 71.0+/-20.9, AC 58.2+/-17.9, CC 58+/-10, P=0.04) CONCLUSION: AA genotype of A 1166C polymorphism in the ATR1 gene may be associated with hypotension and decline in sympathetic tone during HUT. Its role in genetic predisposition to vasovagal syncope cannot be excluded.]
Identify how '[syncope,DiseaseOrPhenotypicFeature]' and '[A 1166C,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Hemodynamic parameters and heart rate variability during a tilt test in relation to gene polymorphism of renin-angiotensin and serotonin system. | PURPOSE: The aim of the study was to evaluate the renin-angiotensin system and serotonin transporter gene polymorphisms in relation to hemodynamic parameters and heart rate variability during a head-up tilt test (HUT) in patients with vasovagal syncope. METHODS: DNA was collected from 191 patients (mean age 44+/-18 years, 61 men, 130 women). The following gene polymorphisms were determined in genomic DNA: angiotensin-converting enzyme insertion/deletion polymorphism (I/D ACE), angiotensinogen gene polymorphism (M 235), angiotensin II receptor type 1 (ATR1) polymorphism (A 11666C), and polymorphism of serotonin transporter gene (5HTTLPR).Heart rate variability during HUT was assessed in 5-minute intervals by low frequency, high frequency, standard deviation of the normal-to-normal (SDNN), and root mean square successive difference parameters. RESULTS: AA genotype of A 1166C polymorphism was associated with lower minimal systolic blood pressure (SBP) and diastolic blood pressure (DBP) during HUT compared with other genotypes (minimal SBP: AA 59.6+/-21,8, AC 79.9+/-22.7, CC 65.4+/-22.7 mmHg, P=0.007), (minimal DBP: AA 36.4+/-22.7, AC 52.3+/-22.9, CC 45.4+/-19.5 mmHg, P=0.007).AA genotype was also associated with higher SDNN compared to other genotypes in the early phase of HUT (SDNN in 5 minutes of tilt: AA 59.7+/-24.6, AC 50.6+/-20.6, CC 46.0+/-13.2, P=0.01) and at syncope occurrence (SDNN: AA 71.0+/-20.9, AC 58.2+/-17.9, CC 58+/-10, P=0.04) CONCLUSION: AA genotype of A 1166C polymorphism in the ATR1 gene may be associated with hypotension and decline in sympathetic tone during HUT. Its role in genetic predisposition to vasovagal syncope cannot be excluded. | {
"name": "syncope",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "A 1166C",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant A 1166C and a disease vasovagal syncope in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[A 1166C,SequenceVariant]' and '[vasovagal syncope,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hemodynamic parameters and heart rate variability during a tilt test in relation to gene polymorphism of renin-angiotensin and serotonin system.
- Abstract of the Paper: [PURPOSE: The aim of the study was to evaluate the renin-angiotensin system and serotonin transporter gene polymorphisms in relation to hemodynamic parameters and heart rate variability during a head-up tilt test (HUT) in patients with vasovagal syncope. METHODS: DNA was collected from 191 patients (mean age 44+/-18 years, 61 men, 130 women). The following gene polymorphisms were determined in genomic DNA: angiotensin-converting enzyme insertion/deletion polymorphism (I/D ACE), angiotensinogen gene polymorphism (M 235), angiotensin II receptor type 1 (ATR1) polymorphism (A 11666C), and polymorphism of serotonin transporter gene (5HTTLPR).Heart rate variability during HUT was assessed in 5-minute intervals by low frequency, high frequency, standard deviation of the normal-to-normal (SDNN), and root mean square successive difference parameters. RESULTS: AA genotype of A 1166C polymorphism was associated with lower minimal systolic blood pressure (SBP) and diastolic blood pressure (DBP) during HUT compared with other genotypes (minimal SBP: AA 59.6+/-21,8, AC 79.9+/-22.7, CC 65.4+/-22.7 mmHg, P=0.007), (minimal DBP: AA 36.4+/-22.7, AC 52.3+/-22.9, CC 45.4+/-19.5 mmHg, P=0.007).AA genotype was also associated with higher SDNN compared to other genotypes in the early phase of HUT (SDNN in 5 minutes of tilt: AA 59.7+/-24.6, AC 50.6+/-20.6, CC 46.0+/-13.2, P=0.01) and at syncope occurrence (SDNN: AA 71.0+/-20.9, AC 58.2+/-17.9, CC 58+/-10, P=0.04) CONCLUSION: AA genotype of A 1166C polymorphism in the ATR1 gene may be associated with hypotension and decline in sympathetic tone during HUT. Its role in genetic predisposition to vasovagal syncope cannot be excluded.]
Identify how '[A 1166C,SequenceVariant]' and '[vasovagal syncope,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hemodynamic parameters and heart rate variability during a tilt test in relation to gene polymorphism of renin-angiotensin and serotonin system. | PURPOSE: The aim of the study was to evaluate the renin-angiotensin system and serotonin transporter gene polymorphisms in relation to hemodynamic parameters and heart rate variability during a head-up tilt test (HUT) in patients with vasovagal syncope. METHODS: DNA was collected from 191 patients (mean age 44+/-18 years, 61 men, 130 women). The following gene polymorphisms were determined in genomic DNA: angiotensin-converting enzyme insertion/deletion polymorphism (I/D ACE), angiotensinogen gene polymorphism (M 235), angiotensin II receptor type 1 (ATR1) polymorphism (A 11666C), and polymorphism of serotonin transporter gene (5HTTLPR).Heart rate variability during HUT was assessed in 5-minute intervals by low frequency, high frequency, standard deviation of the normal-to-normal (SDNN), and root mean square successive difference parameters. RESULTS: AA genotype of A 1166C polymorphism was associated with lower minimal systolic blood pressure (SBP) and diastolic blood pressure (DBP) during HUT compared with other genotypes (minimal SBP: AA 59.6+/-21,8, AC 79.9+/-22.7, CC 65.4+/-22.7 mmHg, P=0.007), (minimal DBP: AA 36.4+/-22.7, AC 52.3+/-22.9, CC 45.4+/-19.5 mmHg, P=0.007).AA genotype was also associated with higher SDNN compared to other genotypes in the early phase of HUT (SDNN in 5 minutes of tilt: AA 59.7+/-24.6, AC 50.6+/-20.6, CC 46.0+/-13.2, P=0.01) and at syncope occurrence (SDNN: AA 71.0+/-20.9, AC 58.2+/-17.9, CC 58+/-10, P=0.04) CONCLUSION: AA genotype of A 1166C polymorphism in the ATR1 gene may be associated with hypotension and decline in sympathetic tone during HUT. Its role in genetic predisposition to vasovagal syncope cannot be excluded. | {
"name": "A 1166C",
"type": "SequenceVariant"
} | {
"name": "vasovagal syncope",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant A 1166C and a disease hypotension in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[A 1166C,SequenceVariant]' and '[hypotension,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hemodynamic parameters and heart rate variability during a tilt test in relation to gene polymorphism of renin-angiotensin and serotonin system.
- Abstract of the Paper: [PURPOSE: The aim of the study was to evaluate the renin-angiotensin system and serotonin transporter gene polymorphisms in relation to hemodynamic parameters and heart rate variability during a head-up tilt test (HUT) in patients with vasovagal syncope. METHODS: DNA was collected from 191 patients (mean age 44+/-18 years, 61 men, 130 women). The following gene polymorphisms were determined in genomic DNA: angiotensin-converting enzyme insertion/deletion polymorphism (I/D ACE), angiotensinogen gene polymorphism (M 235), angiotensin II receptor type 1 (ATR1) polymorphism (A 11666C), and polymorphism of serotonin transporter gene (5HTTLPR).Heart rate variability during HUT was assessed in 5-minute intervals by low frequency, high frequency, standard deviation of the normal-to-normal (SDNN), and root mean square successive difference parameters. RESULTS: AA genotype of A 1166C polymorphism was associated with lower minimal systolic blood pressure (SBP) and diastolic blood pressure (DBP) during HUT compared with other genotypes (minimal SBP: AA 59.6+/-21,8, AC 79.9+/-22.7, CC 65.4+/-22.7 mmHg, P=0.007), (minimal DBP: AA 36.4+/-22.7, AC 52.3+/-22.9, CC 45.4+/-19.5 mmHg, P=0.007).AA genotype was also associated with higher SDNN compared to other genotypes in the early phase of HUT (SDNN in 5 minutes of tilt: AA 59.7+/-24.6, AC 50.6+/-20.6, CC 46.0+/-13.2, P=0.01) and at syncope occurrence (SDNN: AA 71.0+/-20.9, AC 58.2+/-17.9, CC 58+/-10, P=0.04) CONCLUSION: AA genotype of A 1166C polymorphism in the ATR1 gene may be associated with hypotension and decline in sympathetic tone during HUT. Its role in genetic predisposition to vasovagal syncope cannot be excluded.]
Identify how '[A 1166C,SequenceVariant]' and '[hypotension,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Hemodynamic parameters and heart rate variability during a tilt test in relation to gene polymorphism of renin-angiotensin and serotonin system. | PURPOSE: The aim of the study was to evaluate the renin-angiotensin system and serotonin transporter gene polymorphisms in relation to hemodynamic parameters and heart rate variability during a head-up tilt test (HUT) in patients with vasovagal syncope. METHODS: DNA was collected from 191 patients (mean age 44+/-18 years, 61 men, 130 women). The following gene polymorphisms were determined in genomic DNA: angiotensin-converting enzyme insertion/deletion polymorphism (I/D ACE), angiotensinogen gene polymorphism (M 235), angiotensin II receptor type 1 (ATR1) polymorphism (A 11666C), and polymorphism of serotonin transporter gene (5HTTLPR).Heart rate variability during HUT was assessed in 5-minute intervals by low frequency, high frequency, standard deviation of the normal-to-normal (SDNN), and root mean square successive difference parameters. RESULTS: AA genotype of A 1166C polymorphism was associated with lower minimal systolic blood pressure (SBP) and diastolic blood pressure (DBP) during HUT compared with other genotypes (minimal SBP: AA 59.6+/-21,8, AC 79.9+/-22.7, CC 65.4+/-22.7 mmHg, P=0.007), (minimal DBP: AA 36.4+/-22.7, AC 52.3+/-22.9, CC 45.4+/-19.5 mmHg, P=0.007).AA genotype was also associated with higher SDNN compared to other genotypes in the early phase of HUT (SDNN in 5 minutes of tilt: AA 59.7+/-24.6, AC 50.6+/-20.6, CC 46.0+/-13.2, P=0.01) and at syncope occurrence (SDNN: AA 71.0+/-20.9, AC 58.2+/-17.9, CC 58+/-10, P=0.04) CONCLUSION: AA genotype of A 1166C polymorphism in the ATR1 gene may be associated with hypotension and decline in sympathetic tone during HUT. Its role in genetic predisposition to vasovagal syncope cannot be excluded. | {
"name": "A 1166C",
"type": "SequenceVariant"
} | {
"name": "hypotension",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease Joubert syndrome (JBTS) type 6 and a variant p.G821R in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[Joubert syndrome (JBTS) type 6,DiseaseOrPhenotypicFeature]' and '[p.G821R,SequenceVariant]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[Joubert syndrome (JBTS) type 6,DiseaseOrPhenotypicFeature]' and '[p.G821R,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "Joubert syndrome (JBTS) type 6",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "p.G821R",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease Joubert syndrome (JBTS) type 6 and a variant p.C615R in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[Joubert syndrome (JBTS) type 6,DiseaseOrPhenotypicFeature]' and '[p.C615R,SequenceVariant]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[Joubert syndrome (JBTS) type 6,DiseaseOrPhenotypicFeature]' and '[p.C615R,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "Joubert syndrome (JBTS) type 6",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "p.C615R",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease Joubert syndrome (JBTS) type 6 and a variant p.W290L in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[Joubert syndrome (JBTS) type 6,DiseaseOrPhenotypicFeature]' and '[p.W290L,SequenceVariant]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[Joubert syndrome (JBTS) type 6,DiseaseOrPhenotypicFeature]' and '[p.W290L,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "Joubert syndrome (JBTS) type 6",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "p.W290L",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease Meckel-Gruber syndrome (MKS) type 3 and a variant p.G821R in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[Meckel-Gruber syndrome (MKS) type 3,DiseaseOrPhenotypicFeature]' and '[p.G821R,SequenceVariant]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[Meckel-Gruber syndrome (MKS) type 3,DiseaseOrPhenotypicFeature]' and '[p.G821R,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "Meckel-Gruber syndrome (MKS) type 3",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "p.G821R",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease Meckel-Gruber syndrome (MKS) type 3 and a variant p.C615R in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[Meckel-Gruber syndrome (MKS) type 3,DiseaseOrPhenotypicFeature]' and '[p.C615R,SequenceVariant]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[Meckel-Gruber syndrome (MKS) type 3,DiseaseOrPhenotypicFeature]' and '[p.C615R,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "Meckel-Gruber syndrome (MKS) type 3",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "p.C615R",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease Meckel-Gruber syndrome (MKS) type 3 and a variant p.W290L in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[Meckel-Gruber syndrome (MKS) type 3,DiseaseOrPhenotypicFeature]' and '[p.W290L,SequenceVariant]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[Meckel-Gruber syndrome (MKS) type 3,DiseaseOrPhenotypicFeature]' and '[p.W290L,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "Meckel-Gruber syndrome (MKS) type 3",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "p.W290L",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant p.G821S and a disease NPHP in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[p.G821S,SequenceVariant]' and '[NPHP,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[p.G821S,SequenceVariant]' and '[NPHP,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "p.G821S",
"type": "SequenceVariant"
} | {
"name": "NPHP",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant p.G821R and a disease MKS in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[p.G821R,SequenceVariant]' and '[MKS,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[p.G821R,SequenceVariant]' and '[MKS,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "p.G821R",
"type": "SequenceVariant"
} | {
"name": "MKS",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant p.G821R and a disease JBTS in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[p.G821R,SequenceVariant]' and '[JBTS,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[p.G821R,SequenceVariant]' and '[JBTS,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "p.G821R",
"type": "SequenceVariant"
} | {
"name": "JBTS",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant p.G821S and a disease liver fibrosis in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[p.G821S,SequenceVariant]' and '[liver fibrosis,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[p.G821S,SequenceVariant]' and '[liver fibrosis,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "p.G821S",
"type": "SequenceVariant"
} | {
"name": "liver fibrosis",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant p.C615R and a disease NPHP in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[p.C615R,SequenceVariant]' and '[NPHP,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[p.C615R,SequenceVariant]' and '[NPHP,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "p.C615R",
"type": "SequenceVariant"
} | {
"name": "NPHP",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant p.C615R and a disease MKS in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[p.C615R,SequenceVariant]' and '[MKS,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[p.C615R,SequenceVariant]' and '[MKS,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "p.C615R",
"type": "SequenceVariant"
} | {
"name": "MKS",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant p.C615R and a disease Joubert syndrome in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[p.C615R,SequenceVariant]' and '[Joubert syndrome,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[p.C615R,SequenceVariant]' and '[Joubert syndrome,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "p.C615R",
"type": "SequenceVariant"
} | {
"name": "Joubert syndrome",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant p.C615R and a disease liver fibrosis in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[p.C615R,SequenceVariant]' and '[liver fibrosis,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[p.C615R,SequenceVariant]' and '[liver fibrosis,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "p.C615R",
"type": "SequenceVariant"
} | {
"name": "liver fibrosis",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant p.W290L and a disease NPHP in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[p.W290L,SequenceVariant]' and '[NPHP,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[p.W290L,SequenceVariant]' and '[NPHP,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "p.W290L",
"type": "SequenceVariant"
} | {
"name": "NPHP",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant p.W290L and a disease MKS in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[p.W290L,SequenceVariant]' and '[MKS,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[p.W290L,SequenceVariant]' and '[MKS,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "p.W290L",
"type": "SequenceVariant"
} | {
"name": "MKS",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant p.W290L and a disease Joubert syndrome in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[p.W290L,SequenceVariant]' and '[Joubert syndrome,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[p.W290L,SequenceVariant]' and '[Joubert syndrome,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "p.W290L",
"type": "SequenceVariant"
} | {
"name": "Joubert syndrome",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a variant p.W290L and a disease liver fibrosis in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[p.W290L,SequenceVariant]' and '[liver fibrosis,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[p.W290L,SequenceVariant]' and '[liver fibrosis,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "p.W290L",
"type": "SequenceVariant"
} | {
"name": "liver fibrosis",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease NPHP with liver fibrosis and a variant p.G821R in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[NPHP with liver fibrosis,DiseaseOrPhenotypicFeature]' and '[p.G821R,SequenceVariant]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[NPHP with liver fibrosis,DiseaseOrPhenotypicFeature]' and '[p.G821R,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "NPHP with liver fibrosis",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "p.G821R",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease NPHP with liver fibrosis and a variant p.C615R in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[NPHP with liver fibrosis,DiseaseOrPhenotypicFeature]' and '[p.C615R,SequenceVariant]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[NPHP with liver fibrosis,DiseaseOrPhenotypicFeature]' and '[p.C615R,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "NPHP with liver fibrosis",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "p.C615R",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease NPHP11 and a variant p.W290L in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[NPHP11,DiseaseOrPhenotypicFeature]' and '[p.W290L,SequenceVariant]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[NPHP11,DiseaseOrPhenotypicFeature]' and '[p.W290L,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "NPHP11",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "p.W290L",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein TMEM67 and a disease Joubert syndrome (JBTS) type 6 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[TMEM67,GeneOrGeneProduct]' and '[Joubert syndrome (JBTS) type 6,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[TMEM67,GeneOrGeneProduct]' and '[Joubert syndrome (JBTS) type 6,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "TMEM67",
"type": "GeneOrGeneProduct"
} | {
"name": "Joubert syndrome (JBTS) type 6",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein TMEM67 and a disease Meckel-Gruber syndrome (MKS) type 3 in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[TMEM67,GeneOrGeneProduct]' and '[Meckel-Gruber syndrome (MKS) type 3,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[TMEM67,GeneOrGeneProduct]' and '[Meckel-Gruber syndrome (MKS) type 3,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "TMEM67",
"type": "GeneOrGeneProduct"
} | {
"name": "Meckel-Gruber syndrome (MKS) type 3",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein TMEM67 and a disease NPHP in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[TMEM67,GeneOrGeneProduct]' and '[NPHP,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[TMEM67,GeneOrGeneProduct]' and '[NPHP,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "TMEM67",
"type": "GeneOrGeneProduct"
} | {
"name": "NPHP",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein MKS3 and a disease MKS in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[MKS3,GeneOrGeneProduct]' and '[MKS,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[MKS3,GeneOrGeneProduct]' and '[MKS,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "MKS3",
"type": "GeneOrGeneProduct"
} | {
"name": "MKS",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein MKS3 and a disease JBTS in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[MKS3,GeneOrGeneProduct]' and '[JBTS,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[MKS3,GeneOrGeneProduct]' and '[JBTS,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "MKS3",
"type": "GeneOrGeneProduct"
} | {
"name": "JBTS",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein MKS3 and a disease liver fibrosis in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[MKS3,GeneOrGeneProduct]' and '[liver fibrosis,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[MKS3,GeneOrGeneProduct]' and '[liver fibrosis,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "MKS3",
"type": "GeneOrGeneProduct"
} | {
"name": "liver fibrosis",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein TMEM67 and a disease nephronophthisis with liver fibrosis in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[TMEM67,GeneOrGeneProduct]' and '[nephronophthisis with liver fibrosis,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).
- Abstract of the Paper: [BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders.]
Identify how '[TMEM67,GeneOrGeneProduct]' and '[nephronophthisis with liver fibrosis,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11). | BACKGROUND: Nephronophthisis (NPHP), a rare recessive cystic kidney disease, is the most frequent genetic cause of chronic renal failure in children and young adults. Mutations in nine genes (NPHP1-9) have been identified. NPHP can be associated with retinal degeneration (Senior-Loken syndrome), brainstem and cerebellar anomalies (Joubert syndrome), or liver fibrosis. METHODS: To identify a causative gene for the subset of patients with associated liver fibrosis, the authors performed a genome wide linkage search in a consanguineous family with three affected patients using 50K SNP microarrays and homozygosity mapping. RESULTS: The authors obtained a significant maximum parametric LOD (logarithm of odds) score of Z(max) = 3.72 on chromosome 8q22 and identified a homozygous missense mutation in the gene MKS3/TMEM67. When examining a worldwide cohort of 62 independent patients with NPHP and associated liver fibrosis we identified altogether four novel mutations (p.W290L, p.C615R, p.G821S, and p.G821R) in five of them. Mutations of MKS3/TMEM67, found recently in Meckel-Gruber syndrome (MKS) type 3 and Joubert syndrome (JBTS) type 6, are predominantly truncating mutations. In contrast, the mutations detected here in patients with NPHP and associated liver fibrosis are exclusively missense mutations. This suggests that they may represent hypomorphic alleles, leading to a milder phenotype compared with the more severe MKS or JBTS phenotype. Additionally, mutation analysis for MKS3/TMEM67 in 120 patients with JBTS yielded seven different (four novel) mutations in five patients, four of whom also presented with congenital liver fibrosis. CONCLUSIONS: Hypomorphic MKS3/TMEM67 mutations cause NPHP with liver fibrosis (NPHP11). This is the first report of MKS3 mutations in patients with no vermian agenesis and without neurological signs. Thus NPHP, JBTS, and MKS represent allelic disorders. | {
"name": "TMEM67",
"type": "GeneOrGeneProduct"
} | {
"name": "nephronophthisis with liver fibrosis",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a disease PD and a variant insertion/deletion (long allele-L/short allele-S) of 43 bp in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' means that a genetic variant is linked to an increased risk of a disease. This includes cases where the variant is more common in those with the disease, causes abnormal gene expression or non-functionality leading to the disease, results in a disease due to a protein deficiency for which the variant is responsible, contributes to genetic susceptibility to the disease, or has a significant impact on the development of the disease.
'Negative_Correlation' indicates that the variant decreases the risk of the disease.
'Association' means that a genetic variant found in some patients is linked to a lower chance of getting the disease, or it makes them less likely to develop the disease. It also covers relation that don't fit into a positive/negative correlation category or relation that are not clearly defined.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[PD,DiseaseOrPhenotypicFeature]' and '[insertion/deletion (long allele-L/short allele-S) of 43 bp,SequenceVariant]'.
- Title of the Paper: Serotonin transporter gene polymorphic element 5-HTTLPR increases the risk of sporadic Parkinson's disease in Italy.
- Abstract of the Paper: [Parkinson's disease (PD) is a neurodegenerative disorder causing muscular rigidity, resting tremor and bradykinesia. We conducted an association study assessing how PD risk in Italy was influenced by the serotonin transporter gene (SLC6A4) polymorphic region 5-HTTLPR, consisting of an insertion/deletion (long allele-L/short allele-S) of 43 bp in the SLC6A4 promoter region. The SLC6A4 promoter single nucleotide polymorphism rs25531(A-->G) was evaluated too. We collected 837 independent subjects (393 PD, 444 controls). An association between the 5-HTTLPR polymorphism and risk of PD (S/S genotype OR [95% CI]: 1.7[1.2-2.5], p = 0.002) was found. The rs25531 and the haplotype 5-HTTLPR/rs25531 did not associate with risk of PD. Our data indicate that the 5-HTTLPR polymorphic element within the SLC6A4 promoter may govern the genetic risk of PD in Italians.]
Identify how '[PD,DiseaseOrPhenotypicFeature]' and '[insertion/deletion (long allele-L/short allele-S) of 43 bp,SequenceVariant]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Positive_Correlation</s> | Serotonin transporter gene polymorphic element 5-HTTLPR increases the risk of sporadic Parkinson's disease in Italy. | Parkinson's disease (PD) is a neurodegenerative disorder causing muscular rigidity, resting tremor and bradykinesia. We conducted an association study assessing how PD risk in Italy was influenced by the serotonin transporter gene (SLC6A4) polymorphic region 5-HTTLPR, consisting of an insertion/deletion (long allele-L/short allele-S) of 43 bp in the SLC6A4 promoter region. The SLC6A4 promoter single nucleotide polymorphism rs25531(A-->G) was evaluated too. We collected 837 independent subjects (393 PD, 444 controls). An association between the 5-HTTLPR polymorphism and risk of PD (S/S genotype OR [95% CI]: 1.7[1.2-2.5], p = 0.002) was found. The rs25531 and the haplotype 5-HTTLPR/rs25531 did not associate with risk of PD. Our data indicate that the 5-HTTLPR polymorphic element within the SLC6A4 promoter may govern the genetic risk of PD in Italians. | {
"name": "PD",
"type": "DiseaseOrPhenotypicFeature"
} | {
"name": "insertion/deletion (long allele-L/short allele-S) of 43 bp",
"type": "SequenceVariant"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Positive_Correlation |
<s>[INST]<<SYS>>
Your task is to determine the relationship between a gene or protein 5-HTTLPR and a disease Parkinson's disease in a medical text. Choose the correct relation from ['Positive_Correlation', 'Negative_Correlation', 'Association'], based only on the information provided in the text.The meanings of each relation type are as follows: 'Positive_Correlation' here means that the relation between a gene and a disease is direct and increases the likelihood of the disease. This includes cases where too much protein causes the disease, removing the gene prevents the disease, or a side effect from the protein or drug results in the disease.
'Negative_Correlation' indicates that when a protein (or gene) is present, it helps to treat or prevent a disease. Conversely, the absence of this protein or the deactivation of its gene can lead to the disease.
'Association' is used to describe relation that don't clearly fall under categories like positive or negative correlation, or when the nature of the relation lack a clear description.
<</SYS>>
Examine the abstract and title of a medical research paper to determine the relationship between the entities '[5-HTTLPR,GeneOrGeneProduct]' and '[Parkinson's disease,DiseaseOrPhenotypicFeature]'.
- Title of the Paper: Serotonin transporter gene polymorphic element 5-HTTLPR increases the risk of sporadic Parkinson's disease in Italy.
- Abstract of the Paper: [Parkinson's disease (PD) is a neurodegenerative disorder causing muscular rigidity, resting tremor and bradykinesia. We conducted an association study assessing how PD risk in Italy was influenced by the serotonin transporter gene (SLC6A4) polymorphic region 5-HTTLPR, consisting of an insertion/deletion (long allele-L/short allele-S) of 43 bp in the SLC6A4 promoter region. The SLC6A4 promoter single nucleotide polymorphism rs25531(A-->G) was evaluated too. We collected 837 independent subjects (393 PD, 444 controls). An association between the 5-HTTLPR polymorphism and risk of PD (S/S genotype OR [95% CI]: 1.7[1.2-2.5], p = 0.002) was found. The rs25531 and the haplotype 5-HTTLPR/rs25531 did not associate with risk of PD. Our data indicate that the 5-HTTLPR polymorphic element within the SLC6A4 promoter may govern the genetic risk of PD in Italians.]
Identify how '[5-HTTLPR,GeneOrGeneProduct]' and '[Parkinson's disease,DiseaseOrPhenotypicFeature]' are related in the text, focusing on their interactions or associations. Then, select the most accurate relationship type from ['Positive_Correlation', 'Negative_Correlation', 'Association']. [/INST]Association</s> | Serotonin transporter gene polymorphic element 5-HTTLPR increases the risk of sporadic Parkinson's disease in Italy. | Parkinson's disease (PD) is a neurodegenerative disorder causing muscular rigidity, resting tremor and bradykinesia. We conducted an association study assessing how PD risk in Italy was influenced by the serotonin transporter gene (SLC6A4) polymorphic region 5-HTTLPR, consisting of an insertion/deletion (long allele-L/short allele-S) of 43 bp in the SLC6A4 promoter region. The SLC6A4 promoter single nucleotide polymorphism rs25531(A-->G) was evaluated too. We collected 837 independent subjects (393 PD, 444 controls). An association between the 5-HTTLPR polymorphism and risk of PD (S/S genotype OR [95% CI]: 1.7[1.2-2.5], p = 0.002) was found. The rs25531 and the haplotype 5-HTTLPR/rs25531 did not associate with risk of PD. Our data indicate that the 5-HTTLPR polymorphic element within the SLC6A4 promoter may govern the genetic risk of PD in Italians. | {
"name": "5-HTTLPR",
"type": "GeneOrGeneProduct"
} | {
"name": "Parkinson's disease",
"type": "DiseaseOrPhenotypicFeature"
} | [
"Positive_Correlation",
"Negative_Correlation",
"Association"
] | Association |
Subsets and Splits