Predicted Trait | |
Reported Trait | Type 1 diabetes |
Mapped Trait(s) | type I diabetes mellitus (EFO_0001359) |
Score Construction | |
PGS Name | GRS1 |
Variants | |
Original Genome Build | NR |
Number of Variants | 30 |
Development Method | |
Name | SNP associations curated from the literature |
Parameters | HLA Haplotypes called with SNP2HLA using the T1DGC reference panel |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000011 |
Citation (link to publication) | Oram RA et al. Diabetes Care (2015) |
Study Identifiers | Sample Numbers | Sample Ancestry |
---|---|---|
GWAS Catalog: GCST000392 EuropePMC: 1943048 |
16,559 individuals | European |
EuropePMC: 20798335 | [
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European |
Phenotype Definitions and Methods | Participant Follow-up Time | Sample Numbers | Age of Study Participants | Sample Ancestry | Additional Ancestry Description | Cohort(s) | Additional Sample/Cohort Information |
---|---|---|---|---|---|---|---|
Cases = patients [that] received a clinical diagnosis of T1D at ,17 years of age and were treated with insulin from the time of diagnosis. Controls = T2D patients diagnosed between 25 and 75 years of age, were GAD autoantibody negative on testing, and were either treated with diet/oral hypoglycemic agents or had an interval of at least 1 year between diagnosis and the institution of insulin therapy | — | [
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— | European | — | WTCCC | — |
PGS Performance Metric ID (PPM ID) |
PGS Sample Set ID (PSS ID) |
Performance Source | Trait |
PGS Effect Sizes (per SD change) |
PGS Classification Metrics | Other Metrics | Covariates Included in the Model | PGS Performance: Other Relevant Information |
---|---|---|---|---|---|---|---|---|
PPM000041 | PSS000026 | PGP000011 Oram RA et al. (2015) | Reported Trait: Severe insulin deficiency | — | AUROC: 0.96 [0.94, 0.99] | AUROC (without covariates): 0.87 | islet auto-antibody status, body mass index (BMI), age at diagnosis | — |
PPM000132 | PSS000083 | PGP000038 Patel KA et al. (2016) Ext. | Reported Trait: Type 1 diabetes aetiology (non-monogenic) | — | AUROC: 0.87 [0.86, 0.89] | — | — | Testing the ability of the GRS to discriminate between two sets of cases: - Positive: individuals with type 1 diabetes - Negative: individuals with diabetes and a maturity-onset diabetes of young (MODY) mutation |
PPM000046 | PSS000030 | PGP000013 Onengut-Gumuscu S et al. (2019) Ext. | Reported Trait: Type 1 diabetes | — | AUROC: 0.798 | — | — | — |
PPM000049 | PSS000032 | PGP000014 Sharp SA et al. (2019) Ext. | Reported Trait: Type 1 diabetes | — | AUROC: 0.893 | — | — | — |
PGS Sample Set ID (PSS ID) |
Phenotype Definitions and Methods | Participant Follow-up Time | Sample Numbers | Age of Study Participants | Sample Ancestry | Additional Ancestry Description | Cohort(s) | Additional Sample/Cohort Information |
---|---|---|---|---|---|---|---|---|
PSS000026 | Cases were defined on the presence or absence of severe insulin deficiency (requiring insulin treatment at 3 years after diagnosis). We cate- gorized people as severely insulin defi- cient if they received continuous insulin treatment at ,3 years from the time of diagnosis and had a low measured C-peptide level (nonfasting measured ,0.6 nmol/L or equivalent fasting blood glucose level or posthome meal urine C-peptide–to–creatinine ratio) | — | [ ,
46.3 % Male samples |
— | European | — | P2ID | A cross-sectional cohort of people in whom diabetes was diagnosed between the ages of 20 and 40 years (n = 223), who had had diabetes for .3 years, and who had self-reported as white European from Devon and Cornwall in South West England. Known monogenic diabetes and secondary diabetes pa- tients were excluded. |
PSS000083 | Cases were clinically diagnosed with T1D before 17 years of age and treated with insulin from diagnosis. Patients with known MODY or NDM were excluded. | — | [
|
— | European | — | WTCCC | Cases with Type 1 Diabetes |
PSS000083 | MODY patients with a confirmed monogenic etiology on genetic testing (415 patients with HNF1A MODY, 346 with GCK MODY, 42 with HNF4A MODY, and 2 with HNF1B MODY). The median age of diagnosis was 20 years (interquartile range 15, 30), and 532 patients were female. | — | [ ,
33.91 % Male samples |
— | European | — | Maturity-onset diabetes of young (MODY) cases ascertained from the Genetic Βeta Cell Research Bank, Exeter, U.K. | |
PSS000030 | — | — | [
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— | African unspecified | — | 7 cohorts
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PSS000032 | Type 1 Diabetes Case Definition = Clinical diagnosis of diabetes at less than or equal to 20 years of age; On insulin within 1 year from the time of diagnosis; Still on insulin at the time of recruit- ment; Not using oral antihyperglycemic agents; Did not ever self-report as having type 2 diabetes (T2D) | — | [
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— | European | — | UKB | — |