| 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 | [
|
— |
| Detailed Phenotype Description | 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 | — | [
|
— | European | — | WTCCC | — |
Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.
|
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 | — |
| 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 | — | — | — |
| 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 |
|
PGS Sample Set ID (PSS ID) |
Detailed Phenotype Description | 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 | — | — | [
|
— | African unspecified | — | 7 cohorts
|
— |
| 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) | — | [
|
— | European | — | UKB | — |