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(Variants and weights)

Polygenic Score (PGS) ID: PGS000021

Predicted Trait

Reported Trait: Type 1 diabetes
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): type I diabetes mellitus

Score Details

Name: GRS1

Original Genome Build: NR
Number of Variants: 30

PGS Development Method: SNP associations curated from the literature
PGS Development Details/Relevant Parameters: HLA Haplotypes called with SNP2HLA using the T1DGC reference panel

Citation: Oram RA et al. Diabetes Care (2015) | PGS Catalog Publication ID: PGP000011

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
PubMed: 20587799.0
PubMed: 20798335.0 5,365 individuals
[ 3,577 cases, 1,788 controls]
Score Development/Training
Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers 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 3,852 individuals
[ 1,938 cases, 1,914 controls]
European WTCCC

Performance Metrics

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000041 PSS000026 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 Onengut-Gumuscu S et al. (2019) Ext. Reported Trait: Type 1 diabetes AUROC: 0.798
PPM000049 PSS000032 Sharp SA et al. (2019) Ext. Reported Trait: Type 1 diabetes AUROC: 0.893

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers 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) 223 individuals
[ 46 cases, 177 controls]
46.300448430493276 % 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.
PSS000030 3,949 individuals
[ 1,021 cases, 2,928 controls]
African unspecified BDC, CLEAR, GoKinD, NYCP, SEARCH, T1DGC, UAB
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) 374,000 individuals
[ 387 cases, 373,613 controls]
European UKB