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(Variants and weights)

Polygenic Score (PGS) ID: PGS000036

Predicted Trait

Reported Trait: Type 2 diabetes
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): type II diabetes mellitus

Score Details

Name: gePS_T2D

Original Genome Build: GRCh37
Number of Variants: 171,249

PGS Development Method: Pruning + Thresholding
PGS Development Details/Relevant Parameters: P < 0.1; r2 < 0.6

Citation: Mahajan A et al. Nat Genet (2018) | PGS Catalog Publication ID: PGP000023

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
PubMed: 29632382 455,313 individuals
[ 55,005 cases, 400,308 controls]
Other
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
Prevalent T2D status was defined using self-reported medical history and medication 117,946 individuals
[ 5,639 cases, 112,307 controls]
European UKB

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
PPM000080 PSS000054 Udler MS et al. (2019) Ext. Reported Trait: Type 2 diabetes AUROC: 0.66 genotyping array, first 6 PCs of ancestry
PPM000081 PSS000054 Udler MS et al. (2019) Ext. Reported Trait: Type 2 diabetes AUROC: 0.73 age, sex, genotyping array, first 6 PCs of ancestry

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
PSS000054 Prevalent T2D status was defined using self-reported medical history and medication 324,870 individuals
[ 13,480 cases, 311,390 controls]
European UKB