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(Variants and weights)

Polygenic Score (PGS) ID: PGS000014

Predicted Trait

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

Score Details

Name: GPS_T2D

Original Genome Build: hg19
Number of Variants: 6,917,436

PGS Development Method: LDPred
PGS Development Details/Relevant Parameters: ρ = 0.01; LD panel = 503 1000G Europeans

Citation: Khera AV et al. Nat Genet (2018) | PGS Catalog Publication ID: PGP000006

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004774
PubMed: 28566273
159,208 individuals European
GWAS Catalog: GCST004773
PubMed: 28566273
159,208 individuals European
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
Type 2 diabetes ascertainment was based on self-report in an interview with a trained nurse or an ICD-10 code of E11.X in hospitalization records. 120,280 individuals
[ 2,785 cases, 123,065 controls]
European UKB UKB Phase 1

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
PPM000023 PSS000017 Khera AV et al. (2018) Reported Trait: Type 2 diabetes cases AUROC: 0.73 [0.72 - 0.73] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.029 age; sex; Ancestry PC 1-4; genotyping chip

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
PSS000017 Type 2 diabetes ascertainment was based on self-report in an interview with a trained nurse or an ICD-10 code of E11.X in hospitalization records. 288,978 individuals
[ 5,853 cases, 294,831 controls]
European UKB UKB Phase 2