Polygenic Score (PGS) ID: PGS000014

Predicted Trait
Reported Trait Type 2 diabetes
Mapped Trait(s) type II diabetes mellitus (EFO_0001360)
Released in PGS Catalog: Oct. 14, 2019
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Terms and Licenses
Freely available to the academic community for research use. Parties interested in using the scores for commercial purposes should contact the Broad Office of Strategic Alliances and Partnering (partnering@broadinstitute.org).

Score Details

Score Construction
PGS Name GPS_T2D
Variants
Original Genome Build hg19
Number of Variants 6,917,436
Development Method
Name LDPred
Parameters ρ = 0.01; LD panel = 503 1000G Europeans
PGS Source
PGS Catalog Publication (PGP) ID PGP000006
Citation (link to publication) Khera AV et al. Nat Genet (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
318,416 individuals (100%)
Score Development/Training
European: 100%
120,280 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004773
Europe PMC: 28566273
159,208 individuals European
GWAS Catalog: GCST004774
Europe PMC: 28566273
159,208 individuals European
Score Development/Training
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
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.
[
  • 2,785 cases
  • , 117,495 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 ID (PPM)
PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000023 PSS000017|
European Ancestry|
288,978 individuals
PGP000006 |
Khera AV et al. Nat Genet (2018)
Reported Trait: Type 2 diabetes 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 Sample Set ID
(PSS)
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
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.
[
  • 5,853 cases
  • , 283,125 controls
]
European UKB UKB Phase 2