Polygenic Score (PGS) ID: PGS000036

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
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Score Details

Score Construction
PGS Name gePS_T2D
Variants
Original Genome Build GRCh37
Number of Variants 171,249
Development Method
Name Pruning + Thresholding
Parameters P < 0.1; r2 < 0.6
PGS Source
PGS Catalog Publication (PGP) ID PGP000023
Citation (link to publication) Mahajan A et al. Nat Genet (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • European
  • African
  • East Asian
  • Hispanic or Latin American
  • South Asian
455,313 individuals (100%)
Score Development/Training
European: 100%
117,946 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
Europe PMC: 29632382
[
  • 55,005 cases
  • , 400,308 controls
]
European, African American or Afro-Caribbean, East Asian, Hispanic or Latin American, South Asian
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
Prevalent T2D status was defined using self-reported medical history and medication
[
  • 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 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
PPM000080 PSS000054|
European Ancestry|
324,870 individuals
PGP000024 |
Udler MS et al. Endocr Rev (2019)
|Ext.
Reported Trait: Type 2 diabetes AUROC: 0.66 genotyping array, first 6 PCs of ancestry
PPM000081 PSS000054|
European Ancestry|
324,870 individuals
PGP000024 |
Udler MS et al. Endocr Rev (2019)
|Ext.
Reported Trait: Type 2 diabetes AUROC: 0.73 age, sex, genotyping array, first 6 PCs of ancestry

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