Polygenic Score (PGS) ID: PGS000729

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Feb. 23, 2021
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Score Details

Score Construction
Development Method
Name LD thinning
Parameters UKB was used for thinning (bi-allelic SNPs, MAF > 1%, INFO > 0.4, excluding palindromic SNPs); r2 threshold = 0.9
Original Genome Build GRCh37
Number of Variants 2,017,388
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000137
Citation (link to publication) Ritchie SC et al. Nat Metab (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
298,957 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST007517
Europe PMC: 29632382
298,957 individuals European DIAGRAM, GERA, 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
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM001667 PSS000869|
European Ancestry|
3,087 individuals
PGP000137 |
Ritchie SC et al. Nat Metab (2021)
Reported Trait: Incident type 2 diabetes HR: 2.0 [1.36, 2.94] age, sex, 10 genetic PCs

Evaluated Samples

PGS Sample Set ID
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
PSS000869 CALIBER rule-based phenotyping algorithms (https://github.com/spiros/chronological-map-phenotypes#diabetes) Median = 6.9 years
  • 27 cases
  • , 3,060 controls
51.0 % Male samples
Median = 44.0 years
IQR = [30.5, 54.7] years