Polygenic Score (PGS) ID: PGS004226

Predicted Trait
Reported Trait Type 2 diabetes
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Dec. 15, 2023
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Score Details

Score Construction
PGS Name PRS50_T2DEur
Development Method
Name Genome-wide significant SNPs
Parameters MAF>0.5, r2 < 0.8
Variants
Original Genome Build NR
Number of Variants 50
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000526
Citation (link to publication) Liu J et al. Nutrients (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 97.6%
South Asian: 1.2%
East Asian: 1.1%
Hispanic or Latin American: 0.2%
1,713,731 individuals (100%)
PGS Evaluation
East Asian: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST000028
Europe PMC: 17463246
 2,931 individuals European NR
GWAS Catalog: GCST000167
Europe PMC: 18372903
 10,128 individuals European NR
GWAS Catalog: GCST000712
Europe PMC: 20581827
 47,117 individuals European
(U.K.)		 NR
GWAS Catalog: GCST005047
Europe PMC: 22885922
 69,033 individuals European NR
GWAS Catalog: GCST002352
Europe PMC: 24509480
 69,033 individuals European NR
GWAS Catalog: GCST002352
Europe PMC: 24509480
 18,817 individuals East Asian NR
GWAS Catalog: GCST002352
Europe PMC: 24509480
 20,019 individuals South Asian NR
GWAS Catalog: GCST002352
Europe PMC: 24509480
 2,583 individuals Hispanic or Latin American NR
GWAS Catalog: GCST006801
Europe PMC: 26961502
 117,775 individuals European NR
GWAS Catalog: GCST004773
Europe PMC: 28566273
 159,208 individuals European NR
GWAS Catalog: GCST007517
Europe PMC: 29632382
 298,957 individuals European NR
GWAS Catalog: GCST009379
Europe PMC: 30297969
 898,130 individuals European NR

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
PPM020216 PSS011306|
East Asian Ancestry|
5,024 individuals
 PGP000526 |
Liu J et al. Nutrients (2023)
 Reported Trait: Type 2 diabetes — — Hazard ratio (HR, high vs low quintile): 1.69 [1.17, 2.44] age, gender, SBP, DBP, FBG, TC, TG, HDLC, and diabetes family history —

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
PSS011306 — — 5,024 individuals,
40.0 % Male samples
 — East Asian
(Chinese)		 — Wuxi NCDs —