Polygenic Score (PGS) ID: PGS004223

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 PRS139_T2D
Development Method
Name Genome-wide significant SNPs
Parameters NR
Variants
Original Genome Build NR
Number of Variants 139
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000523
Citation (link to publication) Lin J et al. Sci Total Environ (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 99.4%
South Asian: 0.6%
659,316 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: GCST006867
Europe PMC: 30054458
 655,666 individuals European NR
GWAS Catalog: GCST006867
Europe PMC: 30054458
 3,650 individuals South Asian 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
PPM020158 PSS011299|
European Ancestry|
395,809 individuals
 PGP000523 |
Lin J et al. Sci Total Environ (2023)
 Reported Trait: Incident type 2 diabetes HR: 1.5 [1.48, 1.52] — — age, gender, education, Townsend deprivation index, smoking status, alcohol consumption, body mass index, total physical activity, dietary pattern, vitamin D supplement, use of sun/UV protection, PM2.5, hypertension, cardiovascular disease, antihypertensive medications use, cholesterol-lowering medications use, and average outdoor light time —
PPM020159 PSS011299|
European Ancestry|
395,809 individuals
 PGP000523 |
Lin J et al. Sci Total Environ (2023)
 Reported Trait: Incident type 2 diabetes with outdoor light time in summer — — Hazard ratio (HR, outdoor light time in summer >3h/day and PRS in top tertile vs. outdoor light time in summer <2-3 h/day and PRS in bottom tertile): 2.53 [2.39, 2.69] Hb1Ac concentrations at baseline —
PPM020160 PSS011299|
European Ancestry|
395,809 individuals
 PGP000523 |
Lin J et al. Sci Total Environ (2023)
 Reported Trait: Incident type 2 diabetes with outdoor light time in winter — — Hazard ratio (HR, outdoor light time in winter >2 h/day and PRS in top tertile vs. outdoor light time in winter <1-2 h/day and PRS in bottom tertile): 2.56 [2.42, 2.71] Hb1Ac concentrations at baseline —
PPM020161 PSS011299|
European Ancestry|
395,809 individuals
 PGP000523 |
Lin J et al. Sci Total Environ (2023)
 Reported Trait: Incident type 2 diabetes with outdoor light time on average — — Hazard ratio (HR, outdoor light time on average >2.5 h/day and PRS in top tertile vs. outdoor light time on average 1.5-2.5 h/day and PRS in bottom tertile): 2.52 [2.37, 2.67] Hb1Ac concentrations at baseline —

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
PSS011299 T2D ICD-10 code E11 Median = 12.55 years
IQR = [11.72, 13.27] years		 395,809 individuals,
45.8 % Male samples
 Mean = 56.7 years
Sd = 8.0 years		 European — UKB —