Polygenic Score (PGS) ID: PGS003867

Predicted Trait
Reported Trait Type 2 diabetes
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Nov. 1, 2023
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Score Details

Score Construction
PGS Name T2D_PRScs_ARB
Development Method
Name PRS-CS
Parameters a=1,b=0.5,phi=0.0001
Variants
Original Genome Build hg19
Number of Variants 1,068,166
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000501
Citation (link to publication) Shim I et al. Nature Communications (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 51.1%
East Asian: 28.4%
South Asian: 8.3%
African: 6.6%
Hispanic or Latin American: 5.6%
492,192 individuals (100%)
PGS Evaluation
Greater Middle Eastern: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 251,740 individuals European NR
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 139,705 individuals East Asian NR
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 40,737 individuals South Asian NR
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 27,417 individuals Hispanic or Latin American NR
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 30,167 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 2,426 individuals Sub-Saharan African 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
PPM018759 PSS011097|
Greater Middle Eastern Ancestry|
2,669 individuals
 PGP000501 |
Shim I et al. Nature Communications (2023)
 Reported Trait: Type 2 diabetes OR: 1.83 [1.74, 1.92] AUROC: 0.7384 [0.7194, 0.7574] — age, sex, array version, and the first 10 principal components 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
PSS011097 — — 2,669 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian)
(Arab)		 — NR N total after excluding missing values = 2,553