Polygenic Score (PGS) ID: PGS005242

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Oct. 6, 2025
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name T2D_PRS_PRS_CSx_META_T
Development Method
Name PRS-CSx
Parameters This PRS score was developed using meta-analyzed posterior effects with the META=T function in PRS-CSx. The T2D GWAS summary statistics used to develop the PRS were from a South Asian (SAS) population from Mahajan et al., 2022 (doi:10.1038/s41588-022-01058-3) and from European (EUR), African American (AFR), Hispanic (HIS), and Asian (ASN) populations from Vujkovic et al., 2020 (doi:10.1038/s41588-020-0637-y). Linkage disequilibrium (LD) reference panels were based on the 1000 Genomes Project (1KG) Phase 3 participants from AFR, Admixed American (AMR), EAS, EUR, and SAS population samples. GWAS summary statistics from the Mahajan et al. 2022 study are available on the DIAGRAM consortium website (http://diagram-consortium.org). GWAS summary statistics from the Vujkovic et al., 2020 study are available on dbGaP (accession numbers pha004945.1, pha004943.1, pha004946.1, and pha004944.1, respectively).
Variants
Original Genome Build GRCh37
Number of Variants 1,257,036
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000742
Citation (link to publication) Guo B G et al. Nat Commun (2025)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 77%
Multi-ancestry (excluding European): 14.9%
  • East Asian
  • South Asian
African: 3.9%
South Asian: 2.8%
Hispanic or Latin American: 1.4%
1,448,019 individuals (100%)
PGS Evaluation
African: 25%
Hispanic or Latin American: 25%
Additional Asian Ancestries: 25%
European: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90132186
Europe PMC: 35551307
 40,737 individuals South Asian 7 cohorts
  • ITH
  • ,LOLIPOP
  • ,Other
  • ,PROMIS
  • ,RHS
  • ,SINDI
  • ,UKB
GWAS Catalog: GCST010556
Europe PMC: 32541925
 56,092 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST010554
Europe PMC: 32541925
 20,445 individuals Hispanic or Latin American NR
GWAS Catalog: GCST010555
Europe PMC: 32541925
 1,114,458 individuals European NR
GWAS Catalog: GCST010553
Europe PMC: 32541925
 216,287 individuals East Asian, 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
PPM022720 PSS012058|
African Ancestry|
13,161 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 1.56 [1.51, 1.61] AUROC: 0.687 [0.68, 0.693] — age, sex, BMI, sub-study, and first 10 PCs —
PPM022721 PSS012061|
Hispanic or Latin American Ancestry|
22,647 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 1.86 [1.8, 1.92] AUROC: 0.753 [0.747, 0.759] — age, sex, BMI, sub-study, and first 10 PCs —
PPM022722 PSS012059|
Additional Asian Ancestries|
7,498 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 1.9 [1.79, 2.02] AUROC: 0.768 [0.758, 0.779] — age, sex, BMI, sub-study, and first 10 PCs —
PPM022723 PSS012060|
European Ancestry|
22,063 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 1.78 [1.7, 1.87] AUROC: 0.761 [0.754, 0.769] — age, sex, BMI, sub-study, and first 10 PCs —

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
PSS012060 — —
[
  • 4,076 cases
  • , 17,987 controls
]
,
17.1 % Male samples
 Mean = 62.0 years
Sd = 8.96 years		 European
(European)		 — PAGE —
PSS012061 — —
[
  • 9,441 cases
  • , 13,206 controls
]
,
36.8 % Male samples
 Mean = 57.0 years
Sd = 10.3 years		 Hispanic or Latin American — PAGE —
PSS012058 — —
[
  • 5,429 cases
  • , 7,732 controls
]
,
43.8 % Male samples
 Mean = 58.9 years
Sd = 9.99 years		 African unspecified
(African American)		 — PAGE —
PSS012059 — —
[
  • 3,185 cases
  • , 4,313 controls
]
,
49.0 % Male samples
 Mean = 60.5 years
Sd = 8.67 years		 Asian unspecified — PAGE —