Polygenic Score (PGS) ID: PGS005324

Predicted Trait
Reported Trait Type 2 Diabetes Mellitus
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Additional Trait Information Constructed as a weighted combination of ancestry-specific PRSs (AFR, AMR, EAS, EUR, SAS) derived using PRS-CSx; weights correspond to individual ancestry proportions estimated in the HCHS/SOL cohort.
Released in PGS Catalog: Nov. 10, 2025
Download Score FTP directory
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_weighted
Development Method
Name PRS-CSx
Parameters Summary statistics sources: DIAGRAM (EAS, EUR, SAS) and Million Veteran Program (MVP; White [Eur], Black [AFR], Hispanic [AMR]) GWAS, both unadjusted for BMI. DIAGRAM-EUR and MVP-White meta-analyzed via GWAMA (inverse-variance weighted). Ancestry-specific PRSs (AFR, AMR, EAS, EUR, SAS) built with PRS-CSx using 1000 Genomes ancestry-matched LD panels. Global shrinkage parameter φ learned automatically; other parameters default (a = 1, b = 0.5). The weighted PRS was computed as a linear combination of these ancestry-specific scores, weighted by each individual's estimated ancestry proportions from the HCHS/SOL cohort.
Variants
Original Genome Build GRCh38
Number of Variants 1,279,733
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000770
Citation (link to publication) Hrytsenko Y et al. Commun Med (Lond) (2025)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • European
  • East Asian
  • South Asian
  • Hispanic or Latin American
  • African
1,613,298 individuals (100%)
Score Development/Training
European: 83.9%
Not Reported: 5.5%
African: 4.7%
Hispanic or Latin American: 3.9%
Additional Asian Ancestries: 1.9%
Additional Diverse Ancestries: 0.1%
38,745 individuals (100%)
PGS Evaluation
Hispanic or Latin American: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90132183
[
  • 180,834 cases
  • , 1,159,055 controls
]
 European, East Asian, South Asian, Hispanic or Latin American, African American or Afro-Caribbean, Sub-Saharan African NR
GWAS Catalog: GCST010557
 273,409 individuals European, Hispanic or Latin American, East Asian, South Asian, African American or Afro-Caribbean NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 2,120 cases
  • , 30,372 controls
]
 European MGBB — — — — —
—
[
  • 354 cases
  • , 1,473 controls
]
 African American or Afro-Caribbean
(Black)		 MGBB — — — — —
—
[
  • 202 cases
  • , 1,301 controls
]
 Hispanic or Latin American MGBB — — — — —
—
[
  • 61 cases
  • , 692 controls
]
 Asian unspecified MGBB — — — — —
—
[
  • 8 cases
  • , 42 controls
]
 Native American MGBB — — — — —
—
[
  • 189 cases
  • , 1,931 controls
]
 Not reported MGBB — — — — —

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
PPM023076 PSS012112|
Hispanic or Latin American Ancestry|
12,309 individuals
 PGP000770 |
Hrytsenko Y et al. Commun Med (Lond) (2025)
 Reported Trait: Incident Type 2 Diabetes Mellitus OR: 2.77 [2.44, 3.13] — — age, sex, BMI, study center, and genetic PCs Constructed as an unweighted average of ancestry-specific PRSs (AFR, AMR, EAS, EUR, SAS) derived using PRS-CSx; no ancestry-proportion weighting applied.

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
PSS012112 — —
[
  • 2,405 cases
  • , 9,904 controls
]
 — Hispanic or Latin American
(Cuban, Central American, Dominican, Mexican, Puerto Rican, and South American)		 — HCHS-SOL —