Polygenic Score (PGS) ID: PGS005374

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Feb. 26, 2026
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Score Details

Score Construction
PGS Name DPRISM_T2DPRS_trainedforSAS_AMRweights
Development Method
Name PRS-CSx
Parameters T2D GWAS summary statistics and LD reference panels (TagIt SNP set, in-house LD estimations) from AMR ancestry. Best phi: 1e-3.
Variants
Original Genome Build hg19
Number of Variants 1,419,570
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000773
Citation (link to publication) Huerta-Chagoya A et al. medRxiv (2025) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
Hispanic or Latin American: 100%
82,013 individuals (100%)
Score Development/Training
South Asian: 100%
5,715 individuals (100%)
PGS Evaluation
South Asian: 100%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
35551307, 32541925
[
  • 26,802 cases
  • , 55,211 controls
]
 Hispanic or Latin American
(Hispanic American, Mexican)		 11 cohorts
  • BioMe
  • ,HCHS
  • ,LALES
  • ,MACAD
  • ,MESA
  • ,MVP
  • ,NIDDM-Athero
  • ,SAFHS
  • ,SIGMA
  • ,SOL
  • ,WHI
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
—
[
  • 2,019 cases
  • , 3,696 controls
]
 South Asian
(British Indian)		 LOLIPOP — — — — —

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
PPM023385 PSS012146|
South Asian Ancestry|
1,397 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes OR: 2.2 [1.92, 2.51]
β: 0.78618		 AUROC: 0.71851 R²: 0.18837 sex, age, genetic principal components —
PPM023390 PSS012147|
South Asian Ancestry|
426 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes OR: 2.26 [1.74, 2.93]
β: 0.81334		 AUROC: 0.80144 R²: 0.32092 sex, age, genetic principal components —
PPM023395 PSS012157|
South Asian Ancestry|
630 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes OR: 1.77 [1.47, 2.13]
β: 0.56903		 AUROC: 0.67322 R²: 0.11799 sex, age, genetic principal components —
PPM023400 PSS012161|
South Asian Ancestry|
1,858 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes OR: 2.57 [2.23, 2.95]
β: 0.94269		 AUROC: 0.79407 R²: 0.28515 sex, age, genetic principal components —

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
PSS012161 — —
[
  • 465 cases
  • , 1,393 controls
]
 — South Asian
(British Indian)		 — LOLIPOP —
PSS012146 — —
[
  • 793 cases
  • , 604 controls
]
 — South Asian
(Punjabi Sikh)		 — AIDHS, SDS —
PSS012147 — —
[
  • 171 cases
  • , 255 controls
]
 — South Asian — AllofUs —
PSS012157 — —
[
  • 247 cases
  • , 383 controls
]
 — South Asian — BioMe —