Polygenic Score (PGS) ID: PGS005354

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_trainedforAFR_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-4.
Variants
Original Genome Build hg19
Number of Variants 1,642,045
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
African: 100%
6,779 individuals (100%)
PGS Evaluation
African: 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
—
[
  • 1,409 cases
  • , 5,370 controls
]
 African American or Afro-Caribbean
(African American)		 BioVU — — — — —

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
PPM023245 PSS012148|
African Ancestry|
12,352 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Cardiovascular disease OR: 0.99 [0.93, 1.05]
β: -0.01123		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023200 PSS012148|
African Ancestry|
12,352 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes HR: 1.36 [1.21, 1.53]
OR: 1.68 [1.61, 1.76]
β: 0.52067		 AUROC: 0.68035 R²: 0.12691 sex, age, genetic principal components —
PPM023205 PSS012153|
African Ancestry|
2,282 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes OR: 1.71 [1.52, 1.94]
β: 0.53912		 AUROC: 0.64033 R²: 0.07418 sex, age, genetic principal components —
PPM023210 PSS012162|
African Ancestry|
1,155 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes OR: 1.46 [1.28, 1.66]
β: 0.37919		 AUROC: 0.62924 R²: 0.06363 sex, age, genetic principal components —
PPM023215 PSS012168|
African Ancestry|
2,906 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes OR: 2.62 [2.3, 2.97]
β: 0.96137		 AUROC: 0.74575 R²: 0.23196 sex, age, genetic principal components —
PPM023220 PSS012148|
African Ancestry|
12,352 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Proliferative diabetic retinopathy OR: 1.39 [1.17, 1.65]
β: 0.32872		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023225 PSS012148|
African Ancestry|
12,352 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Ischemic stroke OR: 1.01 [0.93, 1.11]
β: 0.01484		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023230 PSS012148|
African Ancestry|
12,352 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: End-stage diabetic nephropathy OR: 1.44 [1.2, 1.74]
β: 0.36742		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023235 PSS012148|
African Ancestry|
12,352 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Diabetic retinopathy OR: 1.28 [1.18, 1.39]
β: 0.24486		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023240 PSS012148|
African Ancestry|
12,352 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Diabetic nephropathy OR: 1.26 [1.13, 1.4]
β: 0.22875		 — — sex, age, genetic principal components Restricted to T2D cases only.

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
PSS012168 — —
[
  • 1,060 cases
  • , 1,846 controls
]
 — African unspecified
(African)		 — UKB —
PSS012153 — —
[
  • 773 cases
  • , 1,509 controls
]
 — African American or Afro-Caribbean
(African American)		 — BioMe —
PSS012162 — —
[
  • 376 cases
  • , 779 controls
]
 — African American or Afro-Caribbean — MGBB —
PSS012148 — —
[
  • 5,366 cases
  • , 6,986 controls
]
 — African American or Afro-Caribbean
(African American)		 — AllofUs —