Polygenic Score (PGS) ID: PGS005359

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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Terms and Licenses
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Score Details

Score Construction
PGS Name DPRISM_T2DPRS_trainedforAMR_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 1,427,746
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
Hispanic or Latin American: 100%
5,747 individuals (100%)
PGS Evaluation
Hispanic or Latin American: 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
—
[
  • 2,964 cases
  • , 2,783 controls
]
 Hispanic or Latin American
(Hispanic American, Mexican)		 SIGMA — — — — —

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
PPM023250 PSS012151|
Hispanic or Latin American Ancestry|
8,608 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes HR: 2.13 [1.8, 2.52]
OR: 2.86 [2.68, 3.06]
β: 1.05143		 AUROC: 0.76555 R²: 0.27402 sex, age, genetic principal components —
PPM023260 PSS012164|
Hispanic or Latin American Ancestry|
1,086 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes OR: 2.6 [2.15, 3.14]
β: 0.95481		 AUROC: 0.72125 R²: 0.17352 sex, age, genetic principal components —
PPM023265 PSS012165|
Hispanic or Latin American Ancestry|
1,683 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes OR: 2.15 [1.85, 2.5]
β: 0.76689		 AUROC: 0.71248 R²: 0.16347 sex, age, genetic principal components —
PPM023270 PSS012151|
Hispanic or Latin American Ancestry|
8,608 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Proliferative diabetic retinopathy OR: 2.08 [1.73, 2.51]
β: 0.73382		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023275 PSS012151|
Hispanic or Latin American Ancestry|
8,608 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Ischemic stroke OR: 1.05 [0.93, 1.18]
β: 0.04638		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023280 PSS012151|
Hispanic or Latin American Ancestry|
8,608 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: End-stage diabetic nephropathy OR: 1.87 [1.56, 2.22]
β: 0.6235		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023285 PSS012151|
Hispanic or Latin American Ancestry|
8,608 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Diabetic retinopathy OR: 1.57 [1.43, 1.73]
β: 0.45344		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023290 PSS012151|
Hispanic or Latin American Ancestry|
8,608 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Diabetic nephropathy OR: 1.58 [1.41, 1.78]
β: 0.45816		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023295 PSS012151|
Hispanic or Latin American Ancestry|
8,608 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Cardiovascular disease OR: 1.16 [1.08, 1.25]
β: 0.14943		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023255 PSS012156|
Hispanic or Latin American Ancestry|
4,126 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes OR: 3.48 [3.02, 4.01]
β: 1.24666		 AUROC: 0.72336 R²: 0.17962 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
PSS012151 — —
[
  • 3,691 cases
  • , 4,917 controls
]
 — Hispanic or Latin American
(Hispanic American)		 — AllofUs —
PSS012156 — —
[
  • 1,340 cases
  • , 2,786 controls
]
 — Hispanic or Latin American
(Hispanic American)		 — BioMe —
PSS012164 — —
[
  • 307 cases
  • , 779 controls
]
 — Hispanic or Latin American — MGBB —
PSS012165 — —
[
  • 396 cases
  • , 1,287 controls
]
 — Hispanic or Latin American
(Mexican)		 — MXBB —