Polygenic Score (PGS) ID: PGS005371

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_trainedforEUR_EURweights
Development Method
Name PRS-CSx
Parameters T2D GWAS summary statistics and LD reference panels (TagIt SNP set, in-house LD estimations) from EUR ancestry. Best phi: 1e-3.
Variants
Original Genome Build hg19
Number of Variants 1,444,665
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)
European: 100%
1,486,934 individuals (100%)
Score Development/Training
European: 100%
21,706 individuals (100%)
PGS Evaluation
European: 100%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 30297969
[
  • 201,262 cases
  • , 1,285,672 controls
]
 European
(European American, Icelandic, French, Swedish, Estonian, Finish, German, British, Greek, Dutch, Danish)		 28 cohorts
  • BioMe
  • ,DGDG
  • ,DGI
  • ,EGCUT
  • ,FHS
  • ,FUSION
  • ,FinnGen
  • ,GCKD
  • ,GENOA
  • ,GERA
  • ,GOMAP
  • ,GoDARTS
  • ,HPFS
  • ,InterAct
  • ,KORA
  • ,MESA
  • ,METSIM
  • ,MGI
  • ,MVP
  • ,NHS
  • ,Nugene
  • ,PIVUS
  • ,PROSPER
  • ,RS
  • ,UKB
  • ,ULSAM
  • ,WTCCC
  • ,deCODE
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
—
[
  • 3,694 cases
  • , 18,012 controls
]
 European
(European 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
PPM023337 PSS012150|
European Ancestry|
41,736 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes HR: 2.18 [2.05, 2.33]
OR: 2.64 [2.56, 2.72]
β: 0.96963		 AUROC: 0.7571 R²: 0.2129 sex, age, genetic principal components —
PPM023342 PSS012155|
European Ancestry|
7,573 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes OR: 1.96 [1.81, 2.12]
β: 0.67282		 AUROC: 0.69233 R²: 0.10551 sex, age, genetic principal components —
PPM023347 PSS012158|
European Ancestry|
21,769 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes OR: 2.16 [2.07, 2.25]
β: 0.76796		 AUROC: 0.72142 R²: 0.14038 sex, age, genetic principal components —
PPM023352 PSS012163|
European Ancestry|
23,183 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Type 2 diabetes OR: 2.23 [2.15, 2.32]
β: 0.80251		 AUROC: 0.72972 R²: 0.13778 sex, age, genetic principal components —
PPM023357 PSS012150|
European Ancestry|
41,736 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Proliferative diabetic retinopathy OR: 1.67 [1.44, 1.93]
β: 0.51204		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023362 PSS012150|
European Ancestry|
41,736 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Ischemic stroke OR: 1.02 [0.96, 1.07]
β: 0.01517		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023367 PSS012150|
European Ancestry|
41,736 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: End-stage diabetic nephropathy OR: 1.46 [1.28, 1.68]
β: 0.37999		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023372 PSS012150|
European Ancestry|
41,736 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Diabetic retinopathy OR: 1.42 [1.34, 1.5]
β: 0.34732		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023377 PSS012150|
European Ancestry|
41,736 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Diabetic nephropathy OR: 1.25 [1.18, 1.32]
β: 0.2209		 — — sex, age, genetic principal components Restricted to T2D cases only.
PPM023382 PSS012150|
European Ancestry|
41,736 individuals
 PGP000773 |
Huerta-Chagoya A et al. medRxiv (2025)
|Pre		 Reported Trait: Cardiovascular disease OR: 1.03 [0.99, 1.06]
β: 0.02493		 — — 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
PSS012150 — —
[
  • 8,924 cases
  • , 32,812 controls
]
 — European
(European American)		 — AllofUs —
PSS012163 — —
[
  • 2,530 cases
  • , 20,653 controls
]
 — European
(European American)		 — MGBB —
PSS012158 — —
[
  • 3,694 cases
  • , 18,075 controls
]
 — European
(European American)		 — BioVU —
PSS012155 — —
[
  • 1,165 cases
  • , 6,408 controls
]
 — European
(European American)		 — BioMe —