Polygenic Score (PGS) ID: PGS005023

Predicted Trait
Reported Trait Type 2 diabetes (T2D) (PheCode 250.2)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Oct. 8, 2024
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Score Details

Score Construction
PGS Name Phe_250_2_ldpred_HISss_amrld
Development Method
Name ldpred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,286,612
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000679
Citation (link to publication) Gunn S et al. HGG Adv (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Not Reported: 50.3%
European: 36.1%
African: 9.5%
Hispanic or Latin American: 4%
1,216,910 individuals (100%)
PGS Evaluation
African: 33.3%
Hispanic or Latin American: 33.3%
European: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 51,469 cases
  • , 64,357 controls
]
 African American or Afro-Caribbean MVP
—
[
  • 156,343 cases
  • , 283,166 controls
]
 European MVP
—
[
  • 19,574 cases
  • , 29,653 controls
]
 Hispanic or Latin American MVP
—
[
  • 229,933 cases
  • , 382,415 controls
]
 Not reported MVP

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
PPM021885 PSS011807|
Hispanic or Latin American Ancestry|
8,102 individuals
 PGP000679 |
Gunn S et al. HGG Adv (2024)
 Reported Trait: Type 2 diabetes OR: 1.656 [1.52, 1.8] C-index: 0.78141 — age, sex, 20 PCs —
PPM021897 PSS011797|
African Ancestry|
10,808 individuals
 PGP000679 |
Gunn S et al. HGG Adv (2024)
 Reported Trait: Type 2 diabetes OR: 1.22 [1.16, 1.28] C-index: 0.71211 — age, sex, 20 PCs —
PPM021891 PSS011817|
European Ancestry|
30,374 individuals
 PGP000679 |
Gunn S et al. HGG Adv (2024)
 Reported Trait: Type 2 diabetes OR: 1.342 [1.3, 1.38] C-index: 0.69576 — age, sex, 20 PCs —

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
PSS011817 — —
[
  • 5,958 cases
  • , 24,416 controls
]
 — European — AllofUs —
PSS011797 — —
[
  • 3,016 cases
  • , 7,792 controls
]
 — African American or Afro-Caribbean — AllofUs —
PSS011807 — —
[
  • 2,144 cases
  • , 5,958 controls
]
 — Hispanic or Latin American — AllofUs —