Polygenic Score (PGS) ID: PGS005115

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Feb. 4, 2025
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Score Details

Score Construction
PGS Name PGS_T2D_beta_cell
Development Method
Name Bayesian nonnegative matrix factorization using curated T2D GWAS variants and GWAS summary statistics of T2D-related traits
Parameters Minimum cluster weight of 0.75
Variants
Original Genome Build GRCh37
Number of Variants 30
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000701
Citation (link to publication) Loesch DP et al. medRxiv (2024) Preprint
Ancestry Distribution
PGS Evaluation
European: 50%
Multi-ancestry (including European): 50%
  • European
  • East Asian
  • South Asian
  • Hispanic or Latin American
  • African
2 Sample Sets

Development Samples

No sample information available.

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
PPM022306 PSS011911|
Multi-ancestry (including European)|
48,603 individuals
 PGP000701 |
Loesch DP et al. medRxiv (2024)
|Pre		 Reported Trait: type 2 diabetes OR: 1.27 [1.23, 1.31] — — age, age^2, sex, UKB centre, array, genetic PCS 1-20 —
PPM022317 PSS011912|
European Ancestry|
45,356 individuals
 PGP000701 |
Loesch DP et al. medRxiv (2024)
|Pre		 Reported Trait: type 2 diabetes OR: 1.27 [1.23, 1.31] — — age, age^2, sex, UKB centre, array, genetic PCS 1-20 —

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
PSS011911 ICD10: E11 for T2D, N18 for CKD, first occurence of I20-125 for CAD. BMI: baseline body mass index Median = 14.8 years 48,603 individuals,
46.0 % Male samples
 Mean = 56.8 years
Sd = 8.2 years		 European, East Asian, South Asian, Hispanic or Latin American, African unspecified — UKB —
PSS011912 ICD10: E11 for T2D, N18 for CKD, first occurence of I20-125 for CAD, K76.0 for NAFLD. BMI: baseline body mass index Median = 14.8 years 45,356 individuals,
46.0 % Male samples
 Mean = 57.1 years
Sd = 8.1 years		 European — UKB —