Polygenic Score (PGS) ID: PGS002780

Predicted Trait
Reported Trait Incident type 2 diabetes
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Dec. 20, 2022
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Terms and Licenses
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)

Score Details

Score Construction
PGS Name GTG_T2D_SCT
Development Method
Name Stacked clumping and thresholding (SCT)
Parameters SCT(bigsnpr) using default hyperparameters
Variants
Original Genome Build hg19
Number of Variants 419,209
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000365
Citation (link to publication) Wong CK et al. PLoS One (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
159,208 individuals (100%)
Score Development/Training
European: 100%
12,768 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004773
Europe PMC: 28566273
 159,208 individuals European NR
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
—
[
  • 2,128 cases
  • , 10,640 controls
]
,
55.0 % Male samples
 European UKB We used the disease definitions described in the supplement of Eastwood et al (2016). PMID: 27631769 — — —

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
PPM014980 PSS009943|
European Ancestry|
5,472 individuals
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Reported Trait: Incident type 2 diabetes OR: 1.41 [1.31, 1.51] AUROC: 0.595 [0.575, 0.615] — — —

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
PSS009943 We used the disease definitions described in the supplement of Eastwood et al (2016). PMID: 27631769 —
[
  • 912 cases
  • , 4,560 controls
]
,
45.0 % Male samples
 European — UKB —