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(Variants and weights)

Polygenic Score (PGS) ID: PGS000031

Predicted Trait

Reported Trait: Type 2 diabetes
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): type II diabetes mellitus

Score Details

Name: GRSt

Original Genome Build: NCBI36
Number of Variants: 62

PGS Development Method: Genome-wide significant SNPs
PGS Development Details/Relevant Parameters: Index SNPs or their proxies

Citation: Vassy JL et al. Diabetes (2014) | PGS Catalog Publication ID: PGP000020

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST005047
PubMed: 22885922
69,033 individuals European

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000062 PSS000044 Vassy JL et al. (2014) Reported Trait: Incident type 2 diabetes cases HR: 1.06 [1.04 - 1.08] C-index: 0.906 [0.892 - 0.92] age, sex, family history (parents), body mass index, systolic blood pressure, fasting glucose, log-HDL cholesterol, log-triglyceride levels Results from the "Clinical model"
PPM000063 PSS000043 Vassy JL et al. (2014) Reported Trait: Incident type 2 diabetes cases HR: 1.06 [1.02 - 1.1] C-index: 0.853 [0.81 - 0.896] age, sex, family history (parents), body mass index, systolic blood pressure, fasting glucose, log-HDL cholesterol, log-triglyceride levels Results from the "Clinical model"
PPM000064 PSS000042 Vassy JL et al. (2014) Reported Trait: Incident type 2 diabetes cases HR: 1.05 [1.0 - 1.09] C-index: 0.771 [0.727 - 0.814] age, sex, family history (parents), body mass index, systolic blood pressure, fasting glucose, log-HDL cholesterol, log-triglyceride levels Results from the "Clinical model", SNPs were not weighted by their effect size as the betas were measure in Europeans

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000042 T2D was defined by a fasting plasma glucose ≥7.0 mmol/L (≥126 mg/dL) or report of taking diabetes medications 820 individuals
[ 118 cases, 702 controls]
38.8 % Male samples
African American or Afro-Caribbean CARDIA
PSS000043 T2D was defined by a fasting plasma glucose ≥7.0 mmol/L (≥126 mg/dL) or report of taking diabetes medications 1,650 individuals
[ 97 cases, 1,553 controls]
46.5 % Male samples
European CARDIA
PSS000044 T2D was defined by a fasting plasma glucose ≥7.0 mmol/L (≥126 mg/dL) or report of taking diabetes medications 3,471 individuals
[ 446 cases, 3,025 controls]
46.6 % Male samples
European FOS