Polygenic Score (PGS) ID: PGS000031

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Oct. 14, 2019
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Score Details

Score Construction
PGS Name GRSt
Development Method
Name Genome-wide significant variants
Parameters Index SNPs or their proxies
Variants
Original Genome Build NCBI36
Number of Variants 62
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000020
Citation (link to publication) Vassy JL et al. Diabetes (2014)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
69,033 individuals (100%)
PGS Evaluation
European: 66.7%
African: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST005047
Europe PMC: 22885922
 69,033 individuals European NR

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
PPM000062 PSS000044|
European Ancestry|
3,471 individuals
 PGP000020 |
Vassy JL et al. Diabetes (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|
European Ancestry|
1,650 individuals
 PGP000020 |
Vassy JL et al. Diabetes (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|
African Ancestry|
820 individuals
 PGP000020 |
Vassy JL et al. Diabetes (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 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
PSS000044 T2D was defined by a fasting plasma glucose ≥7.0 mmol/L (≥126 mg/dL) or report of taking diabetes medications —
[
  • 446 cases
  • , 3,025 controls
]
,
46.6 % Male samples
 — European — FOS —
PSS000042 T2D was defined by a fasting plasma glucose ≥7.0 mmol/L (≥126 mg/dL) or report of taking diabetes medications —
[
  • 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 —
[
  • 97 cases
  • , 1,553 controls
]
,
46.5 % Male samples
 — European — CARDIA —