Polygenic Score (PGS) ID: PGS000031

Predicted Trait
Reported Trait Type 2 diabetes
Mapped Trait(s) type II diabetes mellitus (EFO_0001360)
Released in PGS: Oct. 14, 2019

Score Details

Score Construction
PGS Name GRSt
Variants
Original Genome Build NCBI36
Number of Variants 62
Development Method
Name Genome-wide significant SNPs
Parameters Index SNPs or their proxies
PGS Source
PGS Catalog Publication (PGP) ID PGP000020
Citation (link to publication) Vassy JL et al. Diabetes (2014)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST005047
EuropePMC: 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 ID
(PPM ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000064 PSS000042 PGP000020
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
PPM000063 PSS000043 PGP000020
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"
PPM000062 PSS000044 PGP000020
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"

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description 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