Publication: Polygenic type 2 diabetes prediction at the limit of common variant detection.

Information

PGS Catalog Publication (PGP) ID: PGP000020
PubMed ID: 24520119
doi: 10.2337/db13-1663

Publication Date: Feb. 11, 2014

Journal: Diabetes

Authors: Vassy JL, Hivert MF, Porneala B, Dauriz M, Florez JC, Dupuis J, Siscovick DS, Fornage M, Rasmussen-Torvik LJ, Bouchard C, Meigs JB.

PGS Associated with PGP000020

PGS Developed By This Study

Polygenic Score (PGS) ID PGS Name Publication ID Reported Trait Mapped Trait(s) (EFO) Number of Variants PGS Download Links
PGS000031 GRSt Vassy JL et al. Diabetes (2014) Type 2 diabetes type II diabetes mellitus 62 FTP Link
PGS000032 GRSB Vassy JL et al. Diabetes (2014) Type 2 diabetes (based on SNPs involved in β-cell function) type II diabetes mellitus 20 FTP Link
PGS000033 GRSIR Vassy JL et al. Diabetes (2014) Type 2 diabetes (based on SNPs involved in insulin resistance) type II diabetes mellitus 10 FTP Link

PGS 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 Evaluated Score 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 PGS000031 (GRSt) 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 PGS000031 (GRSt) 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 PGS000031 (GRSt) 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
PPM000065 PGS000032 (GRSB) PSS000044 Vassy JL et al. (2014) Reported Trait: Incident type 2 diabetes cases HR: 1.1 [1.06 - 1.14] age, sex, family history (parents), body mass index, systolic blood pressure, fasting glucose, log-HDL cholesterol, log-triglyceride levels Results from the "Clinical model"
PPM000066 PGS000032 (GRSB) PSS000043 Vassy JL et al. (2014) Reported Trait: Incident type 2 diabetes cases HR: 1.09 [1.02 - 1.17] age, sex, family history (parents), body mass index, systolic blood pressure, fasting glucose, log-HDL cholesterol, log-triglyceride levels Results from the "Clinical model"
PPM000067 PGS000032 (GRSB) PSS000042 Vassy JL et al. (2014) Reported Trait: Incident type 2 diabetes cases HR: 1.06 [0.99 - 1.15] 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
PPM000068 PGS000033 (GRSIR) PSS000044 Vassy JL et al. (2014) Reported Trait: Incident type 2 diabetes cases HR: 0.98 [0.93 - 1.04] age, sex, family history (parents), body mass index, systolic blood pressure, fasting glucose, log-HDL cholesterol, log-triglyceride levels Results from the "Clinical model"
PPM000069 PGS000033 (GRSIR) PSS000043 Vassy JL et al. (2014) Reported Trait: Incident type 2 diabetes cases HR: 1.01 [0.91 - 1.12] age, sex, family history (parents), body mass index, systolic blood pressure, fasting glucose, log-HDL cholesterol, log-triglyceride levels Results from the "Clinical model"
PPM000070 PGS000033 (GRSIR) PSS000042 Vassy JL et al. (2014) Reported Trait: Incident type 2 diabetes cases HR: 1.06 [0.99 - 1.15] 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