PGS Publication: PGP000020

Publication Information (EuropePMC)
Title Polygenic type 2 diabetes prediction at the limit of common variant detection.
PubMed ID 24520119(Europe PMC)
doi 10.2337/db13-1663
Publication Date Feb. 11, 2014
Journal Diabetes
Author(s) Vassy JL, Hivert MF, Porneala B, Dauriz M, Florez JC, Dupuis J, Siscovick DS, Fornage M, Rasmussen-Torvik LJ, Bouchard C, Meigs JB.
Released in PGS: Oct. 14, 2019

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000031 GRSt PGP000020
Vassy JL et al. Diabetes (2014)
Type 2 diabetes type II diabetes mellitus 62 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000031/ScoringFiles/PGS000031.txt.gz
PGS000032 GRSB PGP000020
Vassy JL et al. Diabetes (2014)
Type 2 diabetes (based on SNPs involved in β-cell function) type II diabetes mellitus 20 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000032/ScoringFiles/PGS000032.txt.gz
PGS000033 GRSIR PGP000020
Vassy JL et al. Diabetes (2014)
Type 2 diabetes (based on SNPs involved in insulin resistance) type II diabetes mellitus 10 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000033/ScoringFiles/PGS000033.txt.gz

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 ID
(PPM ID)
Evaluated Score 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
PPM000062 PGS000031 (GRSt) 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"
PPM000063 PGS000031 (GRSt) 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"
PPM000064 PGS000031 (GRSt) 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
PPM000065 PGS000032 (GRSB) PSS000044 PGP000020
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 PGP000020
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 PGP000020
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 PGP000020
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 PGP000020
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 PGP000020
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 Sample Set ID
(PSS ID)
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