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 Catalog: Oct. 14, 2019

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000031
(GRSt)
 PGP000020 |
Vassy JL et al. Diabetes (2014)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 62
-
 https://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 2 diabetes mellitus 20
-
 https://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 2 diabetes mellitus 10
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000033/ScoringFiles/PGS000033.txt.gz

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) 		Evaluated Score 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 PGS000031
(GRSt)
 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 PGS000031
(GRSt)
 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 PGS000031
(GRSt)
 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
PPM000065 PGS000032
(GRSB)
 PSS000044|
European Ancestry|
3,471 individuals
 PGP000020 |
Vassy JL et al. Diabetes (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|
European Ancestry|
1,650 individuals
 PGP000020 |
Vassy JL et al. Diabetes (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|
African Ancestry|
820 individuals
 PGP000020 |
Vassy JL et al. Diabetes (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|
European Ancestry|
3,471 individuals
 PGP000020 |
Vassy JL et al. Diabetes (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|
European Ancestry|
1,650 individuals
 PGP000020 |
Vassy JL et al. Diabetes (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|
African Ancestry|
820 individuals
 PGP000020 |
Vassy JL et al. Diabetes (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) 		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 —