Polygenic Score (PGS) ID: PGS000032

Predicted Trait
Reported Trait Type 2 diabetes (based on SNPs involved in β-cell function)
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 GRSB
Development Method
Name Genome-wide significant variants
Parameters Index SNPs or their proxies (using T2D weights)
Variants
Original Genome Build NR
Number of Variants 20
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: 50%
Not Reported: 25%
African: 25%
4 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
PPM000065 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 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 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
PPM002415 PSS001092|
Ancestry Not Reported|
5,740 individuals
 PGP000214 |
Aksit MA et al. J Clin Endocrinol Metab (2020)
|Ext.		 Reported Trait: Cystic-fibrosis related diabetes onset HR: 1.192 — — PCs(1-4), site of recruitment —

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 —
PSS001092 All individuals had cystic fibrosis with either 2 severe CFTR mutations and/or clinically diagnosed exocrine pancreatic insufficiency. Cases are individuals with cystic fibrosis related diabetes (CFRD).Phenotypes were obtained from extracted medical charts and CF Foundation Patient Registry through 2011. CFRD was defined by clinician diagnosis of diabetes plus insulin treatment for at least 1 year. The onset of CFRD was defined as the date at which insulin was started, if it was subsequently continued for at least 1 year. In approximately 50% of the participants, independent laboratory data (such as oral glucose tolerance test or hemoglobin A1c) were able to independently confirm the diagnosis of CFRD. Diabetes data were censored at the last clinic visit or date of solid organ transplant. —
[
  • 1,341 cases
  • , 4,399 controls
]
,
47.04 % Male samples
 Mean = 20.0 years Not reported — CGS, CWRU, FrGMC, JHU, UNC —
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 —