Predicted Trait | |
Reported Trait | Type 2 diabetes (based on SNPs involved in β-cell function) |
Mapped Trait(s) | type 2 diabetes mellitus (MONDO_0005148) |
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 |
Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
---|---|---|---|
GWAS Catalog: GCST005047 Europe PMC: 22885922 |
69,033 individuals | European | NR |
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 | — |
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 | — | [ ,
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. | — | [ ,
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 | — | [ ,
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 | — | [ ,
46.5 % Male samples |
— | European | — | CARDIA | — |