PGS CatalogTrait: type II diabetes mellitus
Information
Experimental Factor Ontology ID: EFO_0001360
EFO Trait Description: A type of diabetes mellitus that is characterized by insulin resistance or desensitization and increased blood glucose levels. This is a chronic disease that can develop gradually over the life of a patient and can be linked to both environmental factors and heredity. [NCIT: P378]
Associated PGS
| Polygenic Score (PGS) ID | PGS Name | Publication ID | Reported Trait | Mapped Trait(s) (EFO) | Number of Variants | PGS Download Links |
|---|---|---|---|---|---|---|
| PGS000014 | GPS_T2D | Khera AV et al. Nat Genet (2018) | Type 2 diabetes | type II diabetes mellitus | 6,917,436 | FTP Link |
| PGS000020 | dGRS1000 | Läll K et al. Genet Med (2016) | Type 2 diabetes | type II diabetes mellitus | 7,502 | FTP Link |
| 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 |
| PGS000036 | gePS_T2D | Mahajan A et al. Nat Genet (2018) | Type 2 diabetes | type II diabetes mellitus | 171,249 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM000023 | PGS000014 (GPS_T2D) | PSS000017 | Khera AV et al. (2018) | Reported Trait: Type 2 diabetes cases | — | AUROC: 0.73 [0.72 - 0.73] | Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.029 | age; sex; Ancestry PC 1-4; genotyping chip | — |
| PPM000040 | PGS000020 (dGRS1000) | PSS000025 | Läll K et al. (2016) | Reported Trait: Incident type 2 diabetes cases | HR: 1.48 [1.32 - 1.66] | C-index: 0.79 [0.771 - 0.812] | — | BMI category, smoking level, waist-to-hip ratio, waist circumference, physical activity level, history of high blood glucose, fruit and vegetable consumption, and sex. | Cox age-as-time-scale |
| 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 |
| PPM000080 | PGS000036 (gePS_T2D) | PSS000054 | Udler MS et al. (2019) Ext. | Reported Trait: Type 2 diabetes | — | AUROC: 0.66 | — | genotyping array, first 6 PCs of ancestry | — |
| PPM000081 | PGS000036 (gePS_T2D) | PSS000054 | Udler MS et al. (2019) Ext. | Reported Trait: Type 2 diabetes | — | AUROC: 0.73 | — | age, sex, genotyping array, first 6 PCs of ancestry | — |
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 |
|---|---|---|---|---|---|---|
| PSS000017 | Type 2 diabetes ascertainment was based on self-report in an interview with a trained nurse or an ICD-10 code of E11.X in hospitalization records. | 288,978 individuals [ 5,853 cases, 294,831 controls] |
European | — | UKB | UKB Phase 2 |
| PSS000025 | Incident cases of Type 2 Diabetes in 5.63 years follow-up | 6,280 individuals [ 302 cases, 5,978 controls] 55.0 % Male samples |
European(Estonian) | — | EB | — |
| 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 | — |
| PSS000054 | Prevalent T2D status was defined using self-reported medical history and medication | 324,870 individuals [ 13,480 cases, 311,390 controls] |
European | — | UKB | — |