Trait: 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

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