Trait: type II diabetes mellitus

Experimental Factor Ontology (EFO) Information
Identifier EFO_0001360
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]
Trait category
Digestive system disorder
Metabolic disorder
Synonyms 48 synonyms
  • T2DM - Type 2 Diabetes mellitus
  • Diabetes Mellitus, Adult-Onset
  • Adult-Onset Diabetes Mellitus
  • diabetes mellitis type II
  • Diabetes Mellitus, Slow Onset
  • type II diabetes mellitus
  • Type 2 Diabetes
  • Diabetes Mellitus, Type II
  • adult onset diabetes
  • non-insulin dependent diabetes
  • Diabetes Mellitus, Stable
  • Diabetes, Type 2
  • Diabetes Mellitus, Ketosis Resistant
  • Type II Diabetes
  • MODY
  • Diabetes Mellitus, Maturity-Onset
  • T2DM - type 2 diabetes mellitus
  • Type 2 Diabetes Mellitus
  • non-insulin dependent diabetes mellitus
  • Maturity Onset Diabetes Mellitus
  • type 2 diabetes mellitus
  • Diabetes Mellitus, Ketosis-Resistant
  • DIABETES MELLITUS TYPE 02
  • Diabetes Mellitus, Type 2
  • diabetes mellitus type 2
  • Diabetes Mellitus, Maturity Onset
  • diabetes mellitis type 2
  • noninsulin dependent diabetes
  • Ketosis-Resistant Diabetes Mellitus
  • NIDDM
  • adult-onset diabetes
  • type 2 diabetes mellitus non-insulin dependent
  • Diabetes Mellitus, Adult Onset
  • diabetes, type 2
  • Non-Insulin Dependent Diabetes
  • Adult-Onset Diabetes
  • Diabetes Mellitus, Slow-Onset
  • type II diabetes
  • Diabetes Mellitus, Noninsulin Dependent
  • Slow-Onset Diabetes Mellitus
  • Non-Insulin Dependent Diabetes Mellitus
  • type 2 diabetes
  • Type 2 Diabetes Mellitus Non-Insulin Dependent
  • non-insulin-dependent diabetes mellitus
  • Diabetes Mellitus, Non-Insulin-Dependent
  • Diabetes Mellitus, Non Insulin Dependent
  • Stable Diabetes Mellitus
  • Maturity-Onset Diabetes Mellitus
Mapped term(s) 15 mapped terms
  • UMLS:CN244395
  • ICD10:E11
  • SCTID:44054006
  • NCIt:C26747
  • NCIT:C26747
  • SNOMEDCT:44054006
  • KEGG:04930
  • DOID:9352
  • MESH:D003924
  • OMIM:616087
  • COHD:201826
  • OMIM:125853
  • MONDO:0005148
  • OMIM:601283
  • MSH:D003924

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000014 GPS_T2D PGP000006 Khera AV et al. Nat Genet (2018) Type 2 diabetes type II diabetes mellitus 6,917,436 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000014/ScoringFiles/PGS000014.txt.gz - Check Terms/Licenses
PGS000020 dGRS1000 PGP000010 Läll K et al. Genet Med (2016) Type 2 diabetes type II diabetes mellitus 7,502 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000020/ScoringFiles/PGS000020.txt.gz
PGS000031 GRSt PGP000020 Vassy JL et al. Diabetes (2014) Type 2 diabetes type II diabetes mellitus 62 http://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 II diabetes mellitus 20 http://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 II diabetes mellitus 10 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000033/ScoringFiles/PGS000033.txt.gz
PGS000036 gePS_T2D PGP000023 Mahajan A et al. Nat Genet (2018) Type 2 diabetes type II diabetes mellitus 171,249 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000036/ScoringFiles/PGS000036.txt.gz
PGS000125 Qi_T2D_2017 PGP000062 Qi Q et al. Diabetes (2017) Type 2 Diabetes type II diabetes mellitus 80 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000125/ScoringFiles/PGS000125.txt.gz
PGS000330 PRS_T2D PGP000100 Mars N et al. Nat Med (2020) Type 2 diabetes type II diabetes mellitus 6,437,380 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000330/ScoringFiles/PGS000330.txt.gz

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 ID
(PPM ID) 		Evaluated Score PGS Sample Set ID
(PSS ID) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000040 PGS000020 (dGRS1000) PSS000025 PGP000010
Läll K et al. (2016) 		Reported Trait: Incident type 2 diabetes 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 PGP000020
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 PGP000020
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 PGP000020
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 PGP000020
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 PGP000020
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 PGP000020
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 PGP000020
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 PGP000020
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 PGP000020
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 PGP000024
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 PGP000024
Udler MS et al. (2019) Ext. 		Reported Trait: Type 2 diabetes — AUROC: 0.73 — age, sex, genotyping array, first 6 PCs of ancestry —
PPM000404 PGS000125 (Qi_T2D_2017) PSS000232 PGP000062
Qi Q et al. (2017) 		Reported Trait: Type 2 Diabetes — — OR (Odds Ratio, per risk allele): 1.07[1.06, 1.08] center, age, sex, 5 PCs of ancestry Covariance matrices corresponding to genetic relatedness (kinship), household, and census block group were included as random effects in the mixed model analysis
PPM000023 PGS000014 (GPS_T2D) PSS000017 PGP000006
Khera AV et al. (2018) 		Reported Trait: Type 2 diabetes — 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 —
PPM000897 PGS000330 (PRS_T2D) PSS000441 PGP000100
Mars N et al. (2020) 		Reported Trait: Incident type 2 diabetes — C-index: 0.845 — age, sex, BMI, history of stroke or CHD, parental history of diabetes, SBP, DBP, HDL, triglycerides, FINRISK cohort, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000892 PGS000330 (PRS_T2D) PSS000441 PGP000100
Mars N et al. (2020) 		Reported Trait: Incident type 2 diabetes HR: 1.7[1.63, 1.78] C-index: 0.763 — age, sex, FINRISK cohort, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000887 PGS000330 (PRS_T2D) PSS000448 PGP000100
Mars N et al. (2020) 		Reported Trait: Type 2 diabetes (incident and prevalent cases) HR: 1.74[1.72, 1.77] — — genotyping array/batch, 10 ancestry PCs, stratified by sex —

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		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
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. —
[
  • 5,853 cases
  • , 283,125 controls
]
 — European — UKB UKB Phase 2
PSS000054 Prevalent T2D status was defined using self-reported medical history and medication —
[
  • 13,480 cases
  • , 311,390 controls
]
 — European — UKB —
PSS000232 Individuals with T2D were defined as those with fasting time >8 h and fasting glucose levels ≥126 mg/dL, fasting ≤8 h and fasting glucose ≥200 mg/dL, post–oral glucose tolerance test glucose ≥200 mg/dL, HbA1c ≥6.5% (48 mmol/mol), or on current treatment with antihyperglycemia medications. —
[
  • 2,499 cases
  • , 5,247 controls
]
,
39.65 % Male samples
 — Hispanic or Latin American
(Central American, Cuban, Dominican, Mexican, Puerto Rican, South American)		 Ancestry groups were defined based on a combination of self-identified Hispanic/Latino background and genetic similarity HCHS, SOL —
PSS000441 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. —
[
  • 1,346 cases
  • , 19,684 controls
]
,
47.3 % Male samples
 Mean (Age At Baseline) = 48.0 years European
(Finnish)		 — FINRISK FINRISK surveys from 1992, 1997, 2002 and 2007
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 —
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 —
PSS000448 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. —
[
  • 17,519 cases
  • , 117,781 controls
]
,
43.7 % Male samples
 Mean (Age At Baseline) = 59.2 years
Sd = 16.6 years		 European
(Finnish)		 — FinnGen —
PSS000025 Incident cases of Type 2 Diabetes in 5.63 years follow-up —
[
  • 302 cases
  • , 5,978 controls
]
,
55.0 % Male samples
 — European
(Estonian)		 — EB —