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
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Mapped term(s) |
15 mapped terms
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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 |
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 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 | — |
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. | — | [
|
— | European | — | UKB | UKB Phase 2 |
PSS000054 | Prevalent T2D status was defined using self-reported medical history and medication | — | [
|
— | 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. | — | [ ,
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. | — | [ ,
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 | — | [ ,
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 | — |
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 | — |
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. | — | [ ,
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 | — | [ ,
55.0 % Male samples |
— | European (Estonian) |
— | EB | — |