Trait: type I diabetes mellitus

Information

Experimental Factor Ontology ID: EFO_0001359

EFO Trait Description: A chronic condition characterized by minimal or absent production of insulin by the pancreas. [NCIT: C2986]

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
PPM000041 PGS000021 (GRS1) PSS000026 Oram RA et al. (2015) Reported Trait: Severe insulin deficiency AUROC: 0.96 [0.94 - 0.99] AUROC (without covariates): 0.87 islet auto-antibody status, body mass index (BMI), age at diagnosis
PPM000046 PGS000021 (GRS1) PSS000030 Onengut-Gumuscu S et al. (2019) Ext. Reported Trait: Type 1 diabetes AUROC: 0.798
PPM000049 PGS000021 (GRS1) PSS000032 Sharp SA et al. (2019) Ext. Reported Trait: Type 1 diabetes AUROC: 0.893
PPM000042 PGS000022 (T1D_GRS) PSS000029 Perry DJ et al. (2018) Reported Trait: Type 1 diabetes AUROC: 0.8508 AUROCs are reported with respect to unrelated-control samples
PPM000043 PGS000022 (T1D_GRS) PSS000028 Perry DJ et al. (2018) Reported Trait: Type 1 diabetes AUROC: 0.9003 AUROCs are reported with respect to unrelated-control samples
PPM000044 PGS000022 (T1D_GRS) PSS000027 Perry DJ et al. (2018) Reported Trait: Type 1 diabetes AUROC: 0.7522 AUROCs are reported with respect to unrelated-control samples
PPM000045 PGS000023 (AA_GRS) PSS000030 Onengut-Gumuscu S et al. (2019) Reported Trait: Type 1 diabetes AUROC: 0.87 NOTE: Evaluated using cross-validation on training samples (20% heldout, 1000 iterations)
PPM000047 PGS000023 (AA_GRS) PSS000031 Onengut-Gumuscu S et al. (2019) Reported Trait: Type 1 diabetes AUROC: 0.779
PPM000048 PGS000024 (GRS2) PSS000032 Sharp SA et al. (2019) Reported Trait: Type 1 diabetes AUROC: 0.921 Youden index: 0.698

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
PSS000026 Cases were defined on the presence or absence of severe insulin deficiency (requiring insulin treatment at 3 years after diagnosis). We cate- gorized people as severely insulin defi- cient if they received continuous insulin treatment at ,3 years from the time of diagnosis and had a low measured C-peptide level (nonfasting measured ,0.6 nmol/L or equivalent fasting blood glucose level or posthome meal urine C-peptide–to–creatinine ratio) 223 individuals
[ 46 cases, 177 controls]
46.300448430493276 % Male samples
European P2ID A cross-sectional cohort of people in whom diabetes was diagnosed between the ages of 20 and 40 years (n = 223), who had had diabetes for .3 years, and who had self-reported as white European from Devon and Cornwall in South West England. Known monogenic diabetes and secondary diabetes pa- tients were excluded.
PSS000027 Type 1 diabetes status was assigned according to clinician diagnosis. 299 individuals
[ 84 cases, 63 controls]
33.78 % Male samples
African American or Afro-Caribbean UFDI Total sample number contains the number of controls, cases, and includes the number of first/second-degree relatives and samples identified as "at risk" (autoantibody positive) used in other analyses.
PSS000028 Type 1 diabetes status was assigned according to clinician diagnosis. 252 individuals
[ 65 cases, 43 controls]
44.84 % Male samples
Hispanic or Latin American Samples labeled Caucasian (Hispanic ethnicity) in the original publication. UFDI Total sample number contains the number of controls, cases, and includes the number of first/second-degree relatives and samples identified as "at risk" (autoantibody positive) used in other analyses.
PSS000029 Type 1 diabetes status was assigned according to clinician diagnosis. 1,447 individuals
[ 478 cases, 290 controls]
47.34 % Male samples
European Samples labeled Caucasian (non-Hispanic) in the original publication. UFDI Total sample number contains the number of controls, cases, and includes the number of first/second-degree relatives and samples identified as "at risk" (autoantibody positive) used in other analyses.
PSS000030 3,949 individuals
[ 1,021 cases, 2,928 controls]
African unspecified BDC, CLEAR, GoKinD, NYCP, SEARCH, T1DGC, UAB
PSS000031 Cases are diagnosed with type 1 diabetes. 145 individuals
[ 61 cases, 54 controls]
African unspecified UOF
PSS000032 Type 1 Diabetes Case Definition = Clinical diagnosis of diabetes at less than or equal to 20 years of age; On insulin within 1 year from the time of diagnosis; Still on insulin at the time of recruit- ment; Not using oral antihyperglycemic agents; Did not ever self-report as having type 2 diabetes (T2D) 374,000 individuals
[ 387 cases, 373,613 controls]
European UKB