Polygenic Score (PGS) ID: PGS000021

Predicted Trait
Reported Trait Type 1 diabetes (T1D)
Mapped Trait(s) type 1 diabetes mellitus (MONDO_0005147)
Released in PGS Catalog: Oct. 14, 2019
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Score Details

Score Construction
PGS Name GRS1
Development Method
Name SNP associations curated from the literature
Parameters HLA Haplotypes called with SNP2HLA using the T1DGC reference panel
Variants
Original Genome Build NR
Number of Variants 33
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000011
Citation (link to publication) Oram RA et al. Diabetes Care (2015)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
21,924 individuals (100%)
Score Development/Training
European: 100%
3,852 individuals (100%)
PGS Evaluation
European: 75%
African: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST000392
Europe PMC: 1943048
 16,559 individuals European NR
Europe PMC: 20798335
[
  • 3,577 cases
  • , 1,788 controls
]
 European NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 1,938 cases
  • , 1,914 controls
]
 European WTCCC Cases = patients [that] received a clinical diagnosis of T1D at ,17 years of age and were treated with insulin from the time of diagnosis. Controls = T2D patients diagnosed between 25 and 75 years of age, were GAD autoantibody negative on testing, and were either treated with diet/oral hypoglycemic agents or had an interval of at least 1 year between diagnosis and the institution of insulin therapy — — — —

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) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000132 PSS000083|
European Ancestry|
2,768 individuals
 PGP000038 |
Patel KA et al. Diabetes (2016)
|Ext.		 Reported Trait: Type 1 diabetes aetiology (non-monogenic) — AUROC: 0.87 [0.86, 0.89] — — Testing the ability of the GRS to discriminate between two sets of cases: - Positive: individuals with type 1 diabetes - Negative: individuals with diabetes and a maturity-onset diabetes of young (MODY) mutation
PPM000041 PSS000026|
European Ancestry|
223 individuals
 PGP000011 |
Oram RA et al. Diabetes Care (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 PSS000030|
African Ancestry|
3,949 individuals
 PGP000013 |
Onengut-Gumuscu S et al. Diabetes Care (2019)
|Ext.		 Reported Trait: Type 1 diabetes — AUROC: 0.798 — — —
PPM000049 PSS000032|
European Ancestry|
374,000 individuals
 PGP000014 |
Sharp SA et al. Diabetes Care (2019)
|Ext.		 Reported Trait: Type 1 diabetes — AUROC: 0.893 — — —

Evaluated Samples

PGS Sample Set ID
(PSS) 		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
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) —
[
  • 46 cases
  • , 177 controls
]
,
46.3 % 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.
PSS000083 Cases were clinically diagnosed with T1D before 17 years of age and treated with insulin from diagnosis. Patients with known MODY or NDM were excluded. —
[
  • 1,963 cases
  • , 0 controls
]
 — European — WTCCC Cases with Type 1 Diabetes
PSS000083 MODY patients with a confirmed monogenic etiology on genetic testing (415 patients with HNF1A MODY, 346 with GCK MODY, 42 with HNF4A MODY, and 2 with HNF1B MODY). The median age of diagnosis was 20 years (interquartile range 15, 30), and 532 patients were female. —
[
  • 805 cases
  • , 0 controls
]
,
33.91 % Male samples
 — European — NR Maturity-onset diabetes of young (MODY) cases ascertained from the Genetic Βeta Cell Research Bank, Exeter, U.K.
PSS000030 — —
[
  • 1,021 cases
  • , 2,928 controls
]
 — African unspecified — 7 cohorts
  • BDC
  • ,CLEAR
  • ,GoKinD
  • ,NYCP
  • ,SEARCH
  • ,T1DGC
  • ,UAB
 —
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) —
[
  • 387 cases
  • , 373,613 controls
]
 — European — UKB —