Polygenic Score (PGS) ID: PGS000024

Predicted Trait
Reported Trait Type 1 diabetes
Mapped Trait(s) type I diabetes mellitus (EFO_0001359)
Released in PGS Catalog: Oct. 14, 2019
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Score Details

Score Construction
PGS Name GRS2
Variants
Original Genome Build NR
Number of Variants 67
Number of Variant Interaction Terms 18
Development Method
Name Genome-wide significant associations and interaction modelling
Parameters Significance threshold for interactions: p < 10^-4
PGS Source
PGS Catalog Publication (PGP) ID PGP000014
Citation (link to publication) Sharp SA et al. Diabetes Care (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
16,086 individuals (100%)
PGS Evaluation
Not Reported: 50%
European: 50%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST000392
Europe PMC: 19956093
[
  • 6,670 cases
  • , 9,416 controls
]
European

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
PPM000048 PSS000032|
European Ancestry|
374,000 individuals
PGP000014 |
Sharp SA et al. Diabetes Care (2019)
Reported Trait: Type 1 diabetes AUROC: 0.921 Youden index: 0.698
PPM000753 PSS000368|
Ancestry Not Reported|
7,798 individuals
PGP000091 |
Ferrat LA et al. Nat Med (2020)
|Ext.
Reported Trait: Type 1 diabetes (5 years horizon time; landmark age 2 years) AUROC: 0.93 autoantibodies, family history
PPM000754 PSS000368|
Ancestry Not Reported|
7,798 individuals
PGP000091 |
Ferrat LA et al. Nat Med (2020)
|Ext.
Reported Trait: Type 1 diabetes (8 years horizon time; landmark age 2 years) AUROC: 0.87 autoantibodies, family history
PPM000755 PSS000368|
Ancestry Not Reported|
7,798 individuals
PGP000091 |
Ferrat LA et al. Nat Med (2020)
|Ext.
Reported Trait: Type 1 diabetes (5 years horizon time; landmark age 4 years) AUROC: 0.96 autoantibodies, family history
PPM000751 PSS000368|
Ancestry Not Reported|
7,798 individuals
PGP000091 |
Ferrat LA et al. Nat Med (2020)
|Ext.
Reported Trait: Type 1 diabetes (1 year horizon time; landmark age 2 years) AUROC: 0.96 autoantibodies, family history
PPM000752 PSS000368|
Ancestry Not Reported|
7,798 individuals
PGP000091 |
Ferrat LA et al. Nat Med (2020)
|Ext.
Reported Trait: Type 1 diabetes (3 years horizon time; landmark age 2 years) AUROC: 0.94 autoantibodies, family history
PPM000750 PSS000368|
Ancestry Not Reported|
7,798 individuals
PGP000091 |
Ferrat LA et al. Nat Med (2020)
|Ext.
Reported Trait: Type 1 diabetes (by age 8; landmark age 2 years) AUROC: 0.73 [0.7, 0.77]

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
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
PSS000368 TEDDY children were followed prospectively from 3–4 months of age, with visits every 3 months until 4 years of age. Each evaluation tested the three islet antibodies (GADA, IA2A and IAA), changes in family history, as well as other measurements specified by the TEDDY protocol. After 4 years of age, children with any islet autoantibodies remained on quarterly visits, while antibody-negative children were evaluated every 6 months. Children were followed prospectively until 15 years of age or until T1D onset, as defined using the American Diabetes Association’s criteria for diagnosis (doi: 10.1196/annals.1447.062) Median = 9.3 years
Range = [0.0833, 14.0] years
[
  • 305 cases
  • , 7,493 controls
]
,
50.86 % Male samples
Range = [3.0, 4.0] years NR TEDDY From 2004–2010, 424,788 newborns were screened at six US and European centers for high-risk HLA genotypes. TEDDY then enrolled 8,676 eligible infants with the intent to follow them until 15 years of age. The three major eligible HLA DR–DQ haplotypes are DR3–DQA1*0501–DQB1*0201, DR4–DQA1*0301–DQB1*0302 and DR8–DQA1*0401–DQB1*0402.