PGS Publication: PGP000091

Publication Information (EuropePMC)
Title A combined risk score enhances prediction of type 1 diabetes among susceptible children.
PubMed ID 32770166(Europe PMC)
doi 10.1038/s41591-020-0930-4
Publication Date Aug. 7, 2020
Journal Nat Med
Author(s) Ferrat LA, Vehik K, Sharp SA, Lernmark Å, Rewers MJ, She JX, Ziegler AG, Toppari J, Akolkar B, Krischer JP, Weedon MN, Oram RA, Hagopian WA, TEDDY Study Group, Committees.
Released in PGS Catalog: Aug. 19, 2020

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000024
(GRS2)
 PGP000014 |
Sharp SA et al. Diabetes Care (2019)
 Type 1 diabetes (T1D) type 1 diabetes mellitus 85
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000024/ScoringFiles/PGS000024.txt.gz

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) 		Evaluated Score 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
PPM000753 PGS000024
(GRS2)
 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 PGS000024
(GRS2)
 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 PGS000024
(GRS2)
 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 PGS000024
(GRS2)
 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 PGS000024
(GRS2)
 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 PGS000024
(GRS2)
 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
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.