Polygenic Score (PGS) ID: PGS003749

Predicted Trait
Reported Trait Type 1 diabetes (T1D)
Mapped Trait(s) type 1 diabetes mellitus (MONDO_0005147)
Released in PGS Catalog: June 22, 2023
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Score Details

Score Construction
PGS Name ModelT1D_under25
Development Method
Name Genome-wide significant SNPs
Parameters r2<=0.1
Variants
Original Genome Build GRCh37
Number of Variants 6,612
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000472
Citation (link to publication) Shoaib M et al. Genet Epidemiol (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
14,741 individuals (100%)
Score Development/Training
European: 100%
178,911 individuals (100%)
PGS Evaluation
European: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 10.1101/120022
[
  • 5,913 cases
  • , 8,828 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
—
[
  • 296 cases
  • , 178,615 controls
]
 European UKB — — — — —

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
PPM018508 PSS011001|
European Ancestry|
119,273 individuals
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Reported Trait: Type 1 diabetes with age of diagnosis under 25 — AUROC: 0.797 Nagelkerke R2: 0.099 — —
PPM018512 PSS011000|
European Ancestry|
7,067 individuals
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Reported Trait: Discrimination of Type 1 diabetes from Type 2 diabetes — AUROC: 0.792 — — —
PPM018514 PSS010998|
European Ancestry|
2,494 individuals
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Reported Trait: Discrimination of Type 1 diabetes from Type 2 diabetes — AUROC: 0.686 — — —

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
PSS010998 — —
[
  • 1,070 cases
  • , 1,424 controls
]
 — European — MGI —
PSS011000 — —
[
  • 953 cases
  • , 6,114 controls
]
 — European — UKB —
PSS011001 — —
[
  • 198 cases
  • , 119,075 controls
]
 — European — UKB —