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(Variants and weights)

Polygenic Score (PGS) ID: PGS000042

Predicted Trait

Reported Trait: Coeliac disease
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): celiac disease

Score Details

Name: GRS-DQ2.5-CeD-imputed

Original Genome Build: hg18
Number of Variants: 3,317

PGS Development Method: SparSNP
PGS Development Details/Relevant Parameters: Lasso penalised linear SVM on SNPs & imputed HLA alleles (SNP2HLA), 10-fold cross-validation

Citation: Abraham G et al. Genome Med (2015) | PGS Catalog Publication ID: PGP000029

Contributing Samples

Score Development/Training
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
The HLA-DQ2.5-positive subset 5,552 individuals European
(British, Dutch, Italian, Finnish)
Four cohorts (UK2, NL, IT, Finn) combined into one, SNPs

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 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
PPM000101 PSS000065 Abraham G et al. (2015) Reported Trait: Coeliac disease in HLA-DQ2.5 carriers AUROC: 0.73 [0.687 - 0.772]

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
PSS000065 The HLA-DQ2.5-positive subset of NIDDK-CIDR 1,237 individuals
[ 1,094 cases, 143 controls]
European NIDDK HLA alleles were imputed using SNP2HLA