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(Variants and weights)

Polygenic Score (PGS) ID: PGS000040

Predicted Trait

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

Score Details

Name: GRS_CeD

Original Genome Build: hg18
Number of Variants: 228

PGS Development Method: SparSNP
PGS Development Details/Relevant Parameters: Lasso penalised linear SVM, 10-fold cross-validation

Citation: Abraham G et al. PLoS Genet (2014) | PGS Catalog Publication ID: PGP000028

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
6,785 individuals
[ 1,849 cases, 4,936 controls]
European
(British)
B58C UK2 Subset of the GWAS Study

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
PPM000093 PSS000059 Abraham G et al. (2014) Reported Trait: Coeliac disease AUROC: 0.9
PPM000094 PSS000061 Abraham G et al. (2014) Reported Trait: Coeliac disease AUROC: 0.87
PPM000095 PSS000062 Abraham G et al. (2014) Reported Trait: Coeliac disease AUROC: 0.86
PPM000096 PSS000063 Abraham G et al. (2014) Reported Trait: Coeliac disease AUROC: 0.87
PPM000097 PSS000060 Abraham G et al. (2014) Reported Trait: Coeliac disease AUROC: 0.87
PPM000098 PSS000064 Abraham G et al. (2015) Ext. Reported Trait: Coeliac disease AUROC: 0.831 [0.808 - 0.85]
PPM000099 PSS000065 Abraham G et al. (2015) Ext. Reported Trait: Coeliac disease in HLA-DQ2.5 carriers AUROC: 0.669 [0.625 - 0.713]

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
PSS000059 2,476 individuals
[ 647 cases, 1,829 controls]
European
(Finnish)
FINRISK, Health 2000
PSS000060 10,304 individuals
[ 5,907 cases, 4,397 controls]
European
(British)
Immunochip
PSS000061 1,040 individuals
[ 497 cases, 543 controls]
European
(Italian)
PSS000062 1,649 individuals
[ 803 cases, 846 controls]
European
(Dutch)
PSS000063 2,200 individuals
[ 778 cases, 1,422 controls]
European
(British)
PSS000064 1,696 individuals
[ 1,259 cases, 437 controls]
European NIDDK
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