Polygenic Score (PGS) ID: PGS000040

Predicted Trait
Reported Trait Coeliac disease
Mapped Trait(s) celiac disease (EFO_0001060)
Released in PGS: Dec. 18, 2019

Score Details

Score Construction
PGS Name GRS_CeD
Variants
Original Genome Build hg18
Number of Variants 228
Development Method
Name SparSNP
Parameters Lasso penalised linear SVM, 10-fold cross-validation
PGS Source
PGS Catalog Publication (PGP) ID PGP000028
Citation (link to publication) Abraham G et al. PLoS Genet (2014)

Contributing Samples

Score Development/Training
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
[
  • 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 ID
(PPM ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000093 PSS000059 PGP000028
Abraham G et al. (2014)
Reported Trait: Coeliac disease AUROC: 0.9
PPM000094 PSS000061 PGP000028
Abraham G et al. (2014)
Reported Trait: Coeliac disease AUROC: 0.87
PPM000095 PSS000062 PGP000028
Abraham G et al. (2014)
Reported Trait: Coeliac disease AUROC: 0.86
PPM000096 PSS000063 PGP000028
Abraham G et al. (2014)
Reported Trait: Coeliac disease AUROC: 0.87
PPM000097 PSS000060 PGP000028
Abraham G et al. (2014)
Reported Trait: Coeliac disease AUROC: 0.87
PPM000098 PSS000064 PGP000029
Abraham G et al. (2015)
Ext.
Reported Trait: Coeliac disease AUROC: 0.831[0.808, 0.85]
PPM000099 PSS000065 PGP000029
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 Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000059
[
  • 647 cases
  • , 1,829 controls
]
European
(Finnish)
FINRISK, Health 2000
PSS000060
[
  • 5,907 cases
  • , 4,397 controls
]
European
(British)
Immunochip
PSS000061
[
  • 497 cases
  • , 543 controls
]
European
(Italian)
PSS000062
[
  • 803 cases
  • , 846 controls
]
European
(Dutch)
PSS000063
[
  • 778 cases
  • , 1,422 controls
]
European
(British)
PSS000064
[
  • 1,259 cases
  • , 437 controls
]
European NIDDK
PSS000065 The HLA-DQ2.5-positive subset of NIDDK-CIDR
[
  • 1,094 cases
  • , 143 controls
]
European NIDDK HLA alleles were imputed using SNP2HLA