Polygenic Score (PGS) ID: PGS000042

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-DQ2.5-CeD-imputed
Variants
Original Genome Build hg18
Number of Variants 3,317
Development Method
Name SparSNP
Parameters Lasso penalised linear SVM on SNPs & imputed HLA alleles (SNP2HLA), 10-fold cross-validation
PGS Source
PGS Catalog Publication (PGP) ID PGP000029
Citation (link to publication) Abraham G et al. Genome Med (2015)

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
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 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
PPM000101 PSS000065 PGP000029
Abraham G et al. (2015)
Reported Trait: Coeliac disease in HLA-DQ2.5 carriers AUROC: 0.73[0.687, 0.772]

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