Polygenic Score (PGS) ID: PGS000041

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

Score Construction
PGS Name GRS-DQ2.5-CeD
Variants
Original Genome Build hg18
Number of Variants 2,513
Development Method
Name SparSNP
Parameters Lasso penalised linear SVM on SNPs, 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
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
— — 11,912 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
PPM000100 PSS000065 PGP000029 Abraham G et al. (2015) Reported Trait: Coeliac disease in HLA-DQ2.5 carriers — AUROC: 0.718 [0.676, 0.761] — — —

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		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
PSS000065 The HLA-DQ2.5-positive subset of NIDDK-CIDR —
[
  • 1,094 cases
  • , 143 controls
]
 — European — NIDDK HLA alleles were imputed using SNP2HLA