Polygenic Score (PGS) ID: PGS000042

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-imputed
Development Method
Name SparSNP
Parameters Lasso penalised linear SVM on SNPs & imputed HLA alleles (SNP2HLA), 10-fold cross-validation
Variants
Original Genome Build hg18
Number of Variants 3,317
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000029
Citation (link to publication) Abraham G et al. Genome Med (2015)
Ancestry Distribution
Score Development/Training
European: 100%
5,552 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
GWAS Catalog: GCST000612
 5,552 individuals European
(British, Dutch, Italian, Finnish)		 NR The HLA-DQ2.5-positive subset — — — 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) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000101 PSS000065|
European Ancestry|
1,237 individuals
 PGP000029 |
Abraham G et al. Genome Med (2015)
 Reported Trait: Coeliac disease in HLA-DQ2.5 carriers — AUROC: 0.73 [0.687, 0.772] — — —

Evaluated Samples

PGS Sample Set ID
(PSS) 		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