Polygenic Score (PGS) ID: PGS000040

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_CeD
Development Method
Name SparSNP
Parameters Lasso penalised linear SVM, 10-fold cross-validation
Variants
Original Genome Build hg18
Number of Variants 228
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000028
Citation (link to publication) Abraham G et al. PLoS Genet (2014)
Ancestry Distribution
Score Development/Training
European: 100%
6,785 individuals (100%)
PGS Evaluation
European: 100%
7 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
[
  • 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) 		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
PPM000093 PSS000059|
European Ancestry|
2,476 individuals
 PGP000028 |
Abraham G et al. PLoS Genet (2014)
 Reported Trait: Coeliac disease — AUROC: 0.9 — — —
PPM000094 PSS000061|
European Ancestry|
1,040 individuals
 PGP000028 |
Abraham G et al. PLoS Genet (2014)
 Reported Trait: Coeliac disease — AUROC: 0.87 — — —
PPM000095 PSS000062|
European Ancestry|
1,649 individuals
 PGP000028 |
Abraham G et al. PLoS Genet (2014)
 Reported Trait: Coeliac disease — AUROC: 0.86 — — —
PPM000096 PSS000063|
European Ancestry|
2,200 individuals
 PGP000028 |
Abraham G et al. PLoS Genet (2014)
 Reported Trait: Coeliac disease — AUROC: 0.87 — — —
PPM000097 PSS000060|
European Ancestry|
10,304 individuals
 PGP000028 |
Abraham G et al. PLoS Genet (2014)
 Reported Trait: Coeliac disease — AUROC: 0.87 — — —
PPM000098 PSS000064|
European Ancestry|
1,696 individuals
 PGP000029 |
Abraham G et al. Genome Med (2015)
|Ext.		 Reported Trait: Coeliac disease — AUROC: 0.831 [0.808, 0.85] — — —
PPM000099 PSS000065|
European Ancestry|
1,237 individuals
 PGP000029 |
Abraham G et al. Genome Med (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) 		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
PSS000059 — —
[
  • 647 cases
  • , 1,829 controls
]
 — European
(Finnish)		 — FINRISK, Health2000 —
PSS000060 — —
[
  • 5,907 cases
  • , 4,397 controls
]
 — European
(British)		 — NR Immunochip
PSS000061 — —
[
  • 497 cases
  • , 543 controls
]
 — European
(Italian)		 — NR —
PSS000062 — —
[
  • 803 cases
  • , 846 controls
]
 — European
(Dutch)		 — NR —
PSS000063 — —
[
  • 778 cases
  • , 1,422 controls
]
 — European
(British)		 — NR —
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