Polygenic Score (PGS) ID: PGS000316

Predicted Trait
Reported Trait Coeliac disease
Mapped Trait(s) celiac disease (EFO_0001060)
Released in PGS Catalog: Aug. 19, 2020
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Score Details

Score Construction
PGS Name GRS42_Coeliac
Development Method
Name Log‐additive GRS
Parameters Odds ratios derived by logistic regression (adjusted for 5 PCs)
Variants
Original Genome Build NR
Number of Variants 53
Number of Variant Interaction Terms 15
Effect Weight Type ln(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000093
Citation (link to publication) Sharp SA et al. Aliment Pharmacol Ther (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
25,570 individuals (100%)
Score Development/Training
European: 100%
24,269 individuals (100%)
PGS Evaluation
Not Reported: 50%
European: 50%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 1,094 cases
  • , 540 controls
]
 European NR
Europe PMC: 10.1038/ng.3268
[
  • 12,016 cases
  • , 11,920 controls
]
,
38.2 % Male samples
 European NR
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: GCST005523
[
  • 12,041 cases
  • , 12,228 controls
]
 European B58C, UKBS — — — — Case‐control study; also used for variant associations

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
PPM000805 PSS000381|
Ancestry Not Reported|
154 individuals
 PGP000093 |
Sharp SA et al. Aliment Pharmacol Ther (2020)
 Reported Trait: Coeliac disease — AUROC: 0.835 [0.76, 0.911] — — —
PPM000804 PSS000382|
European Ancestry|
379,767 individuals
 PGP000093 |
Sharp SA et al. Aliment Pharmacol Ther (2020)
 Reported Trait: Coeliac disease — AUROC: 0.879 [0.87, 0.888] — — —

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
PSS000381 Control subjects (n = 40) were paediatric general gastroenterology patients whom were negative for coeliac disease by both intestinal biopsy and negative tissue transglutaminase serology. —
[
  • 0 cases
  • , 40 controls
]
,
48.0 % Male samples
 Mean = 4.9 years
Sd = 4.0 years		 NR — STOLLERY_CC —
PSS000381 Diagnosis of coeliac disease was made by a modification of European serological diagnostic guidelines for patients referred to a tertiary paediatric clinic in Alberta, Canada, for consideration of coeliac disease diagnosis —
[
  • 63 cases
  • , 0 controls
]
,
63.0 % Male samples
 Mean = 8.6 years
Sd = 3.9 years		 NR — STOLLERY_CC —
PSS000381 Diagnosis of coeliac disease was made by endoscopy for patients referred to a tertiary paediatric clinic in Alberta, Canada, for consideration of coeliac disease diagnosis —
[
  • 51 cases
  • , 0 controls
]
,
57.0 % Male samples
 Mean = 7.5 years
Sd = 3.8 years		 NR — STOLLERY_CC —
PSS000382 Coeliac disease cases were identified using either hospital admission code and/or self‐reported coeliac disease. —
[
  • 1,237 cases
  • , 378,530 controls
]
 — European — UKB —