PGS Publication: PGP000093

Publication Information (EuropePMC)
Title A single nucleotide polymorphism genetic risk score to aid diagnosis of coeliac disease: a pilot study in clinical care.
PubMed ID 32790217(Europe PMC)
doi 10.1111/apt.15826
Publication Date Aug. 13, 2020
Journal Aliment Pharmacol Ther
Author(s) Sharp SA, Jones SE, Kimmitt RA, Weedon MN, Halpin AM, Wood AR, Beaumont RN, King S, van Heel DA, Campbell PM, Hagopian WA, Turner JM, Oram RA.
Released in PGS Catalog: Aug. 19, 2020

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000316
(GRS42_Coeliac)
 PGP000093 |
Sharp SA et al. Aliment Pharmacol Ther (2020)
 Coeliac disease celiac disease 53
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000316/ScoringFiles/PGS000316.txt.gz

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) 		Evaluated Score 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 PGS000316
(GRS42_Coeliac)
 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 PGS000316
(GRS42_Coeliac)
 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 —