Trait: celiac disease

Experimental Factor Ontology (EFO) Information
Identifier EFO_0001060
Description An autoimmune genetic disorder with an unknown pattern of inheritance that primarily affects the digestive tract. It is caused by intolerance to dietary gluten. Consumption of gluten protein triggers an immune response which damages small intestinal villi and prevents adequate absorption of nutrients. Clinical signs include abdominal cramping, diarrhea or constipation and weight loss. If untreated, the clinical course may progress to malnutrition, anemia, osteoporosis and an increased risk of intestinal malignancies. However, the prognosis is favorable with successful avoidance of gluten in the diet. [NCIT: C26714]
Trait category
Digestive system disorder
Immune system disorder
Synonyms 48 synonyms
  • idiopathic steatorrhea
  • Celiac syndrome
  • Celiac rickets (disorder)
  • Coeliac sprue
  • CS - Celiac sprue
  • Gluten enteropathy
  • Gluten-Induced Enteropathy
  • Celiac disease NOS
  • Celiac disease (disorder)
  • Gluten-Sensitive Enteropathy
  • Coeliac disease
  • GSE - Gluten-sensitive enteropathy
  • Gluten Enteropathies
  • Gluten Sensitive Enteropathy
  • Sprue, Nontropical
  • Non Tropical Sprue
  • Gluten-Sensitive Enteropathies
  • Coeliac disease [Ambiguous]
  • Coeliac disease NOS
  • Sprue, Celiac
  • Disease, Celiac
  • celiac disease
  • CS - Coeliac sprue
  • CELIAC DIS
  • Non-tropical sprue
  • CD - Celiac disease
  • celiac sprue
  • Gluten-responsive sprue
  • Enteropathy, Gluten
  • Celiac disease NOS (disorder)
  • Sprue
  • Celiac rickets
  • Celiac Sprue
  • gluten-induced enteropathy
  • Gluten-induced enteropathy syndrome
  • CD - Coeliac disease
  • Coeliac syndrome
  • Coeliac rickets
  • coeliac disease
  • Enteropathies, Gluten
  • Nontropical Sprue
  • Steatorrhoea - idiopathic
  • non tropical sprue
  • Idiopathic steatorrhoea
  • Wheat-sensitive enteropathy
  • Idiopathic steatorrhea
  • Enteropathies, Gluten-Sensitive
  • Enteropathy, Gluten-Sensitive
Mapped term(s) 18 mapped terms
  • GARD:0011998
  • OMIMPS:212750
  • SCTID:396331005
  • ICD9:579.0
  • ICD10:K90.0
  • OMIM:609755
  • NCIt:C26714
  • NCIT:C26714
  • MESH:D002446
  • DOID:10608
  • COHD:194992
  • OMIM:612011
  • SNOMEDCT:396331005
  • MONDO:0005130
  • OMIM:609753
  • MSH:D002446
  • UMLS:C0007570
  • OMIM:212750

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000040 GRS_CeD PGP000028
Abraham G et al. PLoS Genet (2014)
Coeliac disease celiac disease 228 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000040/ScoringFiles/PGS000040.txt.gz
PGS000041 GRS-DQ2.5-CeD PGP000029
Abraham G et al. Genome Med (2015)
Coeliac disease celiac disease 2,513 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000041/ScoringFiles/PGS000041.txt.gz
PGS000042 GRS-DQ2.5-CeD-imputed PGP000029
Abraham G et al. Genome Med (2015)
Coeliac disease celiac disease 3,317 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000042/ScoringFiles/PGS000042.txt.gz
PGS000316 GRS42_Coeliac PGP000093
Sharp SA et al. Aliment Pharmacol Ther (2020)
Coeliac disease celiac disease 42 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000316/ScoringFiles/PGS000316.txt.gz

PGS 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)
Evaluated Score 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
PPM000093 PGS000040 (GRS_CeD) PSS000059 PGP000028
Abraham G et al. (2014)
Reported Trait: Coeliac disease AUROC: 0.9
PPM000094 PGS000040 (GRS_CeD) PSS000061 PGP000028
Abraham G et al. (2014)
Reported Trait: Coeliac disease AUROC: 0.87
PPM000095 PGS000040 (GRS_CeD) PSS000062 PGP000028
Abraham G et al. (2014)
Reported Trait: Coeliac disease AUROC: 0.86
PPM000096 PGS000040 (GRS_CeD) PSS000063 PGP000028
Abraham G et al. (2014)
Reported Trait: Coeliac disease AUROC: 0.87
PPM000097 PGS000040 (GRS_CeD) PSS000060 PGP000028
Abraham G et al. (2014)
Reported Trait: Coeliac disease AUROC: 0.87
PPM000098 PGS000040 (GRS_CeD) PSS000064 PGP000029
Abraham G et al. (2015)
Ext.
Reported Trait: Coeliac disease AUROC: 0.831[0.808, 0.85]
PPM000099 PGS000040 (GRS_CeD) PSS000065 PGP000029
Abraham G et al. (2015)
Ext.
Reported Trait: Coeliac disease in HLA-DQ2.5 carriers AUROC: 0.669[0.625, 0.713]
PPM000100 PGS000041 (GRS-DQ2.5-CeD) PSS000065 PGP000029
Abraham G et al. (2015)
Reported Trait: Coeliac disease in HLA-DQ2.5 carriers AUROC: 0.718[0.676, 0.761]
PPM000101 PGS000042 (GRS-DQ2.5-CeD-imputed) PSS000065 PGP000029
Abraham G et al. (2015)
Reported Trait: Coeliac disease in HLA-DQ2.5 carriers AUROC: 0.73[0.687, 0.772]
PPM000804 PGS000316 (GRS42_Coeliac) PSS000382 PGP000093
Sharp SA et al. (2020)
Reported Trait: Coeliac disease AUROC: 0.879[0.87, 0.888]
PPM000805 PGS000316 (GRS42_Coeliac) PSS000381 PGP000093
Sharp SA et al. (2020)
Reported Trait: Coeliac disease AUROC: 0.835[0.76, 0.911]

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
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
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
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
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
PSS000059
[
  • 647 cases
  • , 1,829 controls
]
European
(Finnish)
FINRISK, Health 2000
PSS000060
[
  • 5,907 cases
  • , 4,397 controls
]
European
(British)
Immunochip
PSS000061
[
  • 497 cases
  • , 543 controls
]
European
(Italian)
PSS000062
[
  • 803 cases
  • , 846 controls
]
European
(Dutch)
PSS000063
[
  • 778 cases
  • , 1,422 controls
]
European
(British)
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