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
  • CD - Celiac disease
  • CD - Coeliac disease
  • CELIAC DIS
  • CS - Celiac sprue
  • CS - Coeliac sprue
  • Celiac Sprue
  • Celiac disease (disorder)
  • Celiac disease NOS
  • Celiac disease NOS (disorder)
  • Celiac rickets
  • Celiac rickets (disorder)
  • Celiac syndrome
  • Coeliac disease
  • Coeliac disease NOS
  • Coeliac disease [Ambiguous]
  • Coeliac rickets
  • Coeliac sprue
  • Coeliac syndrome
  • Disease, Celiac
  • Enteropathies, Gluten
  • Enteropathies, Gluten-Sensitive
  • Enteropathy, Gluten
  • Enteropathy, Gluten-Sensitive
  • GSE - Gluten-sensitive enteropathy
  • Gluten Enteropathies
  • Gluten Sensitive Enteropathy
  • Gluten enteropathy
  • Gluten-Induced Enteropathy
  • Gluten-Sensitive Enteropathies
  • Gluten-Sensitive Enteropathy
  • Gluten-induced enteropathy syndrome
  • Gluten-responsive sprue
  • Idiopathic steatorrhea
  • Idiopathic steatorrhoea
  • Non Tropical Sprue
  • Non-tropical sprue
  • Nontropical Sprue
  • Sprue
  • Sprue, Celiac
  • Sprue, Nontropical
  • Steatorrhoea - idiopathic
  • Wheat-sensitive enteropathy
  • celiac disease
  • celiac sprue
  • coeliac disease
  • gluten-induced enteropathy
  • idiopathic steatorrhea
  • non tropical sprue
Mapped term(s) 18 mapped terms
  • COHD:194992
  • DOID:10608
  • GARD:0011998
  • ICD10:K90.0
  • ICD9:579.0
  • MESH:D002446
  • MONDO:0005130
  • MeSH:D002446
  • NCIT:C26714
  • NCIt:C26714
  • OMIM:212750
  • OMIM:609753
  • OMIM:609755
  • OMIM:612011
  • OMIMPS:212750
  • SCTID:396331005
  • SNOMEDCT:396331005
  • UMLS:C0007570

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution 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

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
PPM000093 PGS000040
(GRS_CeD)
PSS000059|
European Ancestry|
2,476 individuals
PGP000028 |
Abraham G et al. PLoS Genet (2014)
Reported Trait: Coeliac disease AUROC: 0.9
PPM000094 PGS000040
(GRS_CeD)
PSS000061|
European Ancestry|
1,040 individuals
PGP000028 |
Abraham G et al. PLoS Genet (2014)
Reported Trait: Coeliac disease AUROC: 0.87
PPM000095 PGS000040
(GRS_CeD)
PSS000062|
European Ancestry|
1,649 individuals
PGP000028 |
Abraham G et al. PLoS Genet (2014)
Reported Trait: Coeliac disease AUROC: 0.86
PPM000096 PGS000040
(GRS_CeD)
PSS000063|
European Ancestry|
2,200 individuals
PGP000028 |
Abraham G et al. PLoS Genet (2014)
Reported Trait: Coeliac disease AUROC: 0.87
PPM000097 PGS000040
(GRS_CeD)
PSS000060|
European Ancestry|
10,304 individuals
PGP000028 |
Abraham G et al. PLoS Genet (2014)
Reported Trait: Coeliac disease AUROC: 0.87
PPM000098 PGS000040
(GRS_CeD)
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 PGS000040
(GRS_CeD)
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]
PPM000100 PGS000041
(GRS-DQ2.5-CeD)
PSS000065|
European Ancestry|
1,237 individuals
PGP000029 |
Abraham G et al. Genome Med (2015)
Reported Trait: Coeliac disease in HLA-DQ2.5 carriers AUROC: 0.718 [0.676, 0.761]
PPM000101 PGS000042
(GRS-DQ2.5-CeD-imputed)
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]
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
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