Trait: Crohn's disease

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000384
Description A gastrointestinal disorder characterized by chronic inflammation involving all layers of the intestinal wall, noncaseating granulomas affecting the intestinal wall and regional lymph nodes, and transmural fibrosis. Crohn disease most commonly involves the terminal ileum; the colon is the second most common site of involvement. [NCIT: P378]
Trait categories
Digestive system disorder
Immune system disorder
Synonyms 21 synonyms
  • CROHN DIS
  • CROHNS DIS
  • Colitis, Granulomatous
  • Crohn Disease
  • Crohn disease
  • Crohn's associated gastritis
  • Crohn's disease
  • Crohn's disease of colon
  • Crohn's disease of large bowel
  • Crohns Disease
  • Enteritis, Granulomatous
  • Enteritis, Regional
  • Gastritis Associated with Crohn Disease
  • Gastritis Associated with Crohn's Disease
  • Ileitis, Regional
  • Ileitis, Terminal
  • Ileocolitis
  • granulomatous colitis
  • paediatric Crohn's disease
  • pediatric Crohn's disease
  • regional enteritis
Mapped terms 21 mapped terms
  • DOID:8778
  • ICD10:K50
  • ICD9:555.1
  • MEDGEN:3664
  • MESH:D003424
  • MONDO:0005011
  • MeSH:D003424
  • MedDRA:10011401
  • NANDO:1200444
  • NANDO:1200446
  • NANDO:2200921
  • NCIT:C2965
  • NCIt:C27837
  • NCIt:C2965
  • OMIM:266600
  • Orphanet:206
  • SCTID:34000006
  • SCTID:7620006
  • SNOMEDCT:34000006
  • UMLS:C0010346
  • icd11.foundation:1267652425

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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001330
(GBE_HC1101)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Crohn's disease [regional enteritis] (time-to-event) Crohn's disease 220
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001330/ScoringFiles/PGS001330.txt.gz
PGS001331
(GBE_HC322)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Crohn's disease Crohn's disease 257
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001331/ScoringFiles/PGS001331.txt.gz
PGS004254
(cd_ldpred2)
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Crohn's disease Crohn's disease 744,682
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004254/ScoringFiles/PGS004254.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
PPM009137 PGS001330
(GBE_HC1101)
 PSS004114|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE crohn's disease [regional enteritis] — AUROC: 0.66243 [0.55234, 0.77252] R²: 0.05286
Incremental AUROC (full-covars): -0.02175
PGS R2 (no covariates): 0.00138
PGS AUROC (no covariates): 0.46272 [0.36718, 0.55826]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009138 PGS001330
(GBE_HC1101)
 PSS004115|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE crohn's disease [regional enteritis] — AUROC: 0.86369 [0.7806, 0.94678] R²: 0.13339
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 0.14319
PGS AUROC (no covariates): 0.10664 [0.0, 0.28372]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009139 PGS001330
(GBE_HC1101)
 PSS004116|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE crohn's disease [regional enteritis] — AUROC: 0.60269 [0.55209, 0.65328] R²: 0.01102
Incremental AUROC (full-covars): 0.02413
PGS R2 (no covariates): 0.00621
PGS AUROC (no covariates): 0.57593 [0.52318, 0.62867]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009140 PGS001330
(GBE_HC1101)
 PSS004117|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE crohn's disease [regional enteritis] — AUROC: 0.69933 [0.63548, 0.76318] R²: 0.0344
Incremental AUROC (full-covars): 0.00201
PGS R2 (no covariates): 0.00147
PGS AUROC (no covariates): 0.53846 [0.46042, 0.6165]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009141 PGS001330
(GBE_HC1101)
 PSS004118|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE crohn's disease [regional enteritis] — AUROC: 0.55852 [0.52842, 0.58862] R²: 0.00474
Incremental AUROC (full-covars): 0.07412
PGS R2 (no covariates): 0.00669
PGS AUROC (no covariates): 0.5714 [0.54073, 0.60207]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009142 PGS001331
(GBE_HC322)
 PSS004442|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Crohns disease — AUROC: 0.65892 [0.54485, 0.77299] R²: 0.05502
Incremental AUROC (full-covars): -0.02526
PGS R2 (no covariates): 4e-05
PGS AUROC (no covariates): 0.49152 [0.37858, 0.60446]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009143 PGS001331
(GBE_HC322)
 PSS004444|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Crohns disease — AUROC: 0.61269 [0.55802, 0.66736] R²: 0.01161
Incremental AUROC (full-covars): 0.02705
PGS R2 (no covariates): 0.00677
PGS AUROC (no covariates): 0.57919 [0.52051, 0.63786]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009144 PGS001331
(GBE_HC322)
 PSS004445|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Crohns disease — AUROC: 0.71 [0.64649, 0.7735] R²: 0.03928
Incremental AUROC (full-covars): 0.01378
PGS R2 (no covariates): 0.00366
PGS AUROC (no covariates): 0.56349 [0.47905, 0.64793]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009145 PGS001331
(GBE_HC322)
 PSS004446|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Crohns disease — AUROC: 0.56362 [0.53297, 0.59427] R²: 0.00529
Incremental AUROC (full-covars): 0.06267
PGS R2 (no covariates): 0.0063
PGS AUROC (no covariates): 0.57326 [0.54246, 0.60406]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM020321 PGS004254
(cd_ldpred2)
 PSS011333|
European Ancestry|
5,285 individuals
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Reported Trait: Crohn's disease OR: 1.83 [1.72, 1.95] AUROC: 0.72 [0.69, 0.74] — age at diagnosis/enrollment, sex, genotyping array, 10 PCs —
PPM020322 PGS004254
(cd_ldpred2)
 PSS011332|
European Ancestry|
22,296 individuals
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Reported Trait: Crohn's disease OR: 2.18 [2.05, 2.32] AUROC: 0.72 [0.7, 0.73] — age, sex, 10 PCs —

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
PSS004444 — —
[
  • 105 cases
  • , 24,800 controls
]
 — European non-white British ancestry UKB —
PSS004445 — —
[
  • 42 cases
  • , 7,789 controls
]
 — South Asian — UKB —
PSS004446 — —
[
  • 361 cases
  • , 67,064 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS011332 — —
[
  • 1,420 cases
  • , 20,876 controls
]
 — European — BioVU —
PSS004114 — —
[
  • 20 cases
  • , 6,477 controls
]
 — African unspecified — UKB —
PSS004115 — —
[
  • 2 cases
  • , 1,702 controls
]
 — East Asian — UKB —
PSS004116 — —
[
  • 117 cases
  • , 24,788 controls
]
 — European non-white British ancestry UKB —
PSS004117 — —
[
  • 48 cases
  • , 7,783 controls
]
 — South Asian — UKB —
PSS004118 — —
[
  • 393 cases
  • , 67,032 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS011333 — —
[
  • 394 cases
  • , 4,891 controls
]
 — European — UKB —
PSS004442 — —
[
  • 20 cases
  • , 6,477 controls
]
 — African unspecified — UKB —