Trait: ulcerative colitis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000729
Description An inflammatory bowel disease involving the mucosal surface of the large intestine and rectum. It may present with an acute or slow onset and follows an intermittent or continuous course. Signs and symptoms include abdominal pain, diarrhea, fever, weight loss, and intestinal hemorrhage. [NCIT: P378]
Trait categories
Digestive system disorder
Immune system disorder
Synonyms 13 synonyms
  • Colitis, Ulcerative
  • Left-sided ulcerative (chronic) colitis
  • Left-sided ulcerative colitis
  • Other ulcerative colitis
  • Other ulcerative colitis (disorder)
  • UC
  • UC - ulcerative colitis
  • ULCERATVE COLITIS UNSPCF
  • Ulcerative colitis, unspecified
  • colitis ulcerative
  • ulcerative colitis
  • ulcerative colitis (disease)
  • ulcerative colitis (disorder)
Mapped terms 19 mapped terms
  • DOID:8577
  • HP:0100279
  • ICD10:K51
  • ICD10:K51.9
  • ICD9:556
  • ICD9:556.5
  • ICD9:556.8
  • ICD9:556.9
  • MESH:D003093
  • MONDO:0005101
  • MeSH:D003093
  • MedDRA:10045365
  • MedDRA:10045366
  • NCIT:C2952
  • NCIt:C2952
  • OMIM:266600
  • SCTID:64766004
  • SNOMEDCT:64766004
  • UMLS:C0009324

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 Scoring File (FTP Link)
PGS001306
(GBE_HC201)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Ulcerative colitis ulcerative colitis 179
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001306/ScoringFiles/PGS001306.txt.gz
PGS001307
(GBE_HC1102)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Ulcerative colitis (time-to-event) ulcerative colitis 809
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001307/ScoringFiles/PGS001307.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
PPM009033 PGS001307
(GBE_HC1102)
PSS004123|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE ulcerative colitis AUROC: 0.63965 [0.62036, 0.65895] : 0.02376
Incremental AUROC (full-covars): 0.1085
PGS R2 (no covariates): 0.02383
PGS AUROC (no covariates): 0.63847 [0.61861, 0.65833]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009032 PGS001307
(GBE_HC1102)
PSS004122|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE ulcerative colitis AUROC: 0.66008 [0.61042, 0.70974] : 0.03192
Incremental AUROC (full-covars): 0.00203
PGS R2 (no covariates): 0.0036
PGS AUROC (no covariates): 0.55808 [0.506, 0.61016]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009031 PGS001307
(GBE_HC1102)
PSS004121|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE ulcerative colitis AUROC: 0.65578 [0.62353, 0.68804] : 0.03272
Incremental AUROC (full-covars): 0.04212
PGS R2 (no covariates): 0.0169
PGS AUROC (no covariates): 0.6106 [0.57717, 0.64402]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009030 PGS001307
(GBE_HC1102)
PSS004120|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE ulcerative colitis AUROC: 0.89582 [0.79576, 0.99588] : 0.20607
Incremental AUROC (full-covars): -0.00177
PGS R2 (no covariates): 0.00203
PGS AUROC (no covariates): 0.55433 [0.4473, 0.66136]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009029 PGS001307
(GBE_HC1102)
PSS004119|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE ulcerative colitis AUROC: 0.62873 [0.51002, 0.74744] : 0.04344
Incremental AUROC (full-covars): -0.00895
PGS R2 (no covariates): 0.00027
PGS AUROC (no covariates): 0.50641 [0.39121, 0.62161]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009028 PGS001306
(GBE_HC201)
PSS004343|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ulcerative colitis AUROC: 0.6157 [0.59481, 0.63659] : 0.01676
Incremental AUROC (full-covars): 0.08728
PGS R2 (no covariates): 0.0193
PGS AUROC (no covariates): 0.62452 [0.60374, 0.6453]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009027 PGS001306
(GBE_HC201)
PSS004342|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ulcerative colitis AUROC: 0.67522 [0.62537, 0.72506] : 0.03696
Incremental AUROC (full-covars): 0.01011
PGS R2 (no covariates): 0.00545
PGS AUROC (no covariates): 0.56552 [0.50815, 0.62289]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009026 PGS001306
(GBE_HC201)
PSS004341|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ulcerative colitis AUROC: 0.66162 [0.6277, 0.69554] : 0.03336
Incremental AUROC (full-covars): 0.04247
PGS R2 (no covariates): 0.02036
PGS AUROC (no covariates): 0.63006 [0.5958, 0.66432]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009025 PGS001306
(GBE_HC201)
PSS004340|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ulcerative colitis AUROC: 0.89429 [0.79357, 0.99502] : 0.20499
Incremental AUROC (full-covars): -0.0033
PGS R2 (no covariates): 2e-05
PGS AUROC (no covariates): 0.49111 [0.35854, 0.62368]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009024 PGS001306
(GBE_HC201)
PSS004339|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ulcerative colitis AUROC: 0.62904 [0.5093, 0.74878] : 0.04535
Incremental AUROC (full-covars): -0.00864
PGS R2 (no covariates): 0.00044
PGS AUROC (no covariates): 0.51081 [0.37987, 0.64174]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004343
[
  • 720 cases
  • , 66,705 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004339
[
  • 27 cases
  • , 6,470 controls
]
African unspecified UKB
PSS004340
[
  • 5 cases
  • , 1,699 controls
]
East Asian UKB
PSS004341
[
  • 239 cases
  • , 24,666 controls
]
European non-white British ancestry UKB
PSS004342
[
  • 103 cases
  • , 7,728 controls
]
South Asian UKB
PSS004119
[
  • 27 cases
  • , 6,470 controls
]
African unspecified UKB
PSS004120
[
  • 5 cases
  • , 1,699 controls
]
East Asian UKB
PSS004121
[
  • 260 cases
  • , 24,645 controls
]
European non-white British ancestry UKB
PSS004122
[
  • 113 cases
  • , 7,718 controls
]
South Asian UKB
PSS004123
[
  • 788 cases
  • , 66,637 controls
]
European white British ancestry UKB Testing cohort (heldout set)