Trait: duodenal ulcer

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004607
Description An ulcer in the duodenal wall. [NCIT: P378]
Trait category
Digestive system disorder
Synonyms 5 synonyms
  • curling Ulcer
  • curling's ulcers
  • duodenal ulcer
  • duodenal ulcer (disease)
  • stress Ulcer
Mapped terms 23 mapped terms
  • DOID:1724
  • HP:0002588
  • ICD10:K26
  • ICD10CM:K26
  • ICD9:532
  • MEDGEN:41670
  • MESH:D004381
  • MONDO:0005412
  • MeSH:D004381
  • MedDRA:10013836
  • MedDRA:10013854
  • MedDRA:10013855
  • MedDRA:10013856
  • MedDRA:10013857
  • MedDRA:10013858
  • MedDRA:10013859
  • MedDRA:10055243
  • MedDRA:10055785
  • NCIT:C26755
  • NCIt:C26755
  • SCTID:39755000
  • UMLS:C0013295
  • icd11.foundation:553678663

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)
PGS001390
(GBE_HC1084)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Duodenal ulcer (time-to-event) duodenal ulcer 220
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001390/ScoringFiles/PGS001390.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
PPM005200 PGS001390
(GBE_HC1084)
 PSS004094|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.71018 [0.66062, 0.75975] R²: 0.05605
Incremental AUROC (full-covars): 0.00294
PGS R2 (no covariates): 0.00399
PGS AUROC (no covariates): 0.5623 [0.50635, 0.61825]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005201 PGS001390
(GBE_HC1084)
 PSS004095|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.66565 [0.55325, 0.77805] R²: 0.04606
Incremental AUROC (full-covars): 0.00253
PGS R2 (no covariates): 0.006
PGS AUROC (no covariates): 0.56376 [0.43513, 0.6924]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005202 PGS001390
(GBE_HC1084)
 PSS004096|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.71045 [0.68829, 0.73261] R²: 0.06289
Incremental AUROC (full-covars): 0.0043
PGS R2 (no covariates): 0.0047
PGS AUROC (no covariates): 0.55991 [0.53425, 0.58556]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005203 PGS001390
(GBE_HC1084)
 PSS004097|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.70619 [0.66443, 0.74795] R²: 0.0567
Incremental AUROC (full-covars): 0.00581
PGS R2 (no covariates): 0.00168
PGS AUROC (no covariates): 0.54031 [0.491, 0.58961]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005204 PGS001390
(GBE_HC1084)
 PSS004098|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.68746 [0.67261, 0.70231] R²: 0.04811
Incremental AUROC (full-covars): 0.00644
PGS R2 (no covariates): 0.00484
PGS AUROC (no covariates): 0.56101 [0.54453, 0.5775]		 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
PSS004094 — —
[
  • 95 cases
  • , 6,402 controls
]
 — African unspecified — UKB —
PSS004095 — —
[
  • 24 cases
  • , 1,680 controls
]
 — East Asian — UKB —
PSS004096 — —
[
  • 481 cases
  • , 24,424 controls
]
 — European non-white British ancestry UKB —
PSS004097 — —
[
  • 135 cases
  • , 7,696 controls
]
 — South Asian — UKB —
PSS004098 — —
[
  • 1,164 cases
  • , 66,261 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)