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 19 mapped terms
  • DOID:1724
  • HP:0002588
  • ICD10:K26
  • ICD9:532
  • 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

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)
PGS001390
(GBE_HC1084)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
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. medRxiv (2021)
|Pre
Reported Trait: TTE duodenal ulcer AUROC: 0.71018 [0.66062, 0.75975] : 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. medRxiv (2021)
|Pre
Reported Trait: TTE duodenal ulcer AUROC: 0.66565 [0.55325, 0.77805] : 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. medRxiv (2021)
|Pre
Reported Trait: TTE duodenal ulcer AUROC: 0.71045 [0.68829, 0.73261] : 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. medRxiv (2021)
|Pre
Reported Trait: TTE duodenal ulcer AUROC: 0.70619 [0.66443, 0.74795] : 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. medRxiv (2021)
|Pre
Reported Trait: TTE duodenal ulcer AUROC: 0.68746 [0.67261, 0.70231] : 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)