Trait: Oral ulcer

Trait Information
Identifier HP_0000155
Description Erosion of the mucous mebrane of the mouth with local excavation of the surface, resulting from the sloughing of inflammatory necrotic tissue. [HPO: probinson]
Trait category
Other trait
Synonyms 2 synonyms
  • Mouth ulcer
  • Oral mucosal ulceration
Mapped terms 3 mapped terms
  • MSH:D019226
  • SNOMEDCT_US:26284000
  • UMLS:C0149745

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)
PGS000947
(GBE_BIN_FC1006149)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Mouth ulcers Oral ulcer 1,648
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000947/ScoringFiles/PGS000947.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
PPM007559 PGS000947
(GBE_BIN_FC1006149)
PSS003770|
African Ancestry|
6,343 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Mouth ulcers AUROC: 0.55141 [0.51964, 0.58317] : 0.00728
Incremental AUROC (full-covars): -0.00753
PGS R2 (no covariates): 0.00051
PGS AUROC (no covariates): 0.51475 [0.48253, 0.54697]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007560 PGS000947
(GBE_BIN_FC1006149)
PSS003771|
East Asian Ancestry|
1,639 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Mouth ulcers AUROC: 0.63149 [0.59813, 0.66485] : 0.05269
Incremental AUROC (full-covars): 0.03724
PGS R2 (no covariates): 0.02115
PGS AUROC (no covariates): 0.58992 [0.55615, 0.62368]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007561 PGS000947
(GBE_BIN_FC1006149)
PSS003772|
European Ancestry|
24,793 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Mouth ulcers AUROC: 0.58069 [0.56921, 0.59217] : 0.0168
Incremental AUROC (full-covars): 0.02537
PGS R2 (no covariates): 0.0095
PGS AUROC (no covariates): 0.55995 [0.54815, 0.57175]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007562 PGS000947
(GBE_BIN_FC1006149)
PSS003773|
South Asian Ancestry|
7,528 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Mouth ulcers AUROC: 0.57052 [0.54871, 0.59233] : 0.01201
Incremental AUROC (full-covars): 0.00553
PGS R2 (no covariates): 0.00331
PGS AUROC (no covariates): 0.53756 [0.51499, 0.56013]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007563 PGS000947
(GBE_BIN_FC1006149)
PSS003774|
European Ancestry|
67,277 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Mouth ulcers AUROC: 0.59736 [0.59049, 0.60422] : 0.02317
Incremental AUROC (full-covars): 0.04113
PGS R2 (no covariates): 0.0165
PGS AUROC (no covariates): 0.58211 [0.57518, 0.58904]
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
PSS003772
[
  • 2,657 cases
  • , 22,136 controls
]
European non-white British ancestry UKB
PSS003773
[
  • 724 cases
  • , 6,804 controls
]
South Asian UKB
PSS003774
[
  • 7,329 cases
  • , 59,948 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS003770
[
  • 332 cases
  • , 6,011 controls
]
African unspecified UKB
PSS003771
[
  • 302 cases
  • , 1,337 controls
]
East Asian UKB