Polygenic Score (PGS) ID: PGS000947

Predicted Trait
Reported Trait Mouth ulcers
Mapped Trait(s) Oral ulcer (HP_0000155)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC1006149
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_BIN_FC1006149
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,648
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,150 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 29,073 cases
  • , 240,077 controls
]
 European UKB — — — white British ancestry —

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) 		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 PSS003770|
African Ancestry|
6,343 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mouth ulcers — AUROC: 0.55141 [0.51964, 0.58317] R²: 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 PSS003771|
East Asian Ancestry|
1,639 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mouth ulcers — AUROC: 0.63149 [0.59813, 0.66485] R²: 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 PSS003772|
European Ancestry|
24,793 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mouth ulcers — AUROC: 0.58069 [0.56921, 0.59217] R²: 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 PSS003773|
South Asian Ancestry|
7,528 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mouth ulcers — AUROC: 0.57052 [0.54871, 0.59233] R²: 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 PSS003774|
European Ancestry|
67,277 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mouth ulcers — AUROC: 0.59736 [0.59049, 0.60422] R²: 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 —