Polygenic Score (PGS) ID: PGS000927

Predicted Trait
Reported Trait Other dermatitis (time-to-event)
Mapped Trait(s) dermatitis (MONDO_0002406)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1158
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_HC1158
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 242
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%
269,704 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
—
[
  • 25,682 cases
  • , 244,022 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
PPM007462 PSS004153|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other dermatitis — AUROC: 0.61027 [0.57953, 0.64101] R²: 0.02035
Incremental AUROC (full-covars): 0.00207
PGS R2 (no covariates): 0.00268
PGS AUROC (no covariates): 0.5378 [0.50673, 0.56886]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007463 PSS004154|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other dermatitis — AUROC: 0.57706 [0.52927, 0.62486] R²: 0.02951
Incremental AUROC (full-covars): 0.01147
PGS R2 (no covariates): 0.00458
PGS AUROC (no covariates): 0.5429 [0.49389, 0.59191]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007464 PSS004155|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other dermatitis — AUROC: 0.54587 [0.53304, 0.5587] R²: 0.00506
Incremental AUROC (full-covars): 0.01785
PGS R2 (no covariates): 0.00339
PGS AUROC (no covariates): 0.53939 [0.52639, 0.55239]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007465 PSS004156|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other dermatitis — AUROC: 0.58261 [0.56273, 0.60248] R²: 0.01573
Incremental AUROC (full-covars): 0.00482
PGS R2 (no covariates): 0.00187
PGS AUROC (no covariates): 0.52627 [0.50591, 0.54663]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007466 PSS004157|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other dermatitis — AUROC: 0.56752 [0.56014, 0.57491] R²: 0.01047
Incremental AUROC (full-covars): 0.01697
PGS R2 (no covariates): 0.00542
PGS AUROC (no covariates): 0.54889 [0.54154, 0.55624]		 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
PSS004156 — —
[
  • 850 cases
  • , 6,981 controls
]
 — South Asian — UKB —
PSS004157 — —
[
  • 6,461 cases
  • , 60,964 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004153 — —
[
  • 343 cases
  • , 6,154 controls
]
 — African unspecified — UKB —
PSS004154 — —
[
  • 143 cases
  • , 1,561 controls
]
 — East Asian — UKB —
PSS004155 — —
[
  • 2,053 cases
  • , 22,852 controls
]
 — European non-white British ancestry UKB —