Polygenic Score (PGS) ID: PGS000944

Predicted Trait
Reported Trait Eczema, dermatitis
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC261
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_HC261
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 598
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
—
[
  • 10,381 cases
  • , 259,323 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
PPM007546 PSS004384|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eczema/dermatitis — AUROC: 0.62856 [0.58377, 0.67334] R²: 0.02337
Incremental AUROC (full-covars): 0.00187
PGS R2 (no covariates): 0.00173
PGS AUROC (no covariates): 0.52778 [0.48039, 0.57516]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007547 PSS004385|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eczema/dermatitis — AUROC: 0.59588 [0.52553, 0.66622] R²: 0.02855
Incremental AUROC (full-covars): 0.02432
PGS R2 (no covariates): 0.0116
PGS AUROC (no covariates): 0.58664 [0.52213, 0.65115]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007548 PSS004386|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eczema/dermatitis — AUROC: 0.56459 [0.54541, 0.58377] R²: 0.00802
Incremental AUROC (full-covars): 0.01208
PGS R2 (no covariates): 0.00353
PGS AUROC (no covariates): 0.54597 [0.52632, 0.56561]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007549 PSS004387|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eczema/dermatitis — AUROC: 0.56106 [0.52439, 0.59773] R²: 0.00683
Incremental AUROC (full-covars): -0.0012
PGS R2 (no covariates): 0.00011
PGS AUROC (no covariates): 0.51686 [0.48122, 0.5525]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007550 PSS004388|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eczema/dermatitis — AUROC: 0.57099 [0.55943, 0.58256] R²: 0.00884
Incremental AUROC (full-covars): 0.02521
PGS R2 (no covariates): 0.00527
PGS AUROC (no covariates): 0.5556 [0.54396, 0.56724]		 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
PSS004384 — —
[
  • 157 cases
  • , 6,340 controls
]
 — African unspecified — UKB —
PSS004385 — —
[
  • 66 cases
  • , 1,638 controls
]
 — East Asian — UKB —
PSS004386 — —
[
  • 873 cases
  • , 24,032 controls
]
 — European non-white British ancestry UKB —
PSS004387 — —
[
  • 243 cases
  • , 7,588 controls
]
 — South Asian — UKB —
PSS004388 — —
[
  • 2,514 cases
  • , 64,911 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)