Polygenic Score (PGS) ID: PGS001284

Predicted Trait
Reported Trait Allergic disease (hay fever, allergic rhinitis, or eczema)
Mapped Trait(s) allergic disease (MONDO_0005271)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC10006152
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_BIN_FC10006152
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 6,755
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%
269,382 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
—
[
  • 64,021 cases
  • , 205,361 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
PPM008918 PSS003736|
African Ancestry|
6,348 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever allergic rhinitis or eczema — AUROC: 0.6114 [0.59586, 0.62694] R²: 0.04366
Incremental AUROC (full-covars): 0.00507
PGS R2 (no covariates): 0.0072
PGS AUROC (no covariates): 0.5418 [0.52577, 0.55784]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008919 PSS003737|
East Asian Ancestry|
1,640 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever allergic rhinitis or eczema — AUROC: 0.6017 [0.57412, 0.62927] R²: 0.04656
Incremental AUROC (full-covars): 0.01162
PGS R2 (no covariates): 0.01108
PGS AUROC (no covariates): 0.55514 [0.52697, 0.58332]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008920 PSS003738|
European Ancestry|
24,838 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever allergic rhinitis or eczema — AUROC: 0.63382 [0.62577, 0.64186] R²: 0.06149
Incremental AUROC (full-covars): 0.03904
PGS R2 (no covariates): 0.0337
PGS AUROC (no covariates): 0.60011 [0.59191, 0.60831]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008921 PSS003739|
South Asian Ancestry|
7,556 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever allergic rhinitis or eczema — AUROC: 0.60105 [0.58571, 0.6164] R²: 0.03149
Incremental AUROC (full-covars): 0.04131
PGS R2 (no covariates): 0.02118
PGS AUROC (no covariates): 0.58123 [0.56584, 0.59661]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008922 PSS003740|
European Ancestry|
67,349 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever allergic rhinitis or eczema — AUROC: 0.63735 [0.6325, 0.6422] R²: 0.06354
Incremental AUROC (full-covars): 0.05347
PGS R2 (no covariates): 0.04086
PGS AUROC (no covariates): 0.60988 [0.60494, 0.61483]		 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
PSS003740 — —
[
  • 16,014 cases
  • , 51,335 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003736 — —
[
  • 1,664 cases
  • , 4,684 controls
]
 — African unspecified — UKB —
PSS003737 — —
[
  • 656 cases
  • , 984 controls
]
 — East Asian — UKB —
PSS003738 — —
[
  • 5,888 cases
  • , 18,950 controls
]
 — European non-white British ancestry UKB —
PSS003739 — —
[
  • 1,629 cases
  • , 5,927 controls
]
 — South Asian — UKB —