Polygenic Score (PGS) ID: PGS001286

Predicted Trait
Reported Trait Allergic disease (hay fever or allergic rhinitis) (diagnosed by doctor)
Mapped Trait(s) allergic disease (MONDO_0005271)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN22126
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_BIN22126
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 466
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%
68,835 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
—
[
  • 15,686 cases
  • , 53,149 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
PPM008928 PSS003671|
African Ancestry|
516 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Doctor diagnosed hayfever or allergic rhinitis — AUROC: 0.59048 [0.53845, 0.6425] R²: 0.04417
Incremental AUROC (full-covars): -0.00133
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.49458 [0.44138, 0.54777]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008929 PSS003672|
East Asian Ancestry|
245 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Doctor diagnosed hayfever or allergic rhinitis — AUROC: 0.64171 [0.57232, 0.7111] R²: 0.10104
Incremental AUROC (full-covars): 0.0021
PGS R2 (no covariates): 0.00195
PGS AUROC (no covariates): 0.53214 [0.45762, 0.60665]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008930 PSS003673|
European Ancestry|
5,959 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Doctor diagnosed hayfever or allergic rhinitis — AUROC: 0.57725 [0.56045, 0.59405] R²: 0.02043
Incremental AUROC (full-covars): 0.01152
PGS R2 (no covariates): 0.00603
PGS AUROC (no covariates): 0.53991 [0.52259, 0.55722]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008931 PSS003674|
South Asian Ancestry|
707 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Doctor diagnosed hayfever or allergic rhinitis — AUROC: 0.62831 [0.58265, 0.67397] R²: 0.06246
Incremental AUROC (full-covars): 0.0031
PGS R2 (no covariates): 0.00591
PGS AUROC (no covariates): 0.54034 [0.49224, 0.58845]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008932 PSS003675|
European Ancestry|
17,244 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Doctor diagnosed hayfever or allergic rhinitis — AUROC: 0.59244 [0.58227, 0.60261] R²: 0.02888
Incremental AUROC (full-covars): 0.02256
PGS R2 (no covariates): 0.01469
PGS AUROC (no covariates): 0.56502 [0.55474, 0.5753]		 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
PSS003671 — —
[
  • 170 cases
  • , 346 controls
]
 — African unspecified — UKB —
PSS003672 — —
[
  • 106 cases
  • , 139 controls
]
 — East Asian — UKB —
PSS003673 — —
[
  • 1,421 cases
  • , 4,538 controls
]
 — European non-white British ancestry UKB —
PSS003674 — —
[
  • 187 cases
  • , 520 controls
]
 — South Asian — UKB —
PSS003675 — —
[
  • 3,857 cases
  • , 13,387 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)