Polygenic Score (PGS) ID: PGS001285

Predicted Trait
Reported Trait Allergic disease (hay fever, rhinitis, or eczema) (diagnosed by doctor)
Mapped Trait(s) allergic disease (MONDO_0005271)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC5006152
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_FC5006152
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 7,313
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%
245,788 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
  • , 181,767 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
PPM008923 PSS003979|
African Ancestry|
5,863 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever rhinitis or eczema diagnosed by doctor — AUROC: 0.61988 [0.60418, 0.63557] R²: 0.05243
Incremental AUROC (full-covars): 0.00361
PGS R2 (no covariates): 0.00809
PGS AUROC (no covariates): 0.5435 [0.52719, 0.55982]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008924 PSS003980|
East Asian Ancestry|
1,575 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever rhinitis or eczema diagnosed by doctor — AUROC: 0.60016 [0.57208, 0.62825] R²: 0.04666
Incremental AUROC (full-covars): 0.00725
PGS R2 (no covariates): 0.0103
PGS AUROC (no covariates): 0.55278 [0.52414, 0.58142]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008925 PSS003981|
European Ancestry|
22,705 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever rhinitis or eczema diagnosed by doctor — AUROC: 0.64037 [0.63223, 0.64852] R²: 0.07055
Incremental AUROC (full-covars): 0.04919
PGS R2 (no covariates): 0.04448
PGS AUROC (no covariates): 0.61233 [0.60403, 0.62062]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008926 PSS003982|
South Asian Ancestry|
6,933 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever rhinitis or eczema diagnosed by doctor — AUROC: 0.61 [0.59463, 0.62537] R²: 0.03824
Incremental AUROC (full-covars): 0.05029
PGS R2 (no covariates): 0.02803
PGS AUROC (no covariates): 0.59248 [0.57698, 0.60797]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008927 PSS003983|
European Ancestry|
61,525 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever rhinitis or eczema diagnosed by doctor — AUROC: 0.64412 [0.63921, 0.64903] R²: 0.07281
Incremental AUROC (full-covars): 0.06352
PGS R2 (no covariates): 0.05108
PGS AUROC (no covariates): 0.62052 [0.61552, 0.62551]		 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
PSS003979 — —
[
  • 1,664 cases
  • , 4,199 controls
]
 — African unspecified — UKB —
PSS003980 — —
[
  • 656 cases
  • , 919 controls
]
 — East Asian — UKB —
PSS003981 — —
[
  • 5,888 cases
  • , 16,817 controls
]
 — European non-white British ancestry UKB —
PSS003982 — —
[
  • 1,629 cases
  • , 5,304 controls
]
 — South Asian — UKB —
PSS003983 — —
[
  • 16,014 cases
  • , 45,511 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)