Polygenic Score (PGS) ID: PGS001259

Predicted Trait
Reported Trait Hayfever/allergic rhinitis
Mapped Trait(s) seasonal allergic rhinitis (EFO_0003956)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC49
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_HC49
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 349
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
—
[
  • 17,482 cases
  • , 252,222 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
PPM008800 PSS004511|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever/allergic rhinitis — AUROC: 0.58821 [0.55886, 0.61757] R²: 0.01784
Incremental AUROC (full-covars): -0.00253
PGS R2 (no covariates): 0.00082
PGS AUROC (no covariates): 0.51547 [0.48626, 0.54467]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008801 PSS004512|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever/allergic rhinitis — AUROC: 0.56313 [0.52505, 0.60122] R²: 0.02281
Incremental AUROC (full-covars): 0.00075
PGS R2 (no covariates): 0.0011
PGS AUROC (no covariates): 0.52627 [0.48539, 0.56716]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008802 PSS004513|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever/allergic rhinitis — AUROC: 0.60641 [0.59175, 0.62107] R²: 0.02043
Incremental AUROC (full-covars): 0.01519
PGS R2 (no covariates): 0.00564
PGS AUROC (no covariates): 0.55414 [0.53891, 0.56936]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008803 PSS004514|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever/allergic rhinitis — AUROC: 0.60093 [0.57427, 0.6276] R²: 0.02041
Incremental AUROC (full-covars): 0.00631
PGS R2 (no covariates): 0.00266
PGS AUROC (no covariates): 0.54086 [0.51259, 0.56913]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008804 PSS004515|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hayfever/allergic rhinitis — AUROC: 0.60078 [0.59218, 0.60937] R²: 0.02042
Incremental AUROC (full-covars): 0.01922
PGS R2 (no covariates): 0.00737
PGS AUROC (no covariates): 0.5597 [0.55096, 0.56843]		 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
PSS004511 — —
[
  • 393 cases
  • , 6,104 controls
]
 — African unspecified — UKB —
PSS004512 — —
[
  • 215 cases
  • , 1,489 controls
]
 — East Asian — UKB —
PSS004513 — —
[
  • 1,438 cases
  • , 23,467 controls
]
 — European non-white British ancestry UKB —
PSS004514 — —
[
  • 435 cases
  • , 7,396 controls
]
 — South Asian — UKB —
PSS004515 — —
[
  • 4,398 cases
  • , 63,027 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)