Polygenic Score (PGS) ID: PGS001343

Predicted Trait
Reported Trait Asthma (algorithmically-defined)
Mapped Trait(s) asthma (MONDO_0004979)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1581
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_HC1581
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 6,425
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
—
[
  • 35,787 cases
  • , 233,917 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
PPM009198 PSS004294|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD asthma — AUROC: 0.63661 [0.62631, 0.6469] R²: 0.04847
Incremental AUROC (full-covars): 0.06318
PGS R2 (no covariates): 0.03703
PGS AUROC (no covariates): 0.61732 [0.60678, 0.62786]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009196 PSS004292|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD asthma — AUROC: 0.61862 [0.59895, 0.63828] R²: 0.038
Incremental AUROC (full-covars): 0.00982
PGS R2 (no covariates): 0.00928
PGS AUROC (no covariates): 0.55801 [0.53701, 0.579]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009197 PSS004293|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD asthma — AUROC: 0.57145 [0.52876, 0.61414] R²: 0.02036
Incremental AUROC (full-covars): -0.02169
PGS R2 (no covariates): 2e-05
PGS AUROC (no covariates): 0.50757 [0.46343, 0.55171]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009199 PSS004295|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD asthma — AUROC: 0.61078 [0.59322, 0.62833] R²: 0.03413
Incremental AUROC (full-covars): 0.03417
PGS R2 (no covariates): 0.02015
PGS AUROC (no covariates): 0.58309 [0.56524, 0.60095]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009200 PSS004296|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD asthma — AUROC: 0.62553 [0.61925, 0.63182] R²: 0.04393
Incremental AUROC (full-covars): 0.07302
PGS R2 (no covariates): 0.03704
PGS AUROC (no covariates): 0.6162 [0.60989, 0.62251]		 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
PSS004292 — —
[
  • 869 cases
  • , 5,628 controls
]
 — African unspecified — UKB —
PSS004293 — —
[
  • 165 cases
  • , 1,539 controls
]
 — East Asian — UKB —
PSS004294 — —
[
  • 3,193 cases
  • , 21,712 controls
]
 — European non-white British ancestry UKB —
PSS004295 — —
[
  • 1,164 cases
  • , 6,667 controls
]
 — South Asian — UKB —
PSS004296 — —
[
  • 8,797 cases
  • , 58,628 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)