Polygenic Score (PGS) ID: PGS001344

Predicted Trait
Reported Trait Asthma (diagnosed by doctor)
Mapped Trait(s) asthma (MONDO_0004979)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC4006152
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_FC4006152
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 6,139
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%
216,121 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
—
[
  • 31,883 cases
  • , 184,238 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
PPM009201 PSS003954|
African Ancestry|
4,956 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Asthma diagnosed by doctor — AUROC: 0.64534 [0.62387, 0.66681] R²: 0.059
Incremental AUROC (full-covars): 0.00716
PGS R2 (no covariates): 0.01177
PGS AUROC (no covariates): 0.56449 [0.5415, 0.58748]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009202 PSS003955|
East Asian Ancestry|
1,072 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Asthma diagnosed by doctor — AUROC: 0.61098 [0.56503, 0.65693] R²: 0.04365
Incremental AUROC (full-covars): -0.00964
PGS R2 (no covariates): 0.00128
PGS AUROC (no covariates): 0.53103 [0.48086, 0.5812]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009203 PSS003956|
European Ancestry|
19,857 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Asthma diagnosed by doctor — AUROC: 0.66621 [0.65552, 0.67691] R²: 0.07596
Incremental AUROC (full-covars): 0.07977
PGS R2 (no covariates): 0.05973
PGS AUROC (no covariates): 0.64568 [0.63475, 0.65662]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009204 PSS003957|
South Asian Ancestry|
6,229 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Asthma diagnosed by doctor — AUROC: 0.61016 [0.59026, 0.63007] R²: 0.03328
Incremental AUROC (full-covars): 0.04929
PGS R2 (no covariates): 0.02494
PGS AUROC (no covariates): 0.59646 [0.57624, 0.61668]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009205 PSS003958|
European Ancestry|
53,936 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Asthma diagnosed by doctor — AUROC: 0.65364 [0.64713, 0.66016] R²: 0.06727
Incremental AUROC (full-covars): 0.09037
PGS R2 (no covariates): 0.05689
PGS AUROC (no covariates): 0.64265 [0.63609, 0.64921]		 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
PSS003954 — —
[
  • 730 cases
  • , 4,226 controls
]
 — African unspecified — UKB —
PSS003955 — —
[
  • 135 cases
  • , 937 controls
]
 — East Asian — UKB —
PSS003956 — —
[
  • 2,872 cases
  • , 16,985 controls
]
 — European non-white British ancestry UKB —
PSS003957 — —
[
  • 901 cases
  • , 5,328 controls
]
 — South Asian — UKB —
PSS003958 — —
[
  • 7,869 cases
  • , 46,067 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)