Polygenic Score (PGS) ID: PGS001346

Predicted Trait
Reported Trait Asthma (time-to-event)
Mapped Trait(s) asthma (MONDO_0004979)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1036
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_HC1036
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 8,508
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
—
[
  • 36,339 cases
  • , 233,365 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
PPM009215 PSS004088|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE asthma — AUROC: 0.62361 [0.61737, 0.62985] R²: 0.04277
Incremental AUROC (full-covars): 0.07368
PGS R2 (no covariates): 0.03644
PGS AUROC (no covariates): 0.61489 [0.60862, 0.62117]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009211 PSS004084|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE asthma — AUROC: 0.60891 [0.58896, 0.62886] R²: 0.03181
Incremental AUROC (full-covars): 0.00272
PGS R2 (no covariates): 0.00692
PGS AUROC (no covariates): 0.55171 [0.53052, 0.5729]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009212 PSS004085|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE asthma — AUROC: 0.58384 [0.54229, 0.62539] R²: 0.02359
Incremental AUROC (full-covars): -0.00999
PGS R2 (no covariates): 0.00084
PGS AUROC (no covariates): 0.52195 [0.47679, 0.5671]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009213 PSS004086|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE asthma — AUROC: 0.63612 [0.62588, 0.64636] R²: 0.04845
Incremental AUROC (full-covars): 0.06586
PGS R2 (no covariates): 0.03759
PGS AUROC (no covariates): 0.61803 [0.60759, 0.62848]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009214 PSS004087|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE asthma — AUROC: 0.6095 [0.59223, 0.62677] R²: 0.03284
Incremental AUROC (full-covars): 0.03317
PGS R2 (no covariates): 0.01873
PGS AUROC (no covariates): 0.58128 [0.56371, 0.59884]		 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
PSS004084 — —
[
  • 851 cases
  • , 5,646 controls
]
 — African unspecified — UKB —
PSS004085 — —
[
  • 166 cases
  • , 1,538 controls
]
 — East Asian — UKB —
PSS004086 — —
[
  • 3,237 cases
  • , 21,668 controls
]
 — European non-white British ancestry UKB —
PSS004087 — —
[
  • 1,196 cases
  • , 6,635 controls
]
 — South Asian — UKB —
PSS004088 — —
[
  • 8,933 cases
  • , 58,492 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)