Polygenic Score (PGS) ID: PGS001009

Predicted Trait
Reported Trait PEF
Mapped Trait(s) peak expiratory flow (EFO_0009718)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI3064
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_INI3064
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9,523
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%
247,832 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
— 247,832 individuals 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
PPM007808 PSS007101|
African Ancestry|
5,865 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PEF — — R²: 0.22035 [0.20256, 0.23814]
Incremental R2 (full-covars): 0.00018
PGS R2 (no covariates): 0.00203 [-0.00015, 0.00422]		 age, sex, UKB array type, Genotype PCs —
PPM007809 PSS007102|
East Asian Ancestry|
1,590 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PEF — — R²: 0.30722 [0.27083, 0.34361]
Incremental R2 (full-covars): -0.00018
PGS R2 (no covariates): 0.00498 [-0.00167, 0.01163]		 age, sex, UKB array type, Genotype PCs —
PPM007810 PSS007103|
European Ancestry|
22,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PEF — — Incremental R2 (full-covars): 0.01492
PGS R2 (no covariates): 0.01342 [0.01058, 0.01626]
R²: 0.36549 [0.35597, 0.37502]		 age, sex, UKB array type, Genotype PCs —
PPM007811 PSS007104|
South Asian Ancestry|
7,147 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PEF — — R²: 0.28496 [0.26806, 0.30186]
Incremental R2 (full-covars): 0.00596
PGS R2 (no covariates): 0.00838 [0.00436, 0.01239]		 age, sex, UKB array type, Genotype PCs —
PPM007812 PSS007105|
European Ancestry|
62,090 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PEF — — R²: 0.37763 [0.37186, 0.38341]
Incremental R2 (full-covars): 0.01833
PGS R2 (no covariates): 0.01842 [0.01641, 0.02043]		 age, sex, UKB array type, Genotype PCs —

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
PSS007101 — — 5,865 individuals — African unspecified — UKB —
PSS007102 — — 1,590 individuals — East Asian — UKB —
PSS007103 — — 22,831 individuals — European non-white British ancestry UKB —
PSS007104 — — 7,147 individuals — South Asian — UKB —
PSS007105 — — 62,090 individuals — European white British ancestry UKB Testing cohort (heldout set)