Polygenic Score (PGS) ID: PGS001237

Predicted Trait
Reported Trait Lung function (FVC)
Mapped Trait(s) vital capacity (EFO_0004312)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI3062
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_INI3062
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 20,921
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
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
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
247,832 individuals European white British ancestry UKB

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
PPM008694 PSS007081|
African Ancestry|
5,865 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: FVC : 0.38605 [0.3675, 0.40459]
Incremental R2 (full-covars): -0.00854
PGS R2 (no covariates): 0.00449 [0.00125, 0.00774]
age, sex, UKB array type, Genotype PCs
PPM008695 PSS007082|
East Asian Ancestry|
1,590 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: FVC : 0.48915 [0.45529, 0.52301]
Incremental R2 (full-covars): 0.0239
PGS R2 (no covariates): 0.03634 [0.01893, 0.05375]
age, sex, UKB array type, Genotype PCs
PPM008696 PSS007083|
European Ancestry|
22,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: FVC : 0.53532 [0.52687, 0.54376]
Incremental R2 (full-covars): 0.04669
PGS R2 (no covariates): 0.04902 [0.04379, 0.05425]
age, sex, UKB array type, Genotype PCs
PPM008697 PSS007084|
South Asian Ancestry|
7,147 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: FVC : 0.42603 [0.40944, 0.44262]
Incremental R2 (full-covars): 0.00884
PGS R2 (no covariates): 0.02153 [0.01517, 0.02789]
age, sex, UKB array type, Genotype PCs
PPM008698 PSS007085|
European Ancestry|
62,090 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: FVC : 0.51644 [0.5112, 0.52169]
Incremental R2 (full-covars): 0.04662
PGS R2 (no covariates): 0.04936 [0.04617, 0.05255]
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
PSS007081 5,865 individuals African unspecified UKB
PSS007082 1,590 individuals East Asian UKB
PSS007083 22,831 individuals European non-white British ancestry UKB
PSS007084 7,147 individuals South Asian UKB
PSS007085 62,090 individuals European white British ancestry UKB Testing cohort (heldout set)