Polygenic Score (PGS) ID: PGS001401

Predicted Trait
Reported Trait Health satisfaction
Mapped Trait(s) health satisfaction measurement (EFO_0009724)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/QT_FC1004548
Released in PGS Catalog: Nov. 25, 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_QT_FC1004548
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,814
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%
106,271 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
106,271 individuals European white British ancestry UKB Training + validation cohort (train_val)

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
PPM007250 PSS007601|
African Ancestry|
3,770 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Health satisfaction : 0.01436 [0.00862, 0.0201]
Incremental R2 (full-covars): -0.00107
PGS R2 (no covariates): 0.00031 [-0.00055, 0.00117]
age, sex, UKB array type, Genotype PCs
PPM007251 PSS007602|
East Asian Ancestry|
773 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Health satisfaction : 0.01047 [0.00087, 0.02006]
Incremental R2 (full-covars): -0.00364
PGS R2 (no covariates): 0.0 [-0.0002, 0.00021]
age, sex, UKB array type, Genotype PCs
PPM007252 PSS007603|
European Ancestry|
10,834 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Health satisfaction : 0.01053 [0.00801, 0.01305]
Incremental R2 (full-covars): 0.00325
PGS R2 (no covariates): 0.00366 [0.00217, 0.00516]
age, sex, UKB array type, Genotype PCs
PPM007253 PSS007604|
South Asian Ancestry|
4,984 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Health satisfaction : 0.01007 [0.00567, 0.01447]
Incremental R2 (full-covars): -0.00147
PGS R2 (no covariates): 0.00014 [-0.00038, 0.00065]
age, sex, UKB array type, Genotype PCs
PPM007254 PSS007605|
European Ancestry|
26,439 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Health satisfaction : 0.00501 [0.00394, 0.00607]
Incremental R2 (full-covars): 0.00135
PGS R2 (no covariates): 0.00204 [0.00136, 0.00272]
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
PSS007601 3,770 individuals African unspecified UKB
PSS007602 773 individuals East Asian UKB
PSS007603 10,834 individuals European non-white British ancestry UKB
PSS007604 4,984 individuals South Asian UKB
PSS007605 26,439 individuals European white British ancestry UKB Testing cohort (heldout set)