Polygenic Score (PGS) ID: PGS001397

Predicted Trait
Reported Trait Frequency of walking for pleasure in last 4 weeks
Mapped Trait(s) physical activity measurement (EFO_0008002)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI971
Released in PGS Catalog: Nov. 25, 2021
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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_INI971
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,276
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%
197,094 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
— 197,094 individuals European UKB — — — white British ancestry 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
PPM007230 PSS007501|
African Ancestry|
3,349 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of walking for pleasure in last 4 weeks — — R²: 0.04503 [0.03518, 0.05487]
Incremental R2 (full-covars): -0.00108
PGS R2 (no covariates): 0.0 [-0.00004, 0.00004]		 age, sex, UKB array type, Genotype PCs —
PPM007231 PSS007502|
East Asian Ancestry|
912 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of walking for pleasure in last 4 weeks — — R²: 0.0431 [0.02428, 0.06193]
Incremental R2 (full-covars): -0.00157
PGS R2 (no covariates): 0.00024 [-0.00122, 0.00169]		 age, sex, UKB array type, Genotype PCs —
PPM007232 PSS007503|
European Ancestry|
17,807 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of walking for pleasure in last 4 weeks — — R²: 0.02317 [0.01948, 0.02686]
Incremental R2 (full-covars): 0.0015
PGS R2 (no covariates): 0.00162 [0.00062, 0.00261]		 age, sex, UKB array type, Genotype PCs —
PPM007233 PSS007504|
South Asian Ancestry|
4,428 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of walking for pleasure in last 4 weeks — — R²: 0.04215 [0.03345, 0.05086]
Incremental R2 (full-covars): 0.00033
PGS R2 (no covariates): 0.00052 [-0.00049, 0.00153]		 age, sex, UKB array type, Genotype PCs —
PPM007234 PSS007505|
European Ancestry|
49,163 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of walking for pleasure in last 4 weeks — — R²: 0.01064 [0.0091, 0.01218]
Incremental R2 (full-covars): 0.00095
PGS R2 (no covariates): 0.00098 [0.00051, 0.00146]		 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
PSS007501 — — 3,349 individuals — African unspecified — UKB —
PSS007502 — — 912 individuals — East Asian — UKB —
PSS007503 — — 17,807 individuals — European non-white British ancestry UKB —
PSS007504 — — 4,428 individuals — South Asian — UKB —
PSS007505 — — 49,163 individuals — European white British ancestry UKB Testing cohort (heldout set)