Polygenic Score (PGS) ID: PGS001074

Predicted Trait
Reported Trait Types of physical activity in last 4 weeks (other exercises)
Mapped Trait(s) physical activity measurement (EFO_0008002)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC30006164
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_BIN_FC30006164
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3,846
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%
150,621 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
—
[
  • 134,747 cases
  • , 15,874 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
PPM008128 PSS003889|
African Ancestry|
3,437 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Types of physical activity in last 4 weeks (other exercises) — AUROC: 0.58685 [0.56691, 0.60678] R²: 0.02734
Incremental AUROC (full-covars): -0.01455
PGS R2 (no covariates): 0.00052
PGS AUROC (no covariates): 0.51078 [0.49041, 0.53114]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008129 PSS003890|
East Asian Ancestry|
925 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Types of physical activity in last 4 weeks (other exercises) — AUROC: 0.53885 [0.4931, 0.58459] R²: 0.01025
Incremental AUROC (full-covars): -0.02118
PGS R2 (no covariates): 0.00013
PGS AUROC (no covariates): 0.49787 [0.45183, 0.54391]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008130 PSS003891|
European Ancestry|
14,151 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Types of physical activity in last 4 weeks (other exercises) — AUROC: 0.62614 [0.61244, 0.63984] R²: 0.04034
Incremental AUROC (full-covars): 0.00763
PGS R2 (no covariates): 0.0082
PGS AUROC (no covariates): 0.5561 [0.54163, 0.57057]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008131 PSS003892|
South Asian Ancestry|
3,751 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Types of physical activity in last 4 weeks (other exercises) — AUROC: 0.56075 [0.54088, 0.58063] R²: 0.01505
Incremental AUROC (full-covars): -0.00611
PGS R2 (no covariates): 0.00193
PGS AUROC (no covariates): 0.52395 [0.50376, 0.54414]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008132 PSS003893|
European Ancestry|
37,995 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Types of physical activity in last 4 weeks (other exercises) — AUROC: 0.59585 [0.58652, 0.60518] R²: 0.0232
Incremental AUROC (full-covars): 0.00711
PGS R2 (no covariates): 0.0069
PGS AUROC (no covariates): 0.55343 [0.54397, 0.56289]		 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
PSS003889 — —
[
  • 2,279 cases
  • , 1,158 controls
]
 — African unspecified — UKB —
PSS003890 — —
[
  • 728 cases
  • , 197 controls
]
 — East Asian — UKB —
PSS003891 — —
[
  • 12,417 cases
  • , 1,734 controls
]
 — European non-white British ancestry UKB —
PSS003892 — —
[
  • 2,623 cases
  • , 1,128 controls
]
 — South Asian — UKB —
PSS003893 — —
[
  • 34,031 cases
  • , 3,964 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)