Polygenic Score (PGS) ID: PGS001019

Predicted Trait
Reported Trait Attending social / leisure activities (regular attendance at a gym or sports club)
Mapped Trait(s) social interaction measurement (EFO_0009592)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC20006160
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_FC20006160
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 11,361
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%
167,225 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
—
[
  • 85,202 cases
  • , 82,023 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
PPM007858 PSS003835|
African Ancestry|
3,021 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leisure/social activities (attend sports club or gym in once a week or more often) — AUROC: 0.54407 [0.52357, 0.56457] R²: 0.00813
Incremental AUROC (full-covars): -0.00783
PGS R2 (no covariates): 0.00123
PGS AUROC (no covariates): 0.51554 [0.49496, 0.53612]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007859 PSS003836|
East Asian Ancestry|
1,085 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leisure/social activities (attend sports club or gym in once a week or more often) — AUROC: 0.58246 [0.5482, 0.61672] R²: 0.0292
Incremental AUROC (full-covars): 0.02535
PGS R2 (no covariates): 0.01412
PGS AUROC (no covariates): 0.55974 [0.52518, 0.5943]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007860 PSS003837|
European Ancestry|
15,258 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leisure/social activities (attend sports club or gym in once a week or more often) — AUROC: 0.57507 [0.56602, 0.58412] R²: 0.02282
Incremental AUROC (full-covars): 0.00636
PGS R2 (no covariates): 0.00715
PGS AUROC (no covariates): 0.54225 [0.53311, 0.55138]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007861 PSS003838|
South Asian Ancestry|
4,460 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leisure/social activities (attend sports club or gym in once a week or more often) — AUROC: 0.5442 [0.527, 0.5614] R²: 0.00767
Incremental AUROC (full-covars): -0.01443
PGS R2 (no covariates): 0.00058
PGS AUROC (no covariates): 0.50999 [0.49273, 0.52726]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007862 PSS003839|
European Ancestry|
41,646 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leisure/social activities (attend sports club or gym in once a week or more often) — AUROC: 0.55465 [0.54914, 0.56015] R²: 0.01246
Incremental AUROC (full-covars): 0.02052
PGS R2 (no covariates): 0.0089
PGS AUROC (no covariates): 0.54635 [0.54083, 0.55186]		 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
PSS003836 — —
[
  • 456 cases
  • , 629 controls
]
 — East Asian — UKB —
PSS003837 — —
[
  • 8,025 cases
  • , 7,233 controls
]
 — European non-white British ancestry UKB —
PSS003838 — —
[
  • 1,790 cases
  • , 2,670 controls
]
 — South Asian — UKB —
PSS003839 — —
[
  • 21,289 cases
  • , 20,357 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003835 — —
[
  • 1,494 cases
  • , 1,527 controls
]
 — African unspecified — UKB —