Polygenic Score (PGS) ID: PGS001020

Predicted Trait
Reported Trait Attending social / leisure activities (regular attendance at an adult education class)
Mapped Trait(s) social interaction measurement (EFO_0009592)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC50006160
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_FC50006160
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 220
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%
105,056 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
—
[
  • 20,834 cases
  • , 84,222 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
PPM007863 PSS003964|
African Ancestry|
2,080 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leisure/social activities (attend adult edication class in once a week or more often) — AUROC: 0.62457 [0.59746, 0.65168] R²: 0.05611
Incremental AUROC (full-covars): -0.00161
PGS R2 (no covariates): 4e-05
PGS AUROC (no covariates): 0.50528 [0.47691, 0.53364]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007864 PSS003965|
East Asian Ancestry|
779 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leisure/social activities (attend adult edication class in once a week or more often) — AUROC: 0.65214 [0.60399, 0.70029] R²: 0.08858
Incremental AUROC (full-covars): -0.016
PGS R2 (no covariates): 0.00657
PGS AUROC (no covariates): 0.44592 [0.39358, 0.49825]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007865 PSS003966|
European Ancestry|
9,800 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leisure/social activities (attend adult edication class in once a week or more often) — AUROC: 0.63249 [0.61991, 0.64506] R²: 0.05833
Incremental AUROC (full-covars): 0.00299
PGS R2 (no covariates): 0.00271
PGS AUROC (no covariates): 0.52692 [0.51362, 0.54021]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007866 PSS003967|
South Asian Ancestry|
3,118 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leisure/social activities (attend adult edication class in once a week or more often) — AUROC: 0.60534 [0.57645, 0.63422] R²: 0.03531
Incremental AUROC (full-covars): 0.00261
PGS R2 (no covariates): 0.00153
PGS AUROC (no covariates): 0.52735 [0.49684, 0.55785]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007867 PSS003968|
European Ancestry|
26,122 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Leisure/social activities (attend adult edication class in once a week or more often) — AUROC: 0.63479 [0.62646, 0.64311] R²: 0.05542
Incremental AUROC (full-covars): 0.00193
PGS R2 (no covariates): 0.00149
PGS AUROC (no covariates): 0.5218 [0.51302, 0.53058]		 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
PSS003964 — —
[
  • 535 cases
  • , 1,545 controls
]
 — African unspecified — UKB —
PSS003965 — —
[
  • 135 cases
  • , 644 controls
]
 — East Asian — UKB —
PSS003966 — —
[
  • 2,403 cases
  • , 7,397 controls
]
 — European non-white British ancestry UKB —
PSS003967 — —
[
  • 405 cases
  • , 2,713 controls
]
 — South Asian — UKB —
PSS003968 — —
[
  • 5,233 cases
  • , 20,889 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)