Polygenic Score (PGS) ID: PGS001091

Predicted Trait
Reported Trait Loneliness
Mapped Trait(s) loneliness measurement (EFO_0007865)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN2020
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_BIN2020
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 660
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%
266,111 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
—
[
  • 48,952 cases
  • , 217,159 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
PPM008198 PSS003657|
African Ancestry|
6,193 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Loneliness, isolation — AUROC: 0.5933 [0.57749, 0.60912] R²: 0.02839
Incremental AUROC (full-covars): -0.00029
PGS R2 (no covariates): 3e-05
PGS AUROC (no covariates): 0.50405 [0.4879, 0.5202]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008199 PSS003658|
East Asian Ancestry|
1,578 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Loneliness, isolation — AUROC: 0.55678 [0.51915, 0.59442] R²: 0.01245
Incremental AUROC (full-covars): 0.00135
PGS R2 (no covariates): 0.00088
PGS AUROC (no covariates): 0.5227 [0.48519, 0.56021]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008200 PSS003659|
European Ancestry|
24,336 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Loneliness, isolation — AUROC: 0.57029 [0.56166, 0.57891] R²: 0.01702
Incremental AUROC (full-covars): 0.00306
PGS R2 (no covariates): 0.00194
PGS AUROC (no covariates): 0.52394 [0.51517, 0.53271]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008201 PSS003660|
South Asian Ancestry|
7,252 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Loneliness, isolation — AUROC: 0.58383 [0.56907, 0.59858] R²: 0.02374
Incremental AUROC (full-covars): 0.00498
PGS R2 (no covariates): 0.00178
PGS AUROC (no covariates): 0.52268 [0.50774, 0.53761]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008202 PSS003661|
European Ancestry|
66,472 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Loneliness, isolation — AUROC: 0.57632 [0.57084, 0.58179] R²: 0.01721
Incremental AUROC (full-covars): 0.00346
PGS R2 (no covariates): 0.00162
PGS AUROC (no covariates): 0.52288 [0.51722, 0.52854]		 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
PSS003657 — —
[
  • 1,686 cases
  • , 4,507 controls
]
 — African unspecified — UKB —
PSS003658 — —
[
  • 273 cases
  • , 1,305 controls
]
 — East Asian — UKB —
PSS003659 — —
[
  • 5,271 cases
  • , 19,065 controls
]
 — European non-white British ancestry UKB —
PSS003660 — —
[
  • 1,963 cases
  • , 5,289 controls
]
 — South Asian — UKB —
PSS003661 — —
[
  • 12,318 cases
  • , 54,154 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)