Trait: loneliness measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0007865
Description Quantification of some aspect of loneliness, such as severity or presence/absence, generally through administration of a standardised questionnaire such as the 3-Item Leave Behind Questionnaire (LBQ).
Trait category
Other measurement

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001091
(GBE_BIN2020)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Loneliness loneliness measurement 660
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001091/ScoringFiles/PGS001091.txt.gz

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) 		Evaluated Score 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 PGS001091
(GBE_BIN2020)
 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 PGS001091
(GBE_BIN2020)
 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 PGS001091
(GBE_BIN2020)
 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 PGS001091
(GBE_BIN2020)
 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 PGS001091
(GBE_BIN2020)
 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)