Polygenic Score (PGS) ID: PGS001090

Predicted Trait
Reported Trait Often felt loved as a child
Mapped Trait(s) wellbeing measurement (EFO_0007869)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC40020489
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_BIN_FC40020489
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 7,555
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%
65,209 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
—
[
  • 46,409 cases
  • , 18,800 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
PPM008193 PSS003939|
African Ancestry|
695 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Often felt loved as a child — AUROC: 0.61181 [0.56997, 0.65365] R²: 0.0544
Incremental AUROC (full-covars): -0.02903
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.5072 [0.46391, 0.55048]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008194 PSS003940|
East Asian Ancestry|
264 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Often felt loved as a child — AUROC: 0.65378 [0.5874, 0.72015] R²: 0.08841
Incremental AUROC (full-covars): -0.03538
PGS R2 (no covariates): 0.0101
PGS AUROC (no covariates): 0.46612 [0.39605, 0.53618]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008195 PSS003941|
European Ancestry|
6,160 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Often felt loved as a child — AUROC: 0.55842 [0.54349, 0.57335] R²: 0.01334
Incremental AUROC (full-covars): 0.0304
PGS R2 (no covariates): 0.01114
PGS AUROC (no covariates): 0.55257 [0.53762, 0.56751]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008196 PSS003942|
South Asian Ancestry|
790 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Often felt loved as a child — AUROC: 0.56556 [0.5235, 0.60762] R²: 0.01512
Incremental AUROC (full-covars): -0.02764
PGS R2 (no covariates): 0.00069
PGS AUROC (no covariates): 0.51244 [0.47037, 0.5545]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008197 PSS003943|
European Ancestry|
16,485 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Often felt loved as a child — AUROC: 0.54953 [0.53996, 0.5591] R²: 0.0088
Incremental AUROC (full-covars): 0.03491
PGS R2 (no covariates): 0.00777
PGS AUROC (no covariates): 0.54645 [0.53688, 0.55602]		 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
PSS003939 — —
[
  • 376 cases
  • , 319 controls
]
 — African unspecified — UKB —
PSS003940 — —
[
  • 122 cases
  • , 142 controls
]
 — East Asian — UKB —
PSS003941 — —
[
  • 3,974 cases
  • , 2,186 controls
]
 — European non-white British ancestry UKB —
PSS003942 — —
[
  • 526 cases
  • , 264 controls
]
 — South Asian — UKB —
PSS003943 — —
[
  • 11,635 cases
  • , 4,850 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)