Polygenic Score (PGS) ID: PGS001298

Predicted Trait
Reported Trait Obesity (time-to-event)
Mapped Trait(s) obesity (EFO_0001073)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC689
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_HC689
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9,227
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%
269,704 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
—
[
  • 18,188 cases
  • , 251,516 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
PPM008987 PSS004590|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE obesity — AUROC: 0.631 [0.60757, 0.65443] R²: 0.03591
Incremental AUROC (full-covars): -0.00374
PGS R2 (no covariates): 0.00346
PGS AUROC (no covariates): 0.54117 [0.51549, 0.56685]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008988 PSS004591|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE obesity — AUROC: 0.65328 [0.53612, 0.77044] R²: 0.04232
Incremental AUROC (full-covars): -0.00574
PGS R2 (no covariates): 0.00287
PGS AUROC (no covariates): 0.54699 [0.43971, 0.65426]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008989 PSS004592|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE obesity — AUROC: 0.59854 [0.58297, 0.61411] R²: 0.01902
Incremental AUROC (full-covars): 0.02082
PGS R2 (no covariates): 0.00911
PGS AUROC (no covariates): 0.56858 [0.5529, 0.58426]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008990 PSS004593|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE obesity — AUROC: 0.61415 [0.59079, 0.6375] R²: 0.02737
Incremental AUROC (full-covars): 0.00377
PGS R2 (no covariates): 0.00603
PGS AUROC (no covariates): 0.55658 [0.53218, 0.58097]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008991 PSS004594|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE obesity — AUROC: 0.59555 [0.58697, 0.60413] R²: 0.01814
Incremental AUROC (full-covars): 0.03355
PGS R2 (no covariates): 0.01146
PGS AUROC (no covariates): 0.57573 [0.56713, 0.58434]		 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
PSS004590 — —
[
  • 536 cases
  • , 5,961 controls
]
 — African unspecified — UKB —
PSS004591 — —
[
  • 27 cases
  • , 1,677 controls
]
 — East Asian — UKB —
PSS004592 — —
[
  • 1,355 cases
  • , 23,550 controls
]
 — European non-white British ancestry UKB —
PSS004593 — —
[
  • 564 cases
  • , 7,267 controls
]
 — South Asian — UKB —
PSS004594 — —
[
  • 4,477 cases
  • , 62,948 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)