Polygenic Score (PGS) ID: PGS001006

Predicted Trait
Reported Trait Weight change compared with 1 year ago
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC1002306
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_FC1002306
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,638
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%
265,770 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
—
[
  • 121,807 cases
  • , 143,963 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
PPM007793 PSS003760|
African Ancestry|
6,079 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Weight change compared with 1 year ago — AUROC: 0.62073 [0.60627, 0.63518] R²: 0.05769
Incremental AUROC (full-covars): -1e-05
PGS R2 (no covariates): 0.00038
PGS AUROC (no covariates): 0.50745 [0.49252, 0.52238]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007794 PSS003761|
East Asian Ancestry|
1,602 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Weight change compared with 1 year ago — AUROC: 0.59942 [0.57137, 0.62747] R²: 0.04761
Incremental AUROC (full-covars): 0.00968
PGS R2 (no covariates): 0.00719
PGS AUROC (no covariates): 0.53616 [0.5075, 0.56482]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007795 PSS003762|
European Ancestry|
24,477 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Weight change compared with 1 year ago — AUROC: 0.57635 [0.56917, 0.58352] R²: 0.02324
Incremental AUROC (full-covars): 0.00533
PGS R2 (no covariates): 0.00365
PGS AUROC (no covariates): 0.5289 [0.52165, 0.53616]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007796 PSS003763|
South Asian Ancestry|
7,281 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Weight change compared with 1 year ago — AUROC: 0.60517 [0.59225, 0.61809] R²: 0.04456
Incremental AUROC (full-covars): -0.00065
PGS R2 (no covariates): 0.00024
PGS AUROC (no covariates): 0.50809 [0.49482, 0.52135]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007797 PSS003764|
European Ancestry|
66,390 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Weight change compared with 1 year ago — AUROC: 0.58453 [0.5802, 0.58886] R²: 0.02896
Incremental AUROC (full-covars): 0.00463
PGS R2 (no covariates): 0.00376
PGS AUROC (no covariates): 0.5295 [0.5251, 0.5339]		 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
PSS003760 — —
[
  • 3,717 cases
  • , 2,362 controls
]
 — African unspecified — UKB —
PSS003761 — —
[
  • 664 cases
  • , 938 controls
]
 — East Asian — UKB —
PSS003762 — —
[
  • 10,994 cases
  • , 13,483 controls
]
 — European non-white British ancestry UKB —
PSS003763 — —
[
  • 3,505 cases
  • , 3,776 controls
]
 — South Asian — UKB —
PSS003764 — —
[
  • 30,581 cases
  • , 35,809 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)