Polygenic Score (PGS) ID: PGS001044

Predicted Trait
Reported Trait Glucosamine intake
Mapped Trait(s) vitamin supplement exposure measurement (EFO_0009116)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC2006179
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_BIN_FC2006179
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 324
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%
269,276 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
—
[
  • 54,349 cases
  • , 214,927 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
PPM007978 PSS003864|
African Ancestry|
6,334 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glucosamine — AUROC: 0.65622 [0.63608, 0.67636] R²: 0.06346
Incremental AUROC (full-covars): 0.00075
PGS R2 (no covariates): 0.00077
PGS AUROC (no covariates): 0.51768 [0.49687, 0.53848]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007979 PSS003865|
East Asian Ancestry|
1,651 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glucosamine — AUROC: 0.68295 [0.65155, 0.71435] R²: 0.10514
Incremental AUROC (full-covars): -1e-05
PGS R2 (no covariates): 0.00024
PGS AUROC (no covariates): 0.50873 [0.47479, 0.54268]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007980 PSS003866|
European Ancestry|
24,820 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glucosamine — AUROC: 0.63822 [0.62937, 0.64707] R²: 0.05449
Incremental AUROC (full-covars): 0.00027
PGS R2 (no covariates): 0.00015
PGS AUROC (no covariates): 0.50748 [0.49816, 0.51681]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007981 PSS003867|
South Asian Ancestry|
7,537 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glucosamine — AUROC: 0.68783 [0.66995, 0.70572] R²: 0.08959
Incremental AUROC (full-covars): -3e-05
PGS R2 (no covariates): 0.00049
PGS AUROC (no covariates): 0.51694 [0.49696, 0.53692]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007982 PSS003868|
European Ancestry|
67,317 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glucosamine — AUROC: 0.62303 [0.61791, 0.62815] R²: 0.04569
Incremental AUROC (full-covars): 0.00058
PGS R2 (no covariates): 0.00054
PGS AUROC (no covariates): 0.51206 [0.50661, 0.51751]		 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
PSS003868 — —
[
  • 13,703 cases
  • , 53,614 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003864 — —
[
  • 842 cases
  • , 5,492 controls
]
 — African unspecified — UKB —
PSS003865 — —
[
  • 334 cases
  • , 1,317 controls
]
 — East Asian — UKB —
PSS003866 — —
[
  • 4,457 cases
  • , 20,363 controls
]
 — European non-white British ancestry UKB —
PSS003867 — —
[
  • 926 cases
  • , 6,611 controls
]
 — South Asian — UKB —