Polygenic Score (PGS) ID: PGS001403

Predicted Trait
Reported Trait Heel bone mineral density (BMD) (L)
Mapped Trait(s) heel bone mineral density (EFO_0009270)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI4105
Released in PGS Catalog: Nov. 25, 2021
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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_INI4105
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 8,285
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%
103,407 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
— 103,407 individuals European UKB — — — white British ancestry Training + validation cohort (train_val)

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
PPM007100 PSS007291|
African Ancestry|
3,558 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) (L) — — R²: 0.02599 [0.01836, 0.03363]
Incremental R2 (full-covars): 0.00518
PGS R2 (no covariates): 0.00667 [0.00273, 0.01062]		 age, sex, UKB array type, Genotype PCs —
PPM007101 PSS007292|
East Asian Ancestry|
781 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) (L) — — R²: 0.10653 [0.07889, 0.13417]
Incremental R2 (full-covars): 0.08652
PGS R2 (no covariates): 0.08516 [0.05986, 0.11046]		 age, sex, UKB array type, Genotype PCs —
PPM007102 PSS007293|
European Ancestry|
10,626 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) (L) — — R²: 0.17743 [0.16883, 0.18604]
Incremental R2 (full-covars): 0.11194
PGS R2 (no covariates): 0.11269 [0.10529, 0.12009]		 age, sex, UKB array type, Genotype PCs —
PPM007103 PSS007294|
South Asian Ancestry|
5,037 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) (L) — — R²: 0.08239 [0.07073, 0.09405]
Incremental R2 (full-covars): 0.05357
PGS R2 (no covariates): 0.05487 [0.04506, 0.06467]		 age, sex, UKB array type, Genotype PCs —
PPM007104 PSS007295|
European Ancestry|
25,706 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) (L) — — R²: 0.18131 [0.17605, 0.18657]
Incremental R2 (full-covars): 0.11744
PGS R2 (no covariates): 0.11656 [0.11201, 0.12112]		 age, sex, UKB array type, Genotype PCs —

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
PSS007292 — — 781 individuals — East Asian — UKB —
PSS007293 — — 10,626 individuals — European non-white British ancestry UKB —
PSS007294 — — 5,037 individuals — South Asian — UKB —
PSS007295 — — 25,706 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS007291 — — 3,558 individuals — African unspecified — UKB —