Polygenic Score (PGS) ID: PGS001404

Predicted Trait
Reported Trait Heel bone mineral density (BMD) (R)
Mapped Trait(s) heel bone mineral density (EFO_0009270)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI4124
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_INI4124
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9,637
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%
103,506 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
— 103,506 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
PPM007110 PSS007321|
African Ancestry|
3,586 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) (R) — — R²: 0.02449 [0.01707, 0.03191]
Incremental R2 (full-covars): 0.00554
PGS R2 (no covariates): 0.00662 [0.00269, 0.01055]		 age, sex, UKB array type, Genotype PCs —
PPM007111 PSS007322|
East Asian Ancestry|
782 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) (R) — — R²: 0.09993 [0.07297, 0.12689]
Incremental R2 (full-covars): 0.0765
PGS R2 (no covariates): 0.0766 [0.05238, 0.10082]		 age, sex, UKB array type, Genotype PCs —
PPM007112 PSS007323|
European Ancestry|
10,627 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) (R) — — R²: 0.17605 [0.16746, 0.18463]
Incremental R2 (full-covars): 0.11134
PGS R2 (no covariates): 0.11225 [0.10487, 0.11964]		 age, sex, UKB array type, Genotype PCs —
PPM007113 PSS007324|
South Asian Ancestry|
5,032 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) (R) — — R²: 0.08461 [0.07282, 0.0964]
Incremental R2 (full-covars): 0.05881
PGS R2 (no covariates): 0.05872 [0.04862, 0.06882]		 age, sex, UKB array type, Genotype PCs —
PPM007114 PSS007325|
European Ancestry|
25,715 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) (R) — — R²: 0.196 [0.19063, 0.20138]
Incremental R2 (full-covars): 0.12507
PGS R2 (no covariates): 0.12352 [0.11887, 0.12817]		 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
PSS007324 — — 5,032 individuals — South Asian — UKB —
PSS007325 — — 25,715 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS007321 — — 3,586 individuals — African unspecified — UKB —
PSS007322 — — 782 individuals — East Asian — UKB —
PSS007323 — — 10,627 individuals — European non-white British ancestry UKB —