Polygenic Score (PGS) ID: PGS001039

Predicted Trait
Reported Trait Right heel bone mineral density (BMD) T-score, automated
Mapped Trait(s) heel bone mineral density (EFO_0009270)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI4125
Released in PGS Catalog: Oct. 21, 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_INI4125
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9,753
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%
103,563 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
— 103,563 individuals 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
PPM007953 PSS007326|
African Ancestry|
3,592 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) T-score, automated (R) — — R²: 0.02463 [0.01719, 0.03207]
Incremental R2 (full-covars): 0.00616
PGS R2 (no covariates): 0.00698 [0.00294, 0.01101]		 age, sex, UKB array type, Genotype PCs —
PPM007954 PSS007327|
East Asian Ancestry|
782 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) T-score, automated (R) — — R²: 0.09885 [0.072, 0.1257]
Incremental R2 (full-covars): 0.07541
PGS R2 (no covariates): 0.07555 [0.05147, 0.09963]		 age, sex, UKB array type, Genotype PCs —
PPM007955 PSS007328|
European Ancestry|
10,633 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) T-score, automated (R) — — R²: 0.1752 [0.16663, 0.18378]
Incremental R2 (full-covars): 0.11145
PGS R2 (no covariates): 0.11271 [0.10531, 0.12011]		 age, sex, UKB array type, Genotype PCs —
PPM007956 PSS007329|
South Asian Ancestry|
5,041 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) T-score, automated (R) — — R²: 0.08262 [0.07095, 0.0943]
Incremental R2 (full-covars): 0.05817
PGS R2 (no covariates): 0.05815 [0.0481, 0.06821]		 age, sex, UKB array type, Genotype PCs —
PPM007957 PSS007330|
European Ancestry|
25,728 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) T-score, automated (R) — — R²: 0.19359 [0.18823, 0.19894]
Incremental R2 (full-covars): 0.1242
PGS R2 (no covariates): 0.12266 [0.11802, 0.1273]		 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
PSS007326 — — 3,592 individuals — African unspecified — UKB —
PSS007327 — — 782 individuals — East Asian — UKB —
PSS007328 — — 10,633 individuals — European non-white British ancestry UKB —
PSS007329 — — 5,041 individuals — South Asian — UKB —
PSS007330 — — 25,728 individuals — European white British ancestry UKB Testing cohort (heldout set)