Polygenic Score (PGS) ID: PGS001402

Predicted Trait
Reported Trait Heel bone mineral density (BMD)
Mapped Trait(s) heel bone mineral density (EFO_0009270)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI3148
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_INI3148
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 14,251
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%
155,452 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
— 155,452 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
PPM007080 PSS007241|
African Ancestry|
2,248 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) — — R²: 0.03461 [0.02588, 0.04334]
Incremental R2 (full-covars): 0.01792
PGS R2 (no covariates): 0.01849 [0.012, 0.02498]		 age, sex, UKB array type, Genotype PCs —
PPM007081 PSS007242|
East Asian Ancestry|
794 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) — — R²: 0.0956 [0.0691, 0.1221]
Incremental R2 (full-covars): 0.06421
PGS R2 (no covariates): 0.06783 [0.04482, 0.09083]		 age, sex, UKB array type, Genotype PCs —
PPM007082 PSS007243|
European Ancestry|
12,374 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) — — R²: 0.18897 [0.18022, 0.19773]
Incremental R2 (full-covars): 0.13548
PGS R2 (no covariates): 0.13714 [0.1292, 0.14508]		 age, sex, UKB array type, Genotype PCs —
PPM007083 PSS007244|
South Asian Ancestry|
2,310 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) — — R²: 0.10415 [0.09135, 0.11695]
Incremental R2 (full-covars): 0.06926
PGS R2 (no covariates): 0.07321 [0.06211, 0.08432]		 age, sex, UKB array type, Genotype PCs —
PPM007084 PSS007245|
European Ancestry|
38,814 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) — — R²: 0.19926 [0.19386, 0.20465]
Incremental R2 (full-covars): 0.14341
PGS R2 (no covariates): 0.14309 [0.1382, 0.14798]		 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
PSS007241 — — 2,248 individuals — African unspecified — UKB —
PSS007242 — — 794 individuals — East Asian — UKB —
PSS007243 — — 12,374 individuals — European non-white British ancestry UKB —
PSS007244 — — 2,310 individuals — South Asian — UKB —
PSS007245 — — 38,814 individuals — European white British ancestry UKB Testing cohort (heldout set)