Polygenic Score (PGS) ID: PGS001038

Predicted Trait
Reported Trait Left 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/INI4106
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_INI4106
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9,275
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%
103,475 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
— 103,475 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
PPM007948 PSS007296|
African Ancestry|
3,560 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) T-score, automated (L) — — R²: 0.02571 [0.01812, 0.03331]
Incremental R2 (full-covars): 0.00529
PGS R2 (no covariates): 0.00688 [0.00288, 0.01089]		 age, sex, UKB array type, Genotype PCs —
PPM007949 PSS007297|
East Asian Ancestry|
781 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) T-score, automated (L) — — R²: 0.10298 [0.0757, 0.13026]
Incremental R2 (full-covars): 0.08297
PGS R2 (no covariates): 0.082 [0.05709, 0.10691]		 age, sex, UKB array type, Genotype PCs —
PPM007950 PSS007298|
European Ancestry|
10,636 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) T-score, automated (L) — — R²: 0.17491 [0.16634, 0.18348]
Incremental R2 (full-covars): 0.11202
PGS R2 (no covariates): 0.11274 [0.10534, 0.12014]		 age, sex, UKB array type, Genotype PCs —
PPM007951 PSS007299|
South Asian Ancestry|
5,043 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) T-score, automated (L) — — R²: 0.08123 [0.06963, 0.09282]
Incremental R2 (full-covars): 0.05296
PGS R2 (no covariates): 0.05415 [0.04441, 0.0639]		 age, sex, UKB array type, Genotype PCs —
PPM007952 PSS007300|
European Ancestry|
25,716 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel bone mineral density (BMD) T-score, automated (L) — — R²: 0.17984 [0.17459, 0.18509]
Incremental R2 (full-covars): 0.11708
PGS R2 (no covariates): 0.11589 [0.11134, 0.12043]		 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
PSS007296 — — 3,560 individuals — African unspecified — UKB —
PSS007297 — — 781 individuals — East Asian — UKB —
PSS007298 — — 10,636 individuals — European non-white British ancestry UKB —
PSS007299 — — 5,043 individuals — South Asian — UKB —
PSS007300 — — 25,716 individuals — European white British ancestry UKB Testing cohort (heldout set)