Polygenic Score (PGS) ID: PGS002632

Predicted Trait
Reported Trait Bone mineral density (BMD)
Mapped Trait(s) bone density (EFO_0003923)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name bmd_HEEL_TSCOREz.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 432,286
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000332
Citation (link to publication) Weissbrod O et al. Nat Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
327,738 individuals (100%)
PGS Evaluation
African: 25%
East Asian: 25%
European: 25%
South Asian: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 327,738 individuals European UKB

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
PPM014348 PSS009703|
African Ancestry|
5,639 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Bone Mineral Density — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0416 age, sex, age*sex, assessment center, genotyping array, 10 PCs See bmd_HEEL_TSCOREz.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014397 PSS009704|
East Asian Ancestry|
889 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Bone Mineral Density — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0991 age, sex, age*sex, assessment center, genotyping array, 10 PCs See bmd_HEEL_TSCOREz.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014446 PSS009705|
European Ancestry|
42,030 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Bone Mineral Density — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.2504 age, sex, age*sex, assessment center, genotyping array, 10 PCs See bmd_HEEL_TSCOREz.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014495 PSS009706|
South Asian Ancestry|
7,588 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Bone Mineral Density — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1707 age, sex, age*sex, assessment center, genotyping array, 10 PCs See bmd_HEEL_TSCOREz.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights

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
PSS009703 — — 5,639 individuals — African unspecified — UKB —
PSS009704 — — 889 individuals — East Asian — UKB —
PSS009705 — — 42,030 individuals — European Non-British European UKB —
PSS009706 — — 7,588 individuals — South Asian — UKB —