Polygenic Score (PGS) ID: PGS000955

Predicted Trait
Reported Trait Right heel broadband ultrasound attenuation
Mapped Trait(s) bone quantitative ultrasound measurement (EFO_0004514)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI4120
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_INI4120
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 7,069
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%
103,558 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
— 103,558 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
PPM007599 PSS007306|
African Ancestry|
3,591 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel broadband ultrasound attenuation (R) — — R²: 0.03102 [0.02273, 0.03932]
Incremental R2 (full-covars): 0.0053
PGS R2 (no covariates): 0.00612 [0.00234, 0.0099]		 age, sex, UKB array type, Genotype PCs —
PPM007600 PSS007307|
East Asian Ancestry|
782 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel broadband ultrasound attenuation (R) — — R²: 0.1074 [0.07968, 0.13512]
Incremental R2 (full-covars): 0.06527
PGS R2 (no covariates): 0.06337 [0.04102, 0.08571]		 age, sex, UKB array type, Genotype PCs —
PPM007601 PSS007308|
European Ancestry|
10,633 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel broadband ultrasound attenuation (R) — — R²: 0.18118 [0.17253, 0.18984]
Incremental R2 (full-covars): 0.09282
PGS R2 (no covariates): 0.09341 [0.08653, 0.10029]		 age, sex, UKB array type, Genotype PCs —
PPM007602 PSS007309|
South Asian Ancestry|
5,040 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel broadband ultrasound attenuation (R) — — R²: 0.08322 [0.07151, 0.09493]
Incremental R2 (full-covars): 0.05145
PGS R2 (no covariates): 0.05095 [0.04147, 0.06044]		 age, sex, UKB array type, Genotype PCs —
PPM007603 PSS007310|
European Ancestry|
25,727 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel broadband ultrasound attenuation (R) — — R²: 0.20708 [0.20164, 0.21253]
Incremental R2 (full-covars): 0.10115
PGS R2 (no covariates): 0.10011 [0.09582, 0.10441]		 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
PSS007306 — — 3,591 individuals — African unspecified — UKB —
PSS007307 — — 782 individuals — East Asian — UKB —
PSS007308 — — 10,633 individuals — European non-white British ancestry UKB —
PSS007309 — — 5,040 individuals — South Asian — UKB —
PSS007310 — — 25,727 individuals — European white British ancestry UKB Testing cohort (heldout set)