Polygenic Score (PGS) ID: PGS000951

Predicted Trait
Reported Trait Heel Broadband ultrasound attenuation, direct entry
Mapped Trait(s) bone quantitative ultrasound measurement (EFO_0004514)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI3144
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
Terms and Licenses
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_INI3144
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 13,735
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%
155,513 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
— 155,513 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
PPM007579 PSS007226|
African Ancestry|
2,252 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — R²: 0.03865 [0.02946, 0.04783]
Incremental R2 (full-covars): 0.01472
PGS R2 (no covariates): 0.01564 [0.00966, 0.02163]		 age, sex, UKB array type, Genotype PCs —
PPM007580 PSS007227|
East Asian Ancestry|
795 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — R²: 0.09355 [0.06728, 0.11982]
Incremental R2 (full-covars): 0.05152
PGS R2 (no covariates): 0.05375 [0.03296, 0.07454]		 age, sex, UKB array type, Genotype PCs —
PPM007581 PSS007228|
European Ancestry|
12,376 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — R²: 0.1963 [0.18746, 0.20514]
Incremental R2 (full-covars): 0.11678
PGS R2 (no covariates): 0.11778 [0.11026, 0.1253]		 age, sex, UKB array type, Genotype PCs —
PPM007582 PSS007229|
South Asian Ancestry|
2,312 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — R²: 0.09722 [0.08476, 0.10969]
Incremental R2 (full-covars): 0.05231
PGS R2 (no covariates): 0.05582 [0.04594, 0.06569]		 age, sex, UKB array type, Genotype PCs —
PPM007583 PSS007230|
European Ancestry|
38,830 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — R²: 0.20634 [0.2009, 0.21179]
Incremental R2 (full-covars): 0.11895
PGS R2 (no covariates): 0.11837 [0.11379, 0.12295]		 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
PSS007228 — — 12,376 individuals — European non-white British ancestry UKB —
PSS007229 — — 2,312 individuals — South Asian — UKB —
PSS007230 — — 38,830 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS007226 — — 2,252 individuals — African unspecified — UKB —
PSS007227 — — 795 individuals — East Asian — UKB —