Polygenic Score (PGS) ID: PGS000952

Predicted Trait
Reported Trait Heel quantitative ultrasound index (QUI), direct entry
Mapped Trait(s) bone quantitative ultrasound measurement (EFO_0004514)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI3147
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_INI3147
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 14,311
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%
155,522 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
— 155,522 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
PPM007584 PSS007236|
African Ancestry|
2,253 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel quantitative ultrasound index (QUI), direct entry — — R²: 0.03462 [0.02589, 0.04335]
Incremental R2 (full-covars): 0.01756
PGS R2 (no covariates): 0.01829 [0.01183, 0.02474]		 age, sex, UKB array type, Genotype PCs —
PPM007585 PSS007237|
East Asian Ancestry|
795 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel quantitative ultrasound index (QUI), direct entry — — R²: 0.09836 [0.07157, 0.12516]
Incremental R2 (full-covars): 0.06627
PGS R2 (no covariates): 0.06933 [0.04611, 0.09255]		 age, sex, UKB array type, Genotype PCs —
PPM007586 PSS007238|
European Ancestry|
12,376 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel quantitative ultrasound index (QUI), direct entry — — R²: 0.18809 [0.17935, 0.19684]
Incremental R2 (full-covars): 0.13505
PGS R2 (no covariates): 0.13677 [0.12885, 0.1447]		 age, sex, UKB array type, Genotype PCs —
PPM007587 PSS007239|
South Asian Ancestry|
2,312 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel quantitative ultrasound index (QUI), direct entry — — R²: 0.10193 [0.08923, 0.11462]
Incremental R2 (full-covars): 0.06757
PGS R2 (no covariates): 0.07119 [0.06022, 0.08216]		 age, sex, UKB array type, Genotype PCs —
PPM007588 PSS007240|
European Ancestry|
38,834 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel quantitative ultrasound index (QUI), direct entry — — R²: 0.1966 [0.19122, 0.20198]
Incremental R2 (full-covars): 0.1419
PGS R2 (no covariates): 0.14158 [0.13671, 0.14646]		 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
PSS007236 — — 2,253 individuals — African unspecified — UKB —
PSS007237 — — 795 individuals — East Asian — UKB —
PSS007238 — — 12,376 individuals — European non-white British ancestry UKB —
PSS007239 — — 2,312 individuals — South Asian — UKB —
PSS007240 — — 38,834 individuals — European white British ancestry UKB Testing cohort (heldout set)