PGS Catalog - PGS001531 / Speed of sound through heel (R) (Polygenic Score)

Polygenic Score (PGS) ID: PGS001531

Predicted Trait
Reported Trait	Speed of sound through heel (R)
Mapped Trait(s)	calcaneal bone quantitative ultrasound measurement (EFO_0007772)
Additional Trait Information	https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI4122

Released in PGS Catalog: Nov. 25, 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_INI4122
Development Method
Name	snpnet
Parameters	NR
Variants
Original Genome Build	GRCh37
Number of Variants	8,912
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% 103,563 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
—	103,563 individuals	European	UKB	—	—	—	white British ancestry	Training + validation cohort (train_val)

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
PPM007105	PSS007311\| African Ancestry\| 3,592 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Speed of sound through heel (R)	—	—	R²: 0.02141 [0.01445, 0.02837] Incremental R2 (full-covars): 0.0063 PGS R2 (no covariates): 0.00698 [0.00295, 0.01101]	age, sex, UKB array type, Genotype PCs	—
PPM007106	PSS007312\| East Asian Ancestry\| 782 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Speed of sound through heel (R)	—	—	R²: 0.09852 [0.07171, 0.12534] Incremental R2 (full-covars): 0.07672 PGS R2 (no covariates): 0.07776 [0.05339, 0.10214]	age, sex, UKB array type, Genotype PCs	—
PPM007107	PSS007313\| European Ancestry\| 10,633 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Speed of sound through heel (R)	—	—	R²: 0.16134 [0.15298, 0.16971] Incremental R2 (full-covars): 0.10988 PGS R2 (no covariates): 0.11176 [0.10439, 0.11914]	age, sex, UKB array type, Genotype PCs	—
PPM007108	PSS007314\| South Asian Ancestry\| 5,041 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Speed of sound through heel (R)	—	—	R²: 0.07785 [0.06646, 0.08924] Incremental R2 (full-covars): 0.05682 PGS R2 (no covariates): 0.05742 [0.04742, 0.06742]	age, sex, UKB array type, Genotype PCs	—
PPM007109	PSS007315\| European Ancestry\| 25,728 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Speed of sound through heel (R)	—	—	R²: 0.17507 [0.16986, 0.18028] Incremental R2 (full-covars): 0.12574 PGS R2 (no covariates): 0.12479 [0.12013, 0.12946]	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
PSS007311	—	—	3,592 individuals	—	African unspecified	—	UKB	—
PSS007312	—	—	782 individuals	—	East Asian	—	UKB	—
PSS007313	—	—	10,633 individuals	—	European	non-white British ancestry	UKB	—
PSS007314	—	—	5,041 individuals	—	South Asian	—	UKB	—
PSS007315	—	—	25,728 individuals	—	European	white British ancestry	UKB	Testing cohort (heldout set)