PGS Catalog - PGS001529 / Speed of sound through heel (Polygenic Score)

Polygenic Score (PGS) ID: PGS001529

Predicted Trait
Reported Trait	Speed of sound through heel
Mapped Trait(s)	calcaneal bone quantitative ultrasound measurement (EFO_0007772)
Additional Trait Information	https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI3146

Released in PGS Catalog: Nov. 25, 2021

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Score Details

Score Construction
PGS Name	GBE_INI3146
Development Method
Name	snpnet
Parameters	NR
Variants
Original Genome Build	GRCh37
Number of Variants	13,172
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% 96,993 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
—	96,993 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
PPM007075	PSS007231\| African Ancestry\| 1,434 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Speed of sound through heel	—	—	R²: 0.03275 [0.02202, 0.04347] Incremental R2 (full-covars): 0.0181 PGS R2 (no covariates): 0.01912 [0.01081, 0.02743]	age, sex, UKB array type, Genotype PCs	—
PPM007076	PSS007232\| East Asian Ancestry\| 500 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Speed of sound through heel	—	—	R²: 0.10987 [0.07399, 0.14575] Incremental R2 (full-covars): 0.07069 PGS R2 (no covariates): 0.08324 [0.05108, 0.11541]	age, sex, UKB array type, Genotype PCs	—
PPM007077	PSS007233\| European Ancestry\| 7,691 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Speed of sound through heel	—	—	R²: 0.17225 [0.16143, 0.18307] Incremental R2 (full-covars): 0.13354 PGS R2 (no covariates): 0.13618 [0.12614, 0.14622]	age, sex, UKB array type, Genotype PCs	—
PPM007078	PSS007234\| South Asian Ancestry\| 1,449 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Speed of sound through heel	—	—	R²: 0.11013 [0.09349, 0.12678] Incremental R2 (full-covars): 0.08026 PGS R2 (no covariates): 0.08576 [0.07067, 0.10085]	age, sex, UKB array type, Genotype PCs	—
PPM007079	PSS007235\| European Ancestry\| 24,146 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Speed of sound through heel	—	—	R²: 0.18117 [0.17451, 0.18783] Incremental R2 (full-covars): 0.13986 PGS R2 (no covariates): 0.14001 [0.13386, 0.14616]	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
PSS007231	—	—	1,434 individuals	—	African unspecified	—	UKB	—
PSS007232	—	—	500 individuals	—	East Asian	—	UKB	—
PSS007233	—	—	7,691 individuals	—	European	non-white British ancestry	UKB	—
PSS007234	—	—	1,449 individuals	—	South Asian	—	UKB	—
PSS007235	—	—	24,146 individuals	—	European	white British ancestry	UKB	Testing cohort (heldout set)