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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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_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 : 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 : 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 : 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 : 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 : 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)