Polygenic Score (PGS) ID: PGS001530

Predicted Trait
Reported Trait Speed of sound through heel (L)
Mapped Trait(s) calcaneal bone quantitative ultrasound measurement (EFO_0007772)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI4103
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_INI4103
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 8,419
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%
103,475 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
103,475 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
PPM007095 PSS007281|
African Ancestry|
3,560 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Speed of sound through heel (L) : 0.02043 [0.01363, 0.02724]
Incremental R2 (full-covars): 0.00372
PGS R2 (no covariates): 0.00552 [0.00193, 0.00911]
age, sex, UKB array type, Genotype PCs
PPM007096 PSS007282|
East Asian Ancestry|
781 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Speed of sound through heel (L) : 0.1024 [0.07518, 0.12962]
Incremental R2 (full-covars): 0.0813
PGS R2 (no covariates): 0.08045 [0.05573, 0.10516]
age, sex, UKB array type, Genotype PCs
PPM007097 PSS007283|
European Ancestry|
10,636 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Speed of sound through heel (L) : 0.16053 [0.15218, 0.16889]
Incremental R2 (full-covars): 0.10916
PGS R2 (no covariates): 0.11118 [0.10382, 0.11854]
age, sex, UKB array type, Genotype PCs
PPM007098 PSS007284|
South Asian Ancestry|
5,043 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Speed of sound through heel (L) : 0.07631 [0.06501, 0.0876]
Incremental R2 (full-covars): 0.05214
PGS R2 (no covariates): 0.05376 [0.04404, 0.06347]
age, sex, UKB array type, Genotype PCs
PPM007099 PSS007285|
European Ancestry|
25,716 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Speed of sound through heel (L) : 0.16377 [0.15866, 0.16887]
Incremental R2 (full-covars): 0.11885
PGS R2 (no covariates): 0.118 [0.11343, 0.12257]
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
PSS007281 3,560 individuals African unspecified UKB
PSS007282 781 individuals East Asian UKB
PSS007283 10,636 individuals European non-white British ancestry UKB
PSS007284 5,043 individuals South Asian UKB
PSS007285 25,716 individuals European white British ancestry UKB Testing cohort (heldout set)