Polygenic Score (PGS) ID: PGS001531

Predicted Trait
Reported Trait Speed of sound through heel (R)
Mapped Trait(s) heel bone mineral density (EFO_0009270)
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)