Polygenic Score (PGS) ID: PGS000954

Predicted Trait
Reported Trait Left heel quantitative ultrasound index (QUI), direct entry
Mapped Trait(s) bone quantitative ultrasound measurement (EFO_0004514)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI4104
Released in PGS Catalog: Oct. 21, 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_INI4104
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9,272
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 —

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
PPM007594 PSS007286|
African Ancestry|
3,560 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel quantitative ultrasound index (QUI), direct entry (L) — — R²: 0.02571 [0.01811, 0.0333]
Incremental R2 (full-covars): 0.00528
PGS R2 (no covariates): 0.00688 [0.00288, 0.01088]		 age, sex, UKB array type, Genotype PCs —
PPM007595 PSS007287|
East Asian Ancestry|
781 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel quantitative ultrasound index (QUI), direct entry (L) — — R²: 0.10298 [0.0757, 0.13026]
Incremental R2 (full-covars): 0.08296
PGS R2 (no covariates): 0.082 [0.05708, 0.10691]		 age, sex, UKB array type, Genotype PCs —
PPM007596 PSS007288|
European Ancestry|
10,636 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel quantitative ultrasound index (QUI), direct entry (L) — — R²: 0.17491 [0.16634, 0.18348]
Incremental R2 (full-covars): 0.11202
PGS R2 (no covariates): 0.11274 [0.10534, 0.12014]		 age, sex, UKB array type, Genotype PCs —
PPM007597 PSS007289|
South Asian Ancestry|
5,043 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel quantitative ultrasound index (QUI), direct entry (L) — — R²: 0.08121 [0.06962, 0.0928]
Incremental R2 (full-covars): 0.05294
PGS R2 (no covariates): 0.05414 [0.0444, 0.06389]		 age, sex, UKB array type, Genotype PCs —
PPM007598 PSS007290|
European Ancestry|
25,716 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel quantitative ultrasound index (QUI), direct entry (L) — — R²: 0.17984 [0.17459, 0.18509]
Incremental R2 (full-covars): 0.11708
PGS R2 (no covariates): 0.11589 [0.11135, 0.12043]		 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
PSS007286 — — 3,560 individuals — African unspecified — UKB —
PSS007287 — — 781 individuals — East Asian — UKB —
PSS007288 — — 10,636 individuals — European non-white British ancestry UKB —
PSS007289 — — 5,043 individuals — South Asian — UKB —
PSS007290 — — 25,716 individuals — European white British ancestry UKB Testing cohort (heldout set)