Polygenic Score (PGS) ID: PGS000953

Predicted Trait
Reported Trait Left heel broadband ultrasound attenuation
Mapped Trait(s) bone quantitative ultrasound measurement (EFO_0004514)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI4101
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_INI4101
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 7,688
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%
103,470 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
— 103,470 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
PPM007591 PSS007278|
European Ancestry|
10,636 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel broadband ultrasound attenuation (L) — — R²: 0.18344 [0.17475, 0.19212]
Incremental R2 (full-covars): 0.09737
PGS R2 (no covariates): 0.09704 [0.09006, 0.10403]		 age, sex, UKB array type, Genotype PCs —
PPM007589 PSS007276|
African Ancestry|
3,559 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel broadband ultrasound attenuation (L) — — R²: 0.03758 [0.02851, 0.04665]
Incremental R2 (full-covars): 0.00859
PGS R2 (no covariates): 0.00936 [0.0047, 0.01402]		 age, sex, UKB array type, Genotype PCs —
PPM007590 PSS007277|
East Asian Ancestry|
781 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel broadband ultrasound attenuation (L) — — Incremental R2 (full-covars): 0.07295
R²: 0.10345 [0.07612, 0.13077]
PGS R2 (no covariates): 0.07189 [0.0483, 0.09547]		 age, sex, UKB array type, Genotype PCs —
PPM007592 PSS007279|
South Asian Ancestry|
5,043 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel broadband ultrasound attenuation (L) — — R²: 0.08632 [0.07443, 0.0982]
Incremental R2 (full-covars): 0.04895
PGS R2 (no covariates): 0.04892 [0.03961, 0.05823]		 age, sex, UKB array type, Genotype PCs —
PPM007593 PSS007280|
European Ancestry|
25,716 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Heel broadband ultrasound attenuation (L) — — R²: 0.19239 [0.18705, 0.19774]
Incremental R2 (full-covars): 0.09654
PGS R2 (no covariates): 0.09575 [0.09152, 0.09997]		 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
PSS007276 — — 3,559 individuals — African unspecified — UKB —
PSS007277 — — 781 individuals — East Asian — UKB —
PSS007278 — — 10,636 individuals — European non-white British ancestry UKB —
PSS007279 — — 5,043 individuals — South Asian — UKB —
PSS007280 — — 25,716 individuals — European white British ancestry UKB Testing cohort (heldout set)