Trait: calcaneal bone quantitative ultrasound measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0007772
Description
  • bone quantitiave ultrasound of the main bone in the heel, recognized as a non-invasive method for evaluation of bone strength and prediction of osteoporotic fracture
Trait category
Other measurement

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000657 gSOS PGP000120 Forgetta V et al. PLoS Med (2020) Heel quantitative ultrasound speed of sound (SOS) calcaneal bone quantitative ultrasound measurement 21,717 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000657/ScoringFiles/PGS000657.txt.gz - Check Terms/Licenses

PGS 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 ID) 		Evaluated Score PGS Sample Set ID
(PSS ID) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM001343 PGS000657 (gSOS) PSS000586 PGP000120
Forgetta V et al. (2020) 		Reported Trait: Heel bone speed of sound — — R²: 0.2318 [0.2266, 0.2369] — —
PPM001344 PGS000657 (gSOS) PSS000585 PGP000120
Forgetta V et al. (2020) 		Reported Trait: Screening incorporating a gSOS-based screening step — — Positive Predictive Value (PPV): 0.954
Reduction in individuals requiring Clinical-Risk-Factor FRAX tests (%): 37.0
Percent reduction in individuals requiring BMD FRAX Tests (%): 41.0		 — —

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		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
PSS000585 — — 4,741 individuals,
47.5 % Male samples
 Mean = 55.8 years
Sd = 7.6 years		 European — UKB —
PSS000585 — — 6,704 individuals,
49.3 % Male samples
 Mean = 62.6 years
Sd = 9.9 years		 European, NR — CLSA —
PSS000585 — — 3,426 individuals,
0.0 % Male samples
 Mean = 71.5 years
Sd = 5.3 years		 European, NR — SOF —
PSS000585 — — 4,657 individuals,
100.0 % Male samples
 Mean = 74.0 years
Sd = 6.0 years		 European — MrOS-USA —
PSS000585 — — 1,880 individuals,
100.0 % Male samples
 Mean = 75.4 years
Sd = 3.2 years		 European
(Swedish)		 — MrOS-SWE —
PSS000586 — — 4,741 individuals,
47.5 % Male samples
 Mean = 55.8 years
Sd = 7.6 years		 European — UKB —