Trait: velocity of sound measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005654
Description quantification of the speed at which sound travels through bone as an indicator of the physical and structural properties of the bone
Trait category
Other measurement

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001957
(portability-PLR_log_heel_SoS)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Speed of sound through heel velocity of sound measurement 65,064
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001957/ScoringFiles/PGS001957.txt.gz
PGS002175
(portability-ldpred2_log_heel_SoS)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Speed of sound through heel velocity of sound measurement 724,667
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002175/ScoringFiles/PGS002175.txt.gz
PGS003537
(cont-decay-log_heel_SoS)
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Speed of sound through heel velocity of sound measurement 979,739
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003537/ScoringFiles/PGS003537.txt.gz

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) 		Evaluated Score 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
PPM010531 PGS001957
(portability-PLR_log_heel_SoS)
 PSS009448|
European Ancestry|
11,504 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.4182 [0.403, 0.4332] sex, age, birth date, deprivation index, 16 PCs —
PPM010532 PGS001957
(portability-PLR_log_heel_SoS)
 PSS009222|
European Ancestry|
2,149 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.403 [0.3668, 0.438] sex, age, birth date, deprivation index, 16 PCs —
PPM010533 PGS001957
(portability-PLR_log_heel_SoS)
 PSS008776|
European Ancestry|
3,470 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.3476 [0.3179, 0.3766] sex, age, birth date, deprivation index, 16 PCs —
PPM010534 PGS001957
(portability-PLR_log_heel_SoS)
 PSS008550|
Greater Middle Eastern Ancestry|
507 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.2669 [0.1823, 0.3475] sex, age, birth date, deprivation index, 16 PCs —
PPM010535 PGS001957
(portability-PLR_log_heel_SoS)
 PSS008328|
South Asian Ancestry|
1,986 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.3007 [0.26, 0.3404] sex, age, birth date, deprivation index, 16 PCs —
PPM010536 PGS001957
(portability-PLR_log_heel_SoS)
 PSS008105|
East Asian Ancestry|
820 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.2977 [0.2332, 0.3596] sex, age, birth date, deprivation index, 16 PCs —
PPM010537 PGS001957
(portability-PLR_log_heel_SoS)
 PSS007892|
African Ancestry|
801 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.1697 [0.1008, 0.237] sex, age, birth date, deprivation index, 16 PCs —
PPM010538 PGS001957
(portability-PLR_log_heel_SoS)
 PSS008996|
African Ancestry|
1,421 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.1551 [0.1035, 0.2058] sex, age, birth date, deprivation index, 16 PCs —
PPM012247 PGS002175
(portability-ldpred2_log_heel_SoS)
 PSS009448|
European Ancestry|
11,504 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.41 [0.3947, 0.4251] sex, age, birth date, deprivation index, 16 PCs —
PPM012248 PGS002175
(portability-ldpred2_log_heel_SoS)
 PSS009222|
European Ancestry|
2,149 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.3934 [0.3568, 0.4287] sex, age, birth date, deprivation index, 16 PCs —
PPM012249 PGS002175
(portability-ldpred2_log_heel_SoS)
 PSS008776|
European Ancestry|
3,470 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.3448 [0.315, 0.3738] sex, age, birth date, deprivation index, 16 PCs —
PPM012250 PGS002175
(portability-ldpred2_log_heel_SoS)
 PSS008550|
Greater Middle Eastern Ancestry|
507 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.2733 [0.1891, 0.3536] sex, age, birth date, deprivation index, 16 PCs —
PPM012251 PGS002175
(portability-ldpred2_log_heel_SoS)
 PSS008328|
South Asian Ancestry|
1,986 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.2963 [0.2554, 0.3361] sex, age, birth date, deprivation index, 16 PCs —
PPM012252 PGS002175
(portability-ldpred2_log_heel_SoS)
 PSS008105|
East Asian Ancestry|
820 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.2873 [0.2224, 0.3496] sex, age, birth date, deprivation index, 16 PCs —
PPM012253 PGS002175
(portability-ldpred2_log_heel_SoS)
 PSS007892|
African Ancestry|
801 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.1599 [0.0908, 0.2275] sex, age, birth date, deprivation index, 16 PCs —
PPM012254 PGS002175
(portability-ldpred2_log_heel_SoS)
 PSS008996|
African Ancestry|
1,421 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Speed of sound through heel — — Partial Correlation (partial-r): 0.1518 [0.1003, 0.2026] sex, age, birth date, deprivation index, 16 PCs —
PPM017465 PGS003537
(cont-decay-log_heel_SoS)
 PSS010901|
European Ancestry|
11,364 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Speed of sound through heel — — partial-R2: 0.17 sex, age, deprivation index, PC1-16 —
PPM017549 PGS003537
(cont-decay-log_heel_SoS)
 PSS010817|
European Ancestry|
2,148 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Speed of sound through heel — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017633 PGS003537
(cont-decay-log_heel_SoS)
 PSS010649|
European Ancestry|
3,393 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Speed of sound through heel — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM017717 PGS003537
(cont-decay-log_heel_SoS)
 PSS010565|
Greater Middle Eastern Ancestry|
488 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Speed of sound through heel — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017801 PGS003537
(cont-decay-log_heel_SoS)
 PSS010229|
European Ancestry|
1,384 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Speed of sound through heel — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017885 PGS003537
(cont-decay-log_heel_SoS)
 PSS010481|
South Asian Ancestry|
1,979 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Speed of sound through heel — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017969 PGS003537
(cont-decay-log_heel_SoS)
 PSS010397|
East Asian Ancestry|
811 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Speed of sound through heel — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM018053 PGS003537
(cont-decay-log_heel_SoS)
 PSS010313|
African Ancestry|
797 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Speed of sound through heel — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM018137 PGS003537
(cont-decay-log_heel_SoS)
 PSS010733|
African Ancestry|
1,412 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Speed of sound through heel — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —

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
PSS008996 — — 1,421 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008550 — — 507 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009222 — — 2,149 individuals — European Poland (NE Europe) UKB —
PSS008776 — — 3,470 individuals — European Italy (South Europe) UKB —
PSS008328 — — 1,986 individuals — South Asian India (South Asia) UKB —
PSS009448 — — 11,504 individuals — European UK (+ Ireland) UKB —
PSS008105 — — 820 individuals — East Asian China (East Asia) UKB —
PSS010817 — — 2,148 individuals,
40.0 % Male samples
 Mean = 54.3 years
Sd = 7.2 years		 European Polish UKB —
PSS010565 — — 488 individuals,
65.0 % Male samples
 Mean = 51.1 years
Sd = 7.6 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010313 — — 797 individuals,
35.0 % Male samples
 Mean = 52.3 years
Sd = 8.2 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010733 — — 1,412 individuals,
49.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS007892 — — 801 individuals — African American or Afro-Caribbean Carribean UKB —
PSS010481 — — 1,979 individuals,
56.0 % Male samples
 Mean = 52.7 years
Sd = 8.2 years		 South Asian Indian UKB —
PSS010229 — — 1,384 individuals,
47.0 % Male samples
 Mean = 57.7 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010901 — — 11,364 individuals,
46.0 % Male samples
 Mean = 56.8 years
Sd = 7.8 years		 European white British UKB —
PSS010649 — — 3,393 individuals,
46.0 % Male samples
 Mean = 54.5 years
Sd = 8.2 years		 European Italian UKB —
PSS010397 — — 811 individuals,
35.0 % Male samples
 Mean = 51.9 years
Sd = 7.5 years		 East Asian Chinese UKB —