Polygenic Score (PGS) ID: PGS002175

Predicted Trait
Reported Trait Speed of sound through heel
Mapped Trait(s) velocity of sound measurement (EFO_0005654)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_log_heel_SoS
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 724,667
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM012247 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 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 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 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 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 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 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 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 —

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 —
PSS007892 — — 801 individuals — African American or Afro-Caribbean Carribean UKB —