Polygenic Score (PGS) ID: PGS003537

Predicted Trait
Reported Trait Speed of sound through heel
Mapped Trait(s) velocity of sound measurement (EFO_0005654)
Released in PGS Catalog: April 12, 2023
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Score Details

Score Construction
PGS Name cont-decay-log_heel_SoS
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
213,090 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 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
— 213,090 individuals,
0.46 % Male samples
 European UKB — Mean = 56.7 years
Sd = 7.9 years		 — white British —

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
PPM017465 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 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 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 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 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 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 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 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 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
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 —
PSS010901 — — 11,364 individuals,
46.0 % Male samples
 Mean = 56.8 years
Sd = 7.8 years		 European white British 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 —
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 —
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 —