Polygenic Score (PGS) ID: PGS003536

Predicted Trait
Reported Trait Heel Broadband ultrasound attenuation, direct entry
Mapped Trait(s) bone quantitative ultrasound measurement (EFO_0004514)
Released in PGS Catalog: April 12, 2023
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name cont-decay-log_heel_BUA
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%
212,712 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
— 212,712 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
PPM017464 PSS010900|
European Ancestry|
11,353 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — partial-R2: 0.17 sex, age, deprivation index, PC1-16 —
PPM017548 PSS010816|
European Ancestry|
2,146 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — partial-R2: 0.17 sex, age, deprivation index, PC1-16 —
PPM017632 PSS010648|
European Ancestry|
3,386 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — partial-R2: 0.13 sex, age, deprivation index, PC1-16 —
PPM017716 PSS010564|
Greater Middle Eastern Ancestry|
486 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017968 PSS010396|
East Asian Ancestry|
810 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM018136 PSS010732|
African Ancestry|
1,395 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM017800 PSS010228|
European Ancestry|
1,382 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — partial-R2: 0.14 sex, age, deprivation index, PC1-16 —
PPM017884 PSS010480|
South Asian Ancestry|
1,961 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM018052 PSS010312|
African Ancestry|
791 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel Broadband ultrasound attenuation, direct entry — — partial-R2: 0.01 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
PSS010816 — — 2,146 individuals,
39.0 % Male samples
 Mean = 54.3 years
Sd = 7.2 years		 European Polish UKB —
PSS010564 — — 486 individuals,
65.0 % Male samples
 Mean = 51.1 years
Sd = 7.6 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010312 — — 791 individuals,
35.0 % Male samples
 Mean = 52.2 years
Sd = 8.2 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010732 — — 1,395 individuals,
49.0 % Male samples
 Mean = 52.0 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010480 — — 1,961 individuals,
56.0 % Male samples
 Mean = 52.7 years
Sd = 8.2 years		 South Asian Indian UKB —
PSS010900 — — 11,353 individuals,
46.0 % Male samples
 Mean = 56.8 years
Sd = 7.8 years		 European white British UKB —
PSS010228 — — 1,382 individuals,
47.0 % Male samples
 Mean = 57.7 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010648 — — 3,386 individuals,
46.0 % Male samples
 Mean = 54.5 years
Sd = 8.2 years		 European Italian UKB —
PSS010396 — — 810 individuals,
35.0 % Male samples
 Mean = 51.9 years
Sd = 7.5 years		 East Asian Chinese UKB —