Polygenic Score (PGS) ID: PGS003535

Predicted Trait
Reported Trait Heel bone mineral density (BMD)
Mapped Trait(s) heel bone mineral density (EFO_0009270)
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_BMD
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%
212,683 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
— 212,683 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
PPM017631 PSS010647|
European Ancestry|
3,384 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel bone mineral density (BMD) — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017799 PSS010227|
European Ancestry|
1,383 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel bone mineral density (BMD) — — partial-R2: 0.17 sex, age, deprivation index, PC1-16 —
PPM017883 PSS010479|
South Asian Ancestry|
1,965 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel bone mineral density (BMD) — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM017967 PSS010395|
East Asian Ancestry|
811 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel bone mineral density (BMD) — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM018051 PSS010311|
African Ancestry|
786 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel bone mineral density (BMD) — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM018135 PSS010731|
African Ancestry|
1,397 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel bone mineral density (BMD) — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM017463 PSS010899|
European Ancestry|
11,350 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel bone mineral density (BMD) — — partial-R2: 0.2 sex, age, deprivation index, PC1-16 —
PPM017547 PSS010815|
European Ancestry|
2,145 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel bone mineral density (BMD) — — partial-R2: 0.19 sex, age, deprivation index, PC1-16 —
PPM017715 PSS010563|
Greater Middle Eastern Ancestry|
487 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Heel bone mineral density (BMD) — — partial-R2: 0.1 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
PSS010815 — — 2,145 individuals,
39.0 % Male samples
 Mean = 54.3 years
Sd = 7.2 years		 European Polish UKB —
PSS010563 — — 487 individuals,
65.0 % Male samples
 Mean = 51.1 years
Sd = 7.6 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010311 — — 786 individuals,
35.0 % Male samples
 Mean = 52.2 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010731 — — 1,397 individuals,
49.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010479 — — 1,965 individuals,
55.0 % Male samples
 Mean = 52.7 years
Sd = 8.2 years		 South Asian Indian UKB —
PSS010227 — — 1,383 individuals,
46.0 % Male samples
 Mean = 57.7 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010899 — — 11,350 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.8 years		 European white British UKB —
PSS010647 — — 3,384 individuals,
46.0 % Male samples
 Mean = 54.5 years
Sd = 8.2 years		 European Italian UKB —
PSS010395 — — 811 individuals,
35.0 % Male samples
 Mean = 51.9 years
Sd = 7.5 years		 East Asian Chinese UKB —