Polygenic Score (PGS) ID: PGS003490

Predicted Trait
Reported Trait Ankle spacing width
Mapped Trait(s) body weights and measures (EFO_0004324)
Released in PGS Catalog: April 12, 2023
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Score Details

Score Construction
PGS Name cont-decay-ankle_spacing
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%
213,066 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
— 213,066 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
PPM017418 PSS010859|
European Ancestry|
11,364 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ankle spacing width — — partial-R2: 0.17 sex, age, deprivation index, PC1-16 —
PPM017502 PSS010775|
European Ancestry|
2,148 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ankle spacing width — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017586 PSS010607|
European Ancestry|
3,392 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ankle spacing width — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017670 PSS010523|
Greater Middle Eastern Ancestry|
488 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ankle spacing width — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM017754 PSS010187|
European Ancestry|
1,381 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ankle spacing width — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017838 PSS010439|
South Asian Ancestry|
1,978 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ankle spacing width — — partial-R2: 0.13 sex, age, deprivation index, PC1-16 —
PPM017922 PSS010355|
East Asian Ancestry|
810 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ankle spacing width — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM018006 PSS010271|
African Ancestry|
797 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ankle spacing width — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM018090 PSS010691|
African Ancestry|
1,412 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ankle spacing width — — 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
PSS010271 — — 797 individuals,
35.0 % Male samples
 Mean = 52.3 years
Sd = 8.2 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010691 — — 1,412 individuals,
49.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010439 — — 1,978 individuals,
56.0 % Male samples
 Mean = 52.7 years
Sd = 8.2 years		 South Asian Indian UKB —
PSS010187 — — 1,381 individuals,
46.0 % Male samples
 Mean = 57.7 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010859 — — 11,364 individuals,
46.0 % Male samples
 Mean = 56.8 years
Sd = 7.8 years		 European white British UKB —
PSS010607 — — 3,392 individuals,
46.0 % Male samples
 Mean = 54.5 years
Sd = 8.2 years		 European Italian UKB —
PSS010355 — — 810 individuals,
35.0 % Male samples
 Mean = 51.9 years
Sd = 7.5 years		 East Asian Chinese UKB —
PSS010775 — — 2,148 individuals,
40.0 % Male samples
 Mean = 54.3 years
Sd = 7.2 years		 European Polish UKB —
PSS010523 — — 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 —