Polygenic Score (PGS) ID: PGS001956

Predicted Trait
Reported Trait Heel Broadband ultrasound attenuation, direct entry
Mapped Trait(s) calcaneal bone quantitative ultrasound measurement (EFO_0007772)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_log_heel_BUA
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 69,537
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM010523 PSS009447|
European Ancestry|
11,485 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Heel Broadband ultrasound attenuation, direct entry Partial Correlation (partial-r): 0.4264 [0.4113, 0.4413] sex, age, birth date, deprivation index, 16 PCs
PPM010524 PSS009221|
European Ancestry|
2,147 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Heel Broadband ultrasound attenuation, direct entry Partial Correlation (partial-r): 0.4076 [0.3715, 0.4424] sex, age, birth date, deprivation index, 16 PCs
PPM010525 PSS008775|
European Ancestry|
3,463 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Heel Broadband ultrasound attenuation, direct entry Partial Correlation (partial-r): 0.3665 [0.3372, 0.395] sex, age, birth date, deprivation index, 16 PCs
PPM010526 PSS008549|
Greater Middle Eastern Ancestry|
505 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Heel Broadband ultrasound attenuation, direct entry Partial Correlation (partial-r): 0.306 [0.223, 0.3845] sex, age, birth date, deprivation index, 16 PCs
PPM010527 PSS008327|
South Asian Ancestry|
1,968 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Heel Broadband ultrasound attenuation, direct entry Partial Correlation (partial-r): 0.3216 [0.2812, 0.3609] sex, age, birth date, deprivation index, 16 PCs
PPM010528 PSS008104|
East Asian Ancestry|
819 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Heel Broadband ultrasound attenuation, direct entry Partial Correlation (partial-r): 0.2762 [0.2109, 0.3391] sex, age, birth date, deprivation index, 16 PCs
PPM010529 PSS007891|
African Ancestry|
795 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Heel Broadband ultrasound attenuation, direct entry Partial Correlation (partial-r): 0.1457 [0.076, 0.2139] sex, age, birth date, deprivation index, 16 PCs
PPM010530 PSS008995|
African Ancestry|
1,404 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Heel Broadband ultrasound attenuation, direct entry Partial Correlation (partial-r): 0.1465 [0.0946, 0.1977] 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
PSS009221 2,147 individuals European Poland (NE Europe) UKB
PSS008549 505 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009447 11,485 individuals European UK (+ Ireland) UKB
PSS008775 3,463 individuals European Italy (South Europe) UKB
PSS008327 1,968 individuals South Asian India (South Asia) UKB
PSS008104 819 individuals East Asian China (East Asia) UKB
PSS007891 795 individuals African American or Afro-Caribbean Carribean UKB
PSS008995 1,404 individuals African unspecified Nigeria (West Africa) UKB