Polygenic Score (PGS) ID: PGS001950

Predicted Trait
Reported Trait Whole body fat-free mass
Mapped Trait(s) lean body mass (EFO_0004995)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
Download Score FTP directory
Terms and Licenses
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 portability-PLR_log_fat_free_mass
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 128,827
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
PPM010476 PSS009217|
European Ancestry|
4,072 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Whole body fat-free mass Partial Correlation (partial-r): 0.449 [0.424, 0.4732] sex, age, birth date, deprivation index, 16 PCs
PPM010477 PSS008771|
European Ancestry|
6,538 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Whole body fat-free mass Partial Correlation (partial-r): 0.4291 [0.4091, 0.4487] sex, age, birth date, deprivation index, 16 PCs
PPM010478 PSS008545|
Greater Middle Eastern Ancestry|
1,152 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Whole body fat-free mass Partial Correlation (partial-r): 0.3709 [0.3195, 0.42] sex, age, birth date, deprivation index, 16 PCs
PPM010479 PSS008323|
South Asian Ancestry|
6,185 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Whole body fat-free mass Partial Correlation (partial-r): 0.3879 [0.3665, 0.4089] sex, age, birth date, deprivation index, 16 PCs
PPM010480 PSS008100|
East Asian Ancestry|
1,782 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Whole body fat-free mass Partial Correlation (partial-r): 0.3154 [0.2727, 0.3568] sex, age, birth date, deprivation index, 16 PCs
PPM010481 PSS007887|
African Ancestry|
2,420 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Whole body fat-free mass Partial Correlation (partial-r): 0.2517 [0.2139, 0.2888] sex, age, birth date, deprivation index, 16 PCs
PPM010482 PSS008991|
African Ancestry|
3,799 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Whole body fat-free mass Partial Correlation (partial-r): 0.1941 [0.1633, 0.2246] sex, age, birth date, deprivation index, 16 PCs
PPM010475 PSS009443|
European Ancestry|
19,637 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Whole body fat-free mass Partial Correlation (partial-r): 0.458 [0.4469, 0.469] 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
PSS008100 1,782 individuals East Asian China (East Asia) UKB
PSS009443 19,637 individuals European UK (+ Ireland) UKB
PSS007887 2,420 individuals African American or Afro-Caribbean Carribean UKB
PSS008771 6,538 individuals European Italy (South Europe) UKB
PSS008991 3,799 individuals African unspecified Nigeria (West Africa) UKB
PSS009217 4,072 individuals European Poland (NE Europe) UKB
PSS008545 1,152 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008323 6,185 individuals South Asian India (South Asia) UKB