Polygenic Score (PGS) ID: PGS002168

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
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Score Details

Score Construction
PGS Name portability-ldpred2_log_fat_free_mass
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 966,825
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
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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM012191 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): 0.447 [0.4358, 0.4581] sex, age, birth date, deprivation index, 16 PCs —
PPM012192 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): 0.4493 [0.4244, 0.4735] sex, age, birth date, deprivation index, 16 PCs —
PPM012193 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): 0.4231 [0.4029, 0.4428] sex, age, birth date, deprivation index, 16 PCs —
PPM012194 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): 0.3653 [0.3138, 0.4148] sex, age, birth date, deprivation index, 16 PCs —
PPM012195 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): 0.3787 [0.3571, 0.3999] sex, age, birth date, deprivation index, 16 PCs —
PPM012196 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): 0.3169 [0.2743, 0.3583] sex, age, birth date, deprivation index, 16 PCs —
PPM012197 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): 0.2494 [0.2115, 0.2866] sex, age, birth date, deprivation index, 16 PCs —
PPM012198 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): 0.1911 [0.1602, 0.2216] 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 —
PSS008323 — — 6,185 individuals — South Asian India (South Asia) UKB —
PSS009443 — — 19,637 individuals — European UK (+ Ireland) UKB —
PSS007887 — — 2,420 individuals — African American or Afro-Caribbean Carribean 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 —
PSS008771 — — 6,538 individuals — European Italy (South Europe) UKB —