Polygenic Score (PGS) ID: PGS003531

Predicted Trait
Reported Trait Whole body fat-free mass
Mapped Trait(s) lean body mass (EFO_0004995)
Released in PGS Catalog: April 12, 2023
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Terms and Licenses
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Score Details

Score Construction
PGS Name cont-decay-log_fat_free_mass
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%
364,393 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
— 364,393 individuals,
0.46 % Male samples
 European UKB — Mean = 56.8 years
Sd = 8.0 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
PPM017459 PSS010895|
European Ancestry|
19,661 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat-free mass — — partial-R2: 0.2 sex, age, deprivation index, PC1-16 —
PPM017543 PSS010811|
European Ancestry|
4,062 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat-free mass — — partial-R2: 0.2 sex, age, deprivation index, PC1-16 —
PPM017627 PSS010643|
European Ancestry|
6,376 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat-free mass — — partial-R2: 0.18 sex, age, deprivation index, PC1-16 —
PPM017711 PSS010559|
Greater Middle Eastern Ancestry|
1,124 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat-free mass — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017795 PSS010223|
European Ancestry|
2,318 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat-free mass — — partial-R2: 0.19 sex, age, deprivation index, PC1-16 —
PPM017879 PSS010475|
South Asian Ancestry|
6,134 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat-free mass — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017963 PSS010391|
East Asian Ancestry|
1,770 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat-free mass — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM018047 PSS010307|
African Ancestry|
2,408 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat-free mass — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM018131 PSS010727|
African Ancestry|
3,771 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat-free mass — — partial-R2: 0.03 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
PSS010559 — — 1,124 individuals,
60.0 % Male samples
 Mean = 52.0 years
Sd = 7.9 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010307 — — 2,408 individuals,
36.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010727 — — 3,771 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010475 — — 6,134 individuals,
54.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010223 — — 2,318 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010895 — — 19,661 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010643 — — 6,376 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010391 — — 1,770 individuals,
34.0 % Male samples
 Mean = 52.4 years
Sd = 7.7 years		 East Asian Chinese UKB —
PSS010811 — — 4,062 individuals,
38.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —