Polygenic Score (PGS) ID: PGS003509

Predicted Trait
Reported Trait Body fat percentage
Mapped Trait(s) body fat percentage (EFO_0007800)
Released in PGS Catalog: April 12, 2023
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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 cont-decay-fat_perc
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%
364,224 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
— 364,224 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
PPM017437 PSS010871|
European Ancestry|
19,650 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Body fat percentage — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017521 PSS010787|
European Ancestry|
4,063 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Body fat percentage — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM017605 PSS010619|
European Ancestry|
6,371 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Body fat percentage — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017689 PSS010535|
Greater Middle Eastern Ancestry|
1,123 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Body fat percentage — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017773 PSS010199|
European Ancestry|
2,315 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Body fat percentage — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM017857 PSS010451|
South Asian Ancestry|
6,129 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Body fat percentage — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM018025 PSS010283|
African Ancestry|
2,406 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Body fat percentage — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018109 PSS010703|
African Ancestry|
3,771 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Body fat percentage — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM017941 PSS010367|
East Asian Ancestry|
1,767 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Body fat percentage — — partial-R2: 0.04 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
PSS010367 — — 1,767 individuals,
33.0 % Male samples
 Mean = 52.4 years
Sd = 7.7 years		 East Asian Chinese UKB —
PSS010787 — — 4,063 individuals,
38.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —
PSS010535 — — 1,123 individuals,
60.0 % Male samples
 Mean = 52.0 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010283 — — 2,406 individuals,
36.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010703 — — 3,771 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010451 — — 6,129 individuals,
54.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010871 — — 19,650 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010619 — — 6,371 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010199 — — 2,315 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —