Polygenic Score (PGS) ID: PGS003532

Predicted Trait
Reported Trait Whole body fat mass
Mapped Trait(s) fat body mass (EFO_0005409)
Released in PGS Catalog: April 12, 2023
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 cont-decay-log_fat_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%
363,831 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
— 363,831 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
PPM017460 PSS010896|
European Ancestry|
19,633 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat mass — — partial-R2: 0.13 sex, age, deprivation index, PC1-16 —
PPM017544 PSS010812|
European Ancestry|
4,055 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat mass — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017628 PSS010644|
European Ancestry|
6,357 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat mass — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM017712 PSS010560|
Greater Middle Eastern Ancestry|
1,121 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat mass — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017796 PSS010224|
European Ancestry|
2,313 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat mass — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM017880 PSS010476|
South Asian Ancestry|
6,122 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat mass — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017964 PSS010392|
East Asian Ancestry|
1,754 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat mass — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM018048 PSS010308|
African Ancestry|
2,406 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat mass — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018132 PSS010728|
African Ancestry|
3,766 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body fat mass — — partial-R2: 0.02 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
PSS010560 — — 1,121 individuals,
60.0 % Male samples
 Mean = 52.0 years
Sd = 7.9 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010308 — — 2,406 individuals,
36.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010728 — — 3,766 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010476 — — 6,122 individuals,
54.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010896 — — 19,633 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010224 — — 2,313 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010644 — — 6,357 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010392 — — 1,754 individuals,
33.0 % Male samples
 Mean = 52.4 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010812 — — 4,055 individuals,
37.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —