Polygenic Score (PGS) ID: PGS001917

Predicted Trait
Reported Trait Body fat percentage
Mapped Trait(s) body fat percentage (EFO_0007800)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_fat_perc
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 107,244
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
PPM010219 PSS009405|
European Ancestry|
19,632 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Body fat percentage Partial Correlation (partial-r): 0.3451 [0.3327, 0.3573] sex, age, birth date, deprivation index, 16 PCs
PPM010220 PSS009179|
European Ancestry|
4,073 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Body fat percentage Partial Correlation (partial-r): 0.3424 [0.3149, 0.3693] sex, age, birth date, deprivation index, 16 PCs
PPM010221 PSS008733|
European Ancestry|
6,533 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Body fat percentage Partial Correlation (partial-r): 0.3184 [0.2964, 0.3401] sex, age, birth date, deprivation index, 16 PCs
PPM010222 PSS008507|
Greater Middle Eastern Ancestry|
1,151 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Body fat percentage Partial Correlation (partial-r): 0.286 [0.2316, 0.3386] sex, age, birth date, deprivation index, 16 PCs
PPM010223 PSS008285|
South Asian Ancestry|
6,180 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Body fat percentage Partial Correlation (partial-r): 0.2751 [0.2518, 0.298] sex, age, birth date, deprivation index, 16 PCs
PPM010224 PSS008062|
East Asian Ancestry|
1,779 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Body fat percentage Partial Correlation (partial-r): 0.2312 [0.1865, 0.275] sex, age, birth date, deprivation index, 16 PCs
PPM010225 PSS007849|
African Ancestry|
2,418 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Body fat percentage Partial Correlation (partial-r): 0.1519 [0.1126, 0.1908] sex, age, birth date, deprivation index, 16 PCs
PPM010226 PSS008953|
African Ancestry|
3,799 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Body fat percentage Partial Correlation (partial-r): 0.1483 [0.1169, 0.1793] 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
PSS008285 6,180 individuals South Asian India (South Asia) UKB
PSS009405 19,632 individuals European UK (+ Ireland) UKB
PSS007849 2,418 individuals African American or Afro-Caribbean Carribean UKB
PSS009179 4,073 individuals European Poland (NE Europe) UKB
PSS008953 3,799 individuals African unspecified Nigeria (West Africa) UKB
PSS008507 1,151 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008733 6,533 individuals European Italy (South Europe) UKB
PSS008062 1,779 individuals East Asian China (East Asia) UKB