Polygenic Score (PGS) ID: PGS002133

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-ldpred2_fat_perc
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 995,419
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: 40%
African: 30%
East Asian: 10%
Greater Middle Eastern: 10%
South Asian: 10%
10 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
PPM011919 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): 0.3443 [0.3319, 0.3566] sex, age, birth date, deprivation index, 16 PCs —
PPM011920 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): 0.3456 [0.3182, 0.3724] sex, age, birth date, deprivation index, 16 PCs —
PPM011921 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): 0.3256 [0.3037, 0.3472] sex, age, birth date, deprivation index, 16 PCs —
PPM011922 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): 0.2896 [0.2353, 0.3421] sex, age, birth date, deprivation index, 16 PCs —
PPM011923 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): 0.273 [0.2497, 0.2959] sex, age, birth date, deprivation index, 16 PCs —
PPM011924 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): 0.2302 [0.1854, 0.274] sex, age, birth date, deprivation index, 16 PCs —
PPM011925 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): 0.153 [0.1136, 0.1918] sex, age, birth date, deprivation index, 16 PCs —
PPM011926 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): 0.1577 [0.1265, 0.1887] sex, age, birth date, deprivation index, 16 PCs —
PPM020884 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.13 [0.94, 1.37] — — — —
PPM020899 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 0.94 [0.76, 1.15] — — — —

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 —
PSS011442 — —
[
  • 181 cases
  • , 383 controls
]
,
77.0 % Male samples
 Mean = 26.7 years European — PDAY —
PSS011441 — —
[
  • 165 cases
  • , 339 controls
]
,
82.0 % Male samples
 Mean = 27.5 years African unspecified — PDAY —
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 —