Polygenic Score (PGS) ID: PGS002169

Predicted Trait
Reported Trait Whole body fat mass
Mapped Trait(s) fat body mass (EFO_0005409)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_log_fat_mass
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 988,292
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
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
PPM012199 PSS009444|
European Ancestry|
19,612 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Whole body fat mass — — Partial Correlation (partial-r): 0.3489 [0.3366, 0.3612] sex, age, birth date, deprivation index, 16 PCs —
PPM012201 PSS008772|
European Ancestry|
6,519 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Whole body fat mass — — Partial Correlation (partial-r): 0.3303 [0.3085, 0.3518] sex, age, birth date, deprivation index, 16 PCs —
PPM012202 PSS008546|
Greater Middle Eastern Ancestry|
1,149 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Whole body fat mass — — Partial Correlation (partial-r): 0.2893 [0.2349, 0.3418] sex, age, birth date, deprivation index, 16 PCs —
PPM012203 PSS008324|
South Asian Ancestry|
6,173 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Whole body fat mass — — Partial Correlation (partial-r): 0.2913 [0.2683, 0.314] sex, age, birth date, deprivation index, 16 PCs —
PPM012204 PSS008101|
East Asian Ancestry|
1,766 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Whole body fat mass — — Partial Correlation (partial-r): 0.2544 [0.21, 0.2978] sex, age, birth date, deprivation index, 16 PCs —
PPM012205 PSS007888|
African Ancestry|
2,418 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Whole body fat mass — — Partial Correlation (partial-r): 0.1745 [0.1355, 0.2131] sex, age, birth date, deprivation index, 16 PCs —
PPM012206 PSS008992|
African Ancestry|
3,794 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Whole body fat mass — — Partial Correlation (partial-r): 0.147 [0.1156, 0.1781] sex, age, birth date, deprivation index, 16 PCs —
PPM012200 PSS009218|
European Ancestry|
4,065 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Whole body fat mass — — Partial Correlation (partial-r): 0.3562 [0.329, 0.3828] 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
PSS009444 — — 19,612 individuals — European UK (+ Ireland) UKB —
PSS008101 — — 1,766 individuals — East Asian China (East Asia) UKB —
PSS008772 — — 6,519 individuals — European Italy (South Europe) UKB —
PSS008324 — — 6,173 individuals — South Asian India (South Asia) UKB —
PSS007888 — — 2,418 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009218 — — 4,065 individuals — European Poland (NE Europe) UKB —
PSS008992 — — 3,794 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008546 — — 1,149 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —