Polygenic Score (PGS) ID: PGS003923

Predicted Trait
Reported Trait Trunk fat-free mass
Mapped Trait(s) lean body mass (EFO_0004995)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI23129
Released in PGS Catalog: Nov. 1, 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 INI23129
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 42,468
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000502
Citation (link to publication) Tanigawa Y et al. AJHG (2023)
Ancestry Distribution
Score Development/Training
Multi-ancestry (including European): 100%
  • European
  • South Asian
  • African
  • Additional Diverse Ancestries
319,738 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
Multi-ancestry (excluding European): 20%
  • East Asian
  • Additional Diverse Ancestries
South Asian: 20%
5 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
319,738 individuals European, South Asian, African unspecified, Other admixed ancestry UKB European, South Asian, African unspecified, Other admixed ancestry

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
PPM018934 PSS011126|
European Ancestry|
66,571 individuals
PGP000502 |
Tanigawa Y et al. AJHG (2023)
Reported Trait: Trunk fat-free mass : 0.77028 [0.76725, 0.77332]
PGS R2 (no covariates): 0.05342 [0.05012, 0.05671]
Incremental R2 (full-covars): 0.05378
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18)
PPM018935 PSS011106|
European Ancestry|
2,836 individuals
PGP000502 |
Tanigawa Y et al. AJHG (2023)
Reported Trait: Trunk fat-free mass : 0.76786 [0.75305, 0.78266]
PGS R2 (no covariates): 0.06983 [0.05194, 0.08772]
Incremental R2 (full-covars): 0.05846
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18)
PPM018936 PSS011116|
South Asian Ancestry|
1,455 individuals
PGP000502 |
Tanigawa Y et al. AJHG (2023)
Reported Trait: Trunk fat-free mass : 0.68418 [0.65769, 0.71067]
PGS R2 (no covariates): 0.02869 [0.012, 0.04537]
Incremental R2 (full-covars): 0.0457
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18)
PPM018937 PSS011157|
African Ancestry|
1,168 individuals
PGP000502 |
Tanigawa Y et al. AJHG (2023)
Reported Trait: Trunk fat-free mass : 0.58996 [0.55462, 0.62531]
PGS R2 (no covariates): 0.00863 [-0.0017, 0.01897]
Incremental R2 (full-covars): 0.00562
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18)
PPM018938 PSS011163|
Multi-ancestry (excluding European)|
7,838 individuals
PGP000502 |
Tanigawa Y et al. AJHG (2023)
Reported Trait: Trunk fat-free mass : 0.75247 [0.74306, 0.76187]
PGS R2 (no covariates): 0.04065 [0.03218, 0.04912]
Incremental R2 (full-covars): 0.04164
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18)

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
PSS011116 1,455 individuals South Asian UKB
PSS011157 1,168 individuals African unspecified UKB
PSS011126 66,571 individuals European
(white British ancestry)
UKB
PSS011163 7,838 individuals East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB
PSS011106 2,836 individuals European
(non-white British ancestry)
UKB