Predicted Trait | |
Reported Trait | Whole body fat-free mass |
Mapped Trait(s) | lean body mass (EFO_0004995) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI23101 |
Score Construction | |
PGS Name | INI23101 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 42,786 |
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 | |
PGS Evaluation |
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 |
---|---|---|---|---|---|---|---|---|
— | 319,944 individuals | European, South Asian, African unspecified, Other admixed ancestry | UKB | — | — | — | European, South Asian, African unspecified, Other admixed ancestry | — |
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 |
---|---|---|---|---|---|---|---|---|
PPM018824 | PSS011150| European Ancestry| 66,614 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Whole body fat-free mass | — | — | R²: 0.7632 [0.76009, 0.76632] PGS R2 (no covariates): 0.0533 [0.05, 0.05659] Incremental R2 (full-covars): 0.05378 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018825 | PSS011108| European Ancestry| 2,835 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Whole body fat-free mass | — | — | R²: 0.76255 [0.74746, 0.77764] PGS R2 (no covariates): 0.06277 [0.04568, 0.07986] Incremental R2 (full-covars): 0.05616 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018826 | PSS011118| South Asian Ancestry| 1,457 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Whole body fat-free mass | — | — | R²: 0.69472 [0.66891, 0.72052] PGS R2 (no covariates): 0.02952 [0.01261, 0.04643] Incremental R2 (full-covars): 0.04458 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018827 | PSS011158| African Ancestry| 1,169 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Whole body fat-free mass | — | — | R²: 0.5853 [0.54969, 0.6209] PGS R2 (no covariates): 0.00696 [-0.00234, 0.01625] Incremental R2 (full-covars): 0.00196 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018828 | PSS011176| Multi-ancestry (excluding European)| 7,842 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Whole body fat-free mass | — | — | R²: 0.75091 [0.74146, 0.76036] PGS R2 (no covariates): 0.03965 [0.03128, 0.04803] Incremental R2 (full-covars): 0.0398 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS011108 | — | — | 2,835 individuals | — | European (non-white British ancestry) |
— | UKB | — |
PSS011176 | — | — | 7,842 individuals | — | East Asian, Other admixed ancestry | East Asian, Other admixed ancestry | UKB | — |
PSS011150 | — | — | 66,614 individuals | — | European (white British ancestry) |
— | UKB | — |
PSS011118 | — | — | 1,457 individuals | — | South Asian | — | UKB | — |
PSS011158 | — | — | 1,169 individuals | — | African unspecified | — | UKB | — |