Predicted Trait | |
Reported Trait | Arm fat-free mass (R) |
Mapped Trait(s) | lean body mass (EFO_0004995) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI23121 |
Score Construction | |
PGS Name | INI23121 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 38,650 |
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 |
---|---|---|---|---|---|---|---|---|
— | 319,885 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 |
---|---|---|---|---|---|---|---|---|
PPM018904 | PSS011135| European Ancestry| 66,605 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Arm fat-free mass (right) | — | — | R²: 0.76312 [0.76, 0.76624] PGS R2 (no covariates): 0.04183 [0.03888, 0.04479] Incremental R2 (full-covars): 0.04246 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018905 | PSS011105| European Ancestry| 2,837 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Arm fat-free mass (right) | — | — | R²: 0.76262 [0.74753, 0.7777] PGS R2 (no covariates): 0.05531 [0.03914, 0.07148] Incremental R2 (full-covars): 0.04628 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018907 | PSS011158| African Ancestry| 1,169 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Arm fat-free mass (right) | — | — | R²: 0.64409 [0.61204, 0.67615] PGS R2 (no covariates): 0.00928 [-0.00143, 0.02] Incremental R2 (full-covars): 0.00249 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018908 | PSS011178| Multi-ancestry (excluding European)| 7,840 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Arm fat-free mass (right) | — | — | R²: 0.76131 [0.75219, 0.77043] PGS R2 (no covariates): 0.03229 [0.02468, 0.0399] Incremental R2 (full-covars): 0.03087 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018906 | PSS011118| South Asian Ancestry| 1,457 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Arm fat-free mass (right) | — | — | R²: 0.72486 [0.70111, 0.74862] PGS R2 (no covariates): 0.02572 [0.00987, 0.04157] Incremental R2 (full-covars): 0.03555 |
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 |
---|---|---|---|---|---|---|---|---|
PSS011178 | — | — | 7,840 individuals | — | East Asian, Other admixed ancestry | East Asian, Other admixed ancestry | UKB | — |
PSS011118 | — | — | 1,457 individuals | — | South Asian | — | UKB | — |
PSS011158 | — | — | 1,169 individuals | — | African unspecified | — | UKB | — |
PSS011135 | — | — | 66,605 individuals | — | European (white British ancestry) |
— | UKB | — |
PSS011105 | — | — | 2,837 individuals | — | European (non-white British ancestry) |
— | UKB | — |