Predicted Trait | |
Reported Trait | Leg fat-free mass (L) |
Mapped Trait(s) | lean body mass (EFO_0004995) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI23117 |
Score Construction | |
PGS Name | INI23117 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 38,764 |
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 |
---|---|---|---|---|---|---|---|---|
— | 319,919 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 |
---|---|---|---|---|---|---|---|---|
PPM018889 | PSS011124| European Ancestry| 66,607 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Leg fat-free mass (left) | — | — | R²: 0.69704 [0.69323, 0.70085] PGS R2 (no covariates): 0.05413 [0.05082, 0.05744] Incremental R2 (full-covars): 0.05384 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018890 | PSS011105| European Ancestry| 2,837 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Leg fat-free mass (left) | — | — | R²: 0.70089 [0.68266, 0.71911] PGS R2 (no covariates): 0.05971 [0.04299, 0.07643] Incremental R2 (full-covars): 0.05733 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018892 | PSS011158| African Ancestry| 1,169 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Leg fat-free mass (left) | — | — | R²: 0.50439 [0.46489, 0.54389] PGS R2 (no covariates): 0.00566 [-0.00274, 0.01405] Incremental R2 (full-covars): -0.00128 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018893 | PSS011177| Multi-ancestry (excluding European)| 7,841 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Leg fat-free mass (left) | — | — | R²: 0.69898 [0.68796, 0.71] PGS R2 (no covariates): 0.03894 [0.03063, 0.04724] Incremental R2 (full-covars): 0.03936 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018891 | PSS011118| South Asian Ancestry| 1,457 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Leg fat-free mass (left) | — | — | R²: 0.65569 [0.62741, 0.68396] PGS R2 (no covariates): 0.02557 [0.00977, 0.04137] Incremental R2 (full-covars): 0.04081 |
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 |
---|---|---|---|---|---|---|---|---|
PSS011177 | — | — | 7,841 individuals | — | East Asian, Other admixed ancestry | East Asian, Other admixed ancestry | UKB | — |
PSS011118 | — | — | 1,457 individuals | — | South Asian | — | UKB | — |
PSS011124 | — | — | 66,607 individuals | — | European (white British ancestry) |
— | UKB | — |
PSS011158 | — | — | 1,169 individuals | — | African unspecified | — | UKB | — |
PSS011105 | — | — | 2,837 individuals | — | European (non-white British ancestry) |
— | UKB | — |