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 |
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 | |
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 |
---|---|---|---|---|---|---|---|---|
— | 319,738 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 |
---|---|---|---|---|---|---|---|---|
PPM018934 | PSS011126| European Ancestry| 66,571 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Trunk fat-free mass | — | — | R²: 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 | — | — | R²: 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 | — | — | R²: 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 | — | — | R²: 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 | — | — | R²: 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) | — |
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 | — |