Predicted Trait | |
Reported Trait | Leg fat mass (R) |
Mapped Trait(s) | fat body mass (EFO_0005409) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI23112 |
Score Construction | |
PGS Name | INI23112 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 30,780 |
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 |
---|---|---|---|---|---|---|---|---|
— | 319,947 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 |
---|---|---|---|---|---|---|---|---|
PPM018869 | PSS011121| European Ancestry| 66,612 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Leg fat mass (right) | — | — | R²: 0.3861 [0.38036, 0.39185] PGS R2 (no covariates): 0.06466 [0.06108, 0.06824] Incremental R2 (full-covars): 0.06497 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018870 | PSS011105| European Ancestry| 2,837 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Leg fat mass (right) | — | — | R²: 0.35972 [0.33178, 0.38767] PGS R2 (no covariates): 0.0599 [0.04316, 0.07665] Incremental R2 (full-covars): 0.07014 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018871 | PSS011118| South Asian Ancestry| 1,457 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Leg fat mass (right) | — | — | R²: 0.46851 [0.43161, 0.5054] PGS R2 (no covariates): 0.05268 [0.03063, 0.07474] Incremental R2 (full-covars): 0.03815 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018872 | PSS011158| African Ancestry| 1,169 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Leg fat mass (right) | — | — | R²: 0.41827 [0.37605, 0.46049] PGS R2 (no covariates): 0.00758 [-0.00212, 0.01727] Incremental R2 (full-covars): -0.02564 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018873 | PSS011177| Multi-ancestry (excluding European)| 7,841 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Leg fat mass (right) | — | — | R²: 0.37114 [0.35436, 0.38791] PGS R2 (no covariates): 0.06443 [0.05403, 0.07483] Incremental R2 (full-covars): 0.04941 |
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 | — |
PSS011121 | — | — | 66,612 individuals | — | European (white British ancestry) |
— | UKB | — |
PSS011158 | — | — | 1,169 individuals | — | African unspecified | — | UKB | — |
PSS011105 | — | — | 2,837 individuals | — | European (non-white British ancestry) |
— | UKB | — |