Predicted Trait | |
Reported Trait | Impedance of leg (R) |
Mapped Trait(s) | body composition measurement (EFO_0005106) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI23107 |
Score Construction | |
PGS Name | INI23107 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 38,218 |
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 |
---|---|---|---|---|---|---|---|---|
— | 319,955 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 |
---|---|---|---|---|---|---|---|---|
PPM018844 | PSS011151| European Ancestry| 66,613 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Impedance of leg (right) | — | — | R²: 0.30322 [0.29744, 0.309] PGS R2 (no covariates): 0.11129 [0.10682, 0.11575] Incremental R2 (full-covars): 0.11033 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018845 | PSS011105| European Ancestry| 2,837 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Impedance of leg (right) | — | — | R²: 0.29712 [0.26924, 0.325] PGS R2 (no covariates): 0.10545 [0.08431, 0.12659] Incremental R2 (full-covars): 0.10793 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018846 | PSS011118| South Asian Ancestry| 1,457 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Impedance of leg (right) | — | — | R²: 0.18556 [0.14998, 0.22114] PGS R2 (no covariates): 0.07372 [0.04821, 0.09923] Incremental R2 (full-covars): 0.07276 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018847 | PSS011158| African Ancestry| 1,169 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Impedance of leg (right) | — | — | R²: 0.07294 [0.04484, 0.10104] PGS R2 (no covariates): 0.01761 [0.00298, 0.03224] Incremental R2 (full-covars): 0.0172 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018848 | PSS011177| Multi-ancestry (excluding European)| 7,841 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Impedance of leg (right) | — | — | R²: 0.282 [0.2653, 0.29869] PGS R2 (no covariates): 0.07892 [0.06759, 0.09025] Incremental R2 (full-covars): 0.06951 |
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 | — |
PSS011151 | — | — | 66,613 individuals | — | European (white British ancestry) |
— | UKB | — |
PSS011158 | — | — | 1,169 individuals | — | African unspecified | — | UKB | — |
PSS011105 | — | — | 2,837 individuals | — | European (non-white British ancestry) |
— | UKB | — |