Predicted Trait | |
Reported Trait | Alanine aminotransferase [U/L] |
Mapped Trait(s) | serum alanine aminotransferase measurement (EFO_0004735) |
Score Construction | |
PGS Name | snpnet.Alanine_aminotransferase |
Development Method | |
Name | snpnet |
Parameters | 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs) |
Variants | |
Original Genome Build | hg19 |
Number of Variants | 12,076 |
Effect Weight Type | beta |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000128 |
Citation (link to publication) | Sinnott-Armstrong N et al. Nat Genet (2021) |
Ancestry Distribution | |
Score Development/Training | European: 100% 255,256 individuals (100%) |
PGS Evaluation | European: 40% African: 20% East Asian: 20% South Asian: 20% 10 Sample Sets |
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 |
---|---|---|---|---|---|---|---|---|
Europe PMC: 10.1038/s41588-020-00757-z |
223,327 individuals | European (British) |
UKB | — | — | — | — | Training |
Europe PMC: 10.1038/s41588-020-00757-z |
31,929 individuals | European (British) |
UKB | — | — | — | — | Validation |
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 |
---|---|---|---|---|---|---|---|---|
PPM001466 | PSS000624| European Ancestry| 23,569 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Alanine aminotransferase [U/L] | — | — | R²: 0.2041 Spearman's ρ: 0.22 |
Age, sex, PCs(1-40) | — |
PPM001501 | PSS000625| South Asian Ancestry| 7,325 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Alanine aminotransferase [U/L] | — | — | R²: 0.18304 Spearman's ρ: 0.198 |
Age, sex, PCs(1-40) | — |
PPM001536 | PSS000626| European Ancestry| 63,766 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Alanine aminotransferase [U/L] | — | — | R²: 0.19165 Spearman's ρ: 0.244 |
Age, sex, PCs(1-40) | — |
PPM001396 | PSS000622| African Ancestry| 6,017 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Alanine aminotransferase [U/L] | — | — | R²: 0.17646 Spearman's ρ: 0.092 |
Age, sex, PCs(1-40) | — |
PPM001431 | PSS000623| East Asian Ancestry| 1,081 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Alanine aminotransferase [U/L] | — | — | R²: 0.1561 Spearman's ρ: 0.145 |
Age, sex, PCs(1-40) | — |
PPM007267 | PSS007078| European Ancestry| 23,758 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Alanine aminotransferase | — | — | R²: 0.07978 [0.07332, 0.08623] Incremental R2 (full-covars): 0.00218 PGS R2 (no covariates): 0.03 [0.02583, 0.03418] |
age, sex, UKB array type, Genotype PCs | — |
PPM007265 | PSS007076| African Ancestry| 6,099 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Alanine aminotransferase | — | — | R²: 0.0977 [0.084, 0.11141] Incremental R2 (full-covars): 0.00077 PGS R2 (no covariates): 0.00447 [0.00124, 0.00771] |
age, sex, UKB array type, Genotype PCs | — |
PPM007266 | PSS007077| East Asian Ancestry| 1,615 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Alanine aminotransferase | — | — | R²: 0.08994 [0.06408, 0.11581] Incremental R2 (full-covars): 0.00177 PGS R2 (no covariates): 0.02382 [0.00954, 0.03809] |
age, sex, UKB array type, Genotype PCs | — |
PPM007268 | PSS007079| South Asian Ancestry| 7,414 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Alanine aminotransferase | — | — | R²: 0.08504 [0.07323, 0.09685] Incremental R2 (full-covars): 0.00213 PGS R2 (no covariates): 0.02862 [0.02135, 0.0359] |
age, sex, UKB array type, Genotype PCs | — |
PPM007269 | PSS007080| European Ancestry| 64,440 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Alanine aminotransferase | — | — | R²: 0.06901 [0.06532, 0.0727] Incremental R2 (full-covars): 0.00284 PGS R2 (no covariates): 0.03994 [0.03705, 0.04284] |
age, sex, UKB array type, Genotype PCs | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS000622 | — | — | 6,017 individuals | — | African unspecified | — | UKB | — |
PSS000623 | — | — | 1,081 individuals | — | East Asian | — | UKB | — |
PSS000624 | — | — | 23,569 individuals | — | European | Non-British White | UKB | — |
PSS000625 | — | — | 7,325 individuals | — | South Asian | — | UKB | — |
PSS000626 | — | — | 63,766 individuals | — | European (British) |
— | UKB | — |
PSS007078 | — | — | 23,758 individuals | — | European | non-white British ancestry | UKB | — |
PSS007076 | — | — | 6,099 individuals | — | African unspecified | — | UKB | — |
PSS007077 | — | — | 1,615 individuals | — | East Asian | — | UKB | — |
PSS007079 | — | — | 7,414 individuals | — | South Asian | — | UKB | — |
PSS007080 | — | — | 64,440 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |