Polygenic Score (PGS) ID: PGS000674

Predicted Trait
Reported Trait AST to ALT ratio
Mapped Trait(s) aspartate aminotransferase to alanine aminotransferase ratio (EFO_0010934)
Released in PGS Catalog: Feb. 3, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.AST_ALT_ratio
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 15,548
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

Development Samples

Score Development/Training
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
223,327 individuals European
(British)		 UKB — — — — Training
31,929 individuals European
(British)		 UKB — — — — Validation

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

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
PPM001402 PSS000617|
African Ancestry|
5,981 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: AST to ALT ratio — — R²: 0.10039
Spearman's ρ: 0.108		 Age, sex, PCs(1-40) —
PPM001437 PSS000618|
East Asian Ancestry|
1,069 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: AST to ALT ratio — — Spearman's ρ: 0.14
R²: 0.16003		 Age, sex, PCs(1-40) —
PPM001472 PSS000619|
European Ancestry|
23,478 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: AST to ALT ratio — — R²: 0.17913
Spearman's ρ: 0.256		 Age, sex, PCs(1-40) —
PPM001507 PSS000620|
South Asian Ancestry|
7,309 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: AST to ALT ratio — — R²: 0.16338
Spearman's ρ: 0.204		 Age, sex, PCs(1-40) —
PPM001542 PSS000621|
European Ancestry|
63,545 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: AST to ALT ratio — — R²: 0.16733
Spearman's ρ: 0.272		 Age, sex, PCs(1-40) —
PPM007295 PSS006906|
African Ancestry|
5,981 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: AST to ALT ratio — — R²: 0.01466 [0.00886, 0.02046]
Incremental R2 (full-covars): 0.00987
PGS R2 (no covariates): 0.01069 [0.00572, 0.01566]		 age, sex, UKB array type, Genotype PCs —
PPM007296 PSS006907|
East Asian Ancestry|
1,564 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: AST to ALT ratio — — R²: 0.02597 [0.01109, 0.04085]
Incremental R2 (full-covars): 0.01695
PGS R2 (no covariates): 0.01781 [0.00539, 0.03023]		 age, sex, UKB array type, Genotype PCs —
PPM007297 PSS006908|
European Ancestry|
23,476 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: AST to ALT ratio — — R²: 0.0729 [0.06668, 0.07911]
Incremental R2 (full-covars): 0.07099
PGS R2 (no covariates): 0.07181 [0.06563, 0.07799]		 age, sex, UKB array type, Genotype PCs —
PPM007298 PSS006909|
South Asian Ancestry|
7,258 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: AST to ALT ratio — — R²: 0.04818 [0.03893, 0.05743]
Incremental R2 (full-covars): 0.04091
PGS R2 (no covariates): 0.04147 [0.03283, 0.05012]		 age, sex, UKB array type, Genotype PCs —
PPM007299 PSS006910|
European Ancestry|
63,540 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: AST to ALT ratio — — R²: 0.07733 [0.07346, 0.08121]
Incremental R2 (full-covars): 0.07732
PGS R2 (no covariates): 0.07746 [0.07358, 0.08133]		 age, sex, UKB array type, Genotype PCs —

Evaluated Samples

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
PSS006908 — — 23,476 individuals — European non-white British ancestry UKB —
PSS006909 — — 7,258 individuals — South Asian — UKB —
PSS000617 — — 5,981 individuals — African unspecified — UKB —
PSS000618 — — 1,069 individuals — East Asian — UKB —
PSS000619 — — 23,478 individuals — European Non-British White UKB —
PSS000620 — — 7,309 individuals — South Asian — UKB —
PSS000621 — — 63,545 individuals — European
(British)		 — UKB —
PSS006910 — — 63,540 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS006906 — — 5,981 individuals — African unspecified — UKB —
PSS006907 — — 1,564 individuals — East Asian — UKB —