Polygenic Score (PGS) ID: PGS000673

Predicted Trait
Reported Trait Aspartate aminotransferase [U/L]
Mapped Trait(s) aspartate aminotransferase measurement (EFO_0004736)
Released in PGS Catalog: Feb. 3, 2021
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Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.Aspartate_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 12,829
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
PPM001401 PSS000647|
African Ancestry|
5,982 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Aspartate aminotransferase [U/L] — — R²: 0.10334
Spearman's ρ: 0.103		 Age, sex, PCs(1-40) —
PPM001436 PSS000648|
East Asian Ancestry|
1,070 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Aspartate aminotransferase [U/L] — — R²: 0.08343
Spearman's ρ: 0.191		 Age, sex, PCs(1-40) —
PPM001506 PSS000650|
South Asian Ancestry|
7,313 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Aspartate aminotransferase [U/L] — — R²: 0.11262
Spearman's ρ: 0.243		 Age, sex, PCs(1-40) —
PPM001541 PSS000651|
European Ancestry|
63,562 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Aspartate aminotransferase [U/L] — — R²: 0.1493
Spearman's ρ: 0.285		 Age, sex, PCs(1-40) —
PPM001471 PSS000649|
European Ancestry|
23,483 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Aspartate aminotransferase [U/L] — — R²: 0.1564
Spearman's ρ: 0.278		 Age, sex, PCs(1-40) —
PPM007290 PSS007106|
African Ancestry|
6,063 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Aspartate aminotransferase — — R²: 0.03615 [0.02724, 0.04506]
Incremental R2 (full-covars): 0.00048
PGS R2 (no covariates): 0.0043 [0.00113, 0.00747]		 age, sex, UKB array type, Genotype PCs —
PPM007291 PSS007107|
East Asian Ancestry|
1,604 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Aspartate aminotransferase — — R²: 0.01565 [0.00398, 0.02731]
Incremental R2 (full-covars): 0.00093
PGS R2 (no covariates): 0.01452 [0.00327, 0.02577]		 age, sex, UKB array type, Genotype PCs —
PPM007292 PSS007108|
European Ancestry|
23,673 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Aspartate aminotransferase — — R²: 0.04146 [0.03661, 0.04631]
Incremental R2 (full-covars): 0.00197
PGS R2 (no covariates): 0.02948 [0.02534, 0.03362]		 age, sex, UKB array type, Genotype PCs —
PPM007293 PSS007109|
South Asian Ancestry|
7,402 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Aspartate aminotransferase — — R²: 0.03584 [0.02776, 0.04393]
Incremental R2 (full-covars): 0.00195
PGS R2 (no covariates): 0.02928 [0.02192, 0.03663]		 age, sex, UKB array type, Genotype PCs —
PPM007294 PSS007110|
European Ancestry|
64,238 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Aspartate aminotransferase — — R²: 0.03244 [0.02981, 0.03507]
Incremental R2 (full-covars): 0.00218
PGS R2 (no covariates): 0.03087 [0.0283, 0.03344]		 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
PSS000647 — — 5,982 individuals — African unspecified — UKB —
PSS000648 — — 1,070 individuals — East Asian — UKB —
PSS000649 — — 23,483 individuals — European Non-British White UKB —
PSS000650 — — 7,313 individuals — South Asian — UKB —
PSS000651 — — 63,562 individuals — European
(British)		 — UKB —
PSS007106 — — 6,063 individuals — African unspecified — UKB —
PSS007107 — — 1,604 individuals — East Asian — UKB —
PSS007108 — — 23,673 individuals — European non-white British ancestry UKB —
PSS007109 — — 7,402 individuals — South Asian — UKB —
PSS007110 — — 64,238 individuals — European white British ancestry UKB Testing cohort (heldout set)