Polygenic Score (PGS) ID: PGS003523

Predicted Trait
Reported Trait Aspartate aminotransferase level
Mapped Trait(s) aspartate aminotransferase measurement (EFO_0004736)
Released in PGS Catalog: April 12, 2023
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Terms and Licenses
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Score Details

Score Construction
PGS Name cont-decay-log_AST
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
352,236 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 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
— 352,236 individuals,
0.46 % Male samples
 European UKB — Mean = 56.8 years
Sd = 8.0 years		 — white British —

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
PPM017451 PSS010886|
European Ancestry|
19,052 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Aspartate aminotransferase — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM017535 PSS010802|
European Ancestry|
3,922 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Aspartate aminotransferase — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM017703 PSS010550|
Greater Middle Eastern Ancestry|
1,095 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Aspartate aminotransferase — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM017871 PSS010466|
South Asian Ancestry|
5,926 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Aspartate aminotransferase — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM017955 PSS010382|
East Asian Ancestry|
1,692 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Aspartate aminotransferase — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018039 PSS010298|
African Ancestry|
2,318 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Aspartate aminotransferase — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM017619 PSS010634|
European Ancestry|
6,155 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Aspartate aminotransferase — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM017787 PSS010214|
European Ancestry|
2,233 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Aspartate aminotransferase — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM018123 PSS010718|
African Ancestry|
3,611 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Aspartate aminotransferase — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —

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
PSS010718 — — 3,611 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010466 — — 5,926 individuals,
54.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010886 — — 19,052 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010214 — — 2,233 individuals,
45.0 % Male samples
 Mean = 58.1 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010634 — — 6,155 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010382 — — 1,692 individuals,
34.0 % Male samples
 Mean = 52.4 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010802 — — 3,922 individuals,
38.0 % Male samples
 Mean = 54.4 years
Sd = 7.5 years		 European Polish UKB —
PSS010550 — — 1,095 individuals,
60.0 % Male samples
 Mean = 51.9 years
Sd = 7.9 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010298 — — 2,318 individuals,
37.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —