Polygenic Score (PGS) ID: PGS002158

Predicted Trait
Reported Trait Alanine aminotransferase
Mapped Trait(s) serum alanine aminotransferase measurement (EFO_0004735)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_log_ALT
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 774,274
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM012112 PSS009201|
European Ancestry|
3,950 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alanine aminotransferase — — Partial Correlation (partial-r): 0.2355 [0.2058, 0.2648] sex, age, birth date, deprivation index, 16 PCs —
PPM012111 PSS009427|
European Ancestry|
18,995 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alanine aminotransferase — — Partial Correlation (partial-r): 0.2622 [0.2489, 0.2754] sex, age, birth date, deprivation index, 16 PCs —
PPM012113 PSS008755|
European Ancestry|
6,321 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alanine aminotransferase — — Partial Correlation (partial-r): 0.2258 [0.2022, 0.2491] sex, age, birth date, deprivation index, 16 PCs —
PPM012114 PSS008529|
Greater Middle Eastern Ancestry|
1,123 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alanine aminotransferase — — Partial Correlation (partial-r): 0.1997 [0.1423, 0.2557] sex, age, birth date, deprivation index, 16 PCs —
PPM012115 PSS008307|
South Asian Ancestry|
5,992 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alanine aminotransferase — — Partial Correlation (partial-r): 0.2086 [0.1842, 0.2328] sex, age, birth date, deprivation index, 16 PCs —
PPM012116 PSS008084|
East Asian Ancestry|
1,716 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alanine aminotransferase — — Partial Correlation (partial-r): 0.194 [0.1478, 0.2394] sex, age, birth date, deprivation index, 16 PCs —
PPM012117 PSS007871|
African Ancestry|
2,345 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alanine aminotransferase — — Partial Correlation (partial-r): 0.1063 [0.0659, 0.1463] sex, age, birth date, deprivation index, 16 PCs —
PPM012118 PSS008975|
African Ancestry|
3,656 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Alanine aminotransferase — — Partial Correlation (partial-r): 0.088 [0.0557, 0.1202] sex, age, birth date, deprivation index, 16 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
PSS008975 — — 3,656 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009201 — — 3,950 individuals — European Poland (NE Europe) UKB —
PSS008529 — — 1,123 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008755 — — 6,321 individuals — European Italy (South Europe) UKB —
PSS008307 — — 5,992 individuals — South Asian India (South Asia) UKB —
PSS009427 — — 18,995 individuals — European UK (+ Ireland) UKB —
PSS008084 — — 1,716 individuals — East Asian China (East Asia) UKB —
PSS007871 — — 2,345 individuals — African American or Afro-Caribbean Carribean UKB —