Polygenic Score (PGS) ID: PGS001940

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-PLR_log_ALT
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 51,849
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM010396 PSS009201|
European Ancestry|
3,950 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.2328 [0.203, 0.2622] sex, age, birth date, deprivation index, 16 PCs
PPM010397 PSS008755|
European Ancestry|
6,321 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.2248 [0.2012, 0.2481] sex, age, birth date, deprivation index, 16 PCs
PPM010399 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): 0.2205 [0.1963, 0.2445] sex, age, birth date, deprivation index, 16 PCs
PPM010400 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): 0.1841 [0.1377, 0.2297] sex, age, birth date, deprivation index, 16 PCs
PPM010401 PSS007871|
African Ancestry|
2,345 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.1008 [0.0604, 0.1409] sex, age, birth date, deprivation index, 16 PCs
PPM010402 PSS008975|
African Ancestry|
3,656 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.1054 [0.0731, 0.1374] sex, age, birth date, deprivation index, 16 PCs
PPM010395 PSS009427|
European Ancestry|
18,995 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.2633 [0.25, 0.2765] sex, age, birth date, deprivation index, 16 PCs
PPM010398 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): 0.1871 [0.1295, 0.2435] 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
PSS008307 5,992 individuals South Asian India (South Asia) UKB
PSS008084 1,716 individuals East Asian China (East Asia) UKB
PSS008755 6,321 individuals European Italy (South Europe) UKB
PSS009427 18,995 individuals European UK (+ Ireland) UKB
PSS007871 2,345 individuals African American or Afro-Caribbean Carribean UKB