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Inferring the heritability of bacterial traits in the era of machine learning
: Quantification of heritability is a fundamental desideratum in genetics, which allows an assessment of the contribution of additive genetic variation to the variability of a trait of interest. The traditional computational approaches for assessing the heritability of a trait have been developed i...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10039732/ https://www.ncbi.nlm.nih.gov/pubmed/36974068 http://dx.doi.org/10.1093/bioadv/vbad027 |
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author | Mai, T Tien Lees, John A Gladstone, Rebecca A Corander, Jukka |
author_facet | Mai, T Tien Lees, John A Gladstone, Rebecca A Corander, Jukka |
author_sort | Mai, T Tien |
collection | PubMed |
description | : Quantification of heritability is a fundamental desideratum in genetics, which allows an assessment of the contribution of additive genetic variation to the variability of a trait of interest. The traditional computational approaches for assessing the heritability of a trait have been developed in the field of quantitative genetics. However, the rise of modern population genomics with large sample sizes has led to the development of several new machine learning-based approaches to inferring heritability. In this article, we systematically summarize recent advances in machine learning which can be used to infer heritability. We focus on an application of these methods to bacterial genomes, where heritability plays a key role in understanding phenotypes such as antibiotic resistance and virulence, which are particularly important due to the rising frequency of antimicrobial resistance. By designing a heritability model incorporating realistic patterns of genome-wide linkage disequilibrium for a frequently recombining bacterial pathogen, we test the performance of a wide spectrum of different inference methods, including also GCTA. In addition to the synthetic data benchmark, we present a comparison of the methods for antibiotic resistance traits for multiple bacterial pathogens. Insights from the benchmarking and real data analyses indicate a highly variable performance of the different methods and suggest that heritability inference would likely benefit from tailoring of the methods to the specific genetic architecture of the target organism. AVAILABILITY AND IMPLEMENTATION: The R codes and data used in the numerical experiments are available at: https://github.com/tienmt/her_MLs. |
format | Online Article Text |
id | pubmed-10039732 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-100397322023-03-26 Inferring the heritability of bacterial traits in the era of machine learning Mai, T Tien Lees, John A Gladstone, Rebecca A Corander, Jukka Bioinform Adv Review : Quantification of heritability is a fundamental desideratum in genetics, which allows an assessment of the contribution of additive genetic variation to the variability of a trait of interest. The traditional computational approaches for assessing the heritability of a trait have been developed in the field of quantitative genetics. However, the rise of modern population genomics with large sample sizes has led to the development of several new machine learning-based approaches to inferring heritability. In this article, we systematically summarize recent advances in machine learning which can be used to infer heritability. We focus on an application of these methods to bacterial genomes, where heritability plays a key role in understanding phenotypes such as antibiotic resistance and virulence, which are particularly important due to the rising frequency of antimicrobial resistance. By designing a heritability model incorporating realistic patterns of genome-wide linkage disequilibrium for a frequently recombining bacterial pathogen, we test the performance of a wide spectrum of different inference methods, including also GCTA. In addition to the synthetic data benchmark, we present a comparison of the methods for antibiotic resistance traits for multiple bacterial pathogens. Insights from the benchmarking and real data analyses indicate a highly variable performance of the different methods and suggest that heritability inference would likely benefit from tailoring of the methods to the specific genetic architecture of the target organism. AVAILABILITY AND IMPLEMENTATION: The R codes and data used in the numerical experiments are available at: https://github.com/tienmt/her_MLs. Oxford University Press 2023-03-14 /pmc/articles/PMC10039732/ /pubmed/36974068 http://dx.doi.org/10.1093/bioadv/vbad027 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Review Mai, T Tien Lees, John A Gladstone, Rebecca A Corander, Jukka Inferring the heritability of bacterial traits in the era of machine learning |
title | Inferring the heritability of bacterial traits in the era of machine learning |
title_full | Inferring the heritability of bacterial traits in the era of machine learning |
title_fullStr | Inferring the heritability of bacterial traits in the era of machine learning |
title_full_unstemmed | Inferring the heritability of bacterial traits in the era of machine learning |
title_short | Inferring the heritability of bacterial traits in the era of machine learning |
title_sort | inferring the heritability of bacterial traits in the era of machine learning |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10039732/ https://www.ncbi.nlm.nih.gov/pubmed/36974068 http://dx.doi.org/10.1093/bioadv/vbad027 |
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