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Improving cellular phylogenies through the integrated use of mutation order and optimality principles

The study of tumor evolution is being revolutionalized by single-cell sequencing technologies that survey the somatic variation of cancer cells. In these endeavors, reliable inference of the evolutionary relationship of single cells is a key step. However, single-cell sequences contain many errors a...

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Autores principales: Miura, Sayaka, Dolker, Tenzin, Sanderford, Maxwell, Kumar, Sudhir
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10432911/
https://www.ncbi.nlm.nih.gov/pubmed/37602230
http://dx.doi.org/10.1016/j.csbj.2023.07.018
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author Miura, Sayaka
Dolker, Tenzin
Sanderford, Maxwell
Kumar, Sudhir
author_facet Miura, Sayaka
Dolker, Tenzin
Sanderford, Maxwell
Kumar, Sudhir
author_sort Miura, Sayaka
collection PubMed
description The study of tumor evolution is being revolutionalized by single-cell sequencing technologies that survey the somatic variation of cancer cells. In these endeavors, reliable inference of the evolutionary relationship of single cells is a key step. However, single-cell sequences contain many errors and missing bases, which necessitate advancing standard molecular phylogenetics approaches for applications in analyzing these datasets. We have developed a computational approach that integratively applies standard phylogenetic optimality principles and patterns of co-occurrence of sequence variations to produce more expansive and accurate cellular phylogenies from single-cell sequence datasets. We found the new approach to also perform well for CRISPR/Cas9 genome editing datasets, suggesting that it can be useful for various applications. We apply the new approach to some empirical datasets to showcase its use for reconstructing recurrent mutations and mutational reversals as well as for phylodynamics analysis to infer metastatic cell migrations between tumors.
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spelling pubmed-104329112023-08-18 Improving cellular phylogenies through the integrated use of mutation order and optimality principles Miura, Sayaka Dolker, Tenzin Sanderford, Maxwell Kumar, Sudhir Comput Struct Biotechnol J Research Article The study of tumor evolution is being revolutionalized by single-cell sequencing technologies that survey the somatic variation of cancer cells. In these endeavors, reliable inference of the evolutionary relationship of single cells is a key step. However, single-cell sequences contain many errors and missing bases, which necessitate advancing standard molecular phylogenetics approaches for applications in analyzing these datasets. We have developed a computational approach that integratively applies standard phylogenetic optimality principles and patterns of co-occurrence of sequence variations to produce more expansive and accurate cellular phylogenies from single-cell sequence datasets. We found the new approach to also perform well for CRISPR/Cas9 genome editing datasets, suggesting that it can be useful for various applications. We apply the new approach to some empirical datasets to showcase its use for reconstructing recurrent mutations and mutational reversals as well as for phylodynamics analysis to infer metastatic cell migrations between tumors. Research Network of Computational and Structural Biotechnology 2023-08-02 /pmc/articles/PMC10432911/ /pubmed/37602230 http://dx.doi.org/10.1016/j.csbj.2023.07.018 Text en © 2023 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Research Article
Miura, Sayaka
Dolker, Tenzin
Sanderford, Maxwell
Kumar, Sudhir
Improving cellular phylogenies through the integrated use of mutation order and optimality principles
title Improving cellular phylogenies through the integrated use of mutation order and optimality principles
title_full Improving cellular phylogenies through the integrated use of mutation order and optimality principles
title_fullStr Improving cellular phylogenies through the integrated use of mutation order and optimality principles
title_full_unstemmed Improving cellular phylogenies through the integrated use of mutation order and optimality principles
title_short Improving cellular phylogenies through the integrated use of mutation order and optimality principles
title_sort improving cellular phylogenies through the integrated use of mutation order and optimality principles
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10432911/
https://www.ncbi.nlm.nih.gov/pubmed/37602230
http://dx.doi.org/10.1016/j.csbj.2023.07.018
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