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COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data

Reconstructing the history of somatic DNA alterations can help understand the evolution of a tumor and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, most existing phylogeneti...

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Autores principales: Sollier, Etienne, Kuipers, Jack, Takahashi, Koichi, Beerenwinkel, Niko, Jahn, Katharina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10427627/
https://www.ncbi.nlm.nih.gov/pubmed/37582954
http://dx.doi.org/10.1038/s41467-023-40378-8
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author Sollier, Etienne
Kuipers, Jack
Takahashi, Koichi
Beerenwinkel, Niko
Jahn, Katharina
author_facet Sollier, Etienne
Kuipers, Jack
Takahashi, Koichi
Beerenwinkel, Niko
Jahn, Katharina
author_sort Sollier, Etienne
collection PubMed
description Reconstructing the history of somatic DNA alterations can help understand the evolution of a tumor and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, most existing phylogenetic methods for scDNAseq data are designed either for single nucleotide variants (SNVs) or for large copy number alterations (CNAs), or are not applicable to targeted sequencing. Here, we develop COMPASS, a computational method for inferring the joint phylogeny of SNVs and CNAs from targeted scDNAseq data. We evaluate COMPASS on simulated data and apply it to several datasets including a cohort of 123 patients with acute myeloid leukemia. COMPASS detected clonal CNAs that could be orthogonally validated with bulk data, in addition to subclonal ones that require single-cell resolution, some of which point toward convergent evolution.
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spelling pubmed-104276272023-08-17 COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data Sollier, Etienne Kuipers, Jack Takahashi, Koichi Beerenwinkel, Niko Jahn, Katharina Nat Commun Article Reconstructing the history of somatic DNA alterations can help understand the evolution of a tumor and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, most existing phylogenetic methods for scDNAseq data are designed either for single nucleotide variants (SNVs) or for large copy number alterations (CNAs), or are not applicable to targeted sequencing. Here, we develop COMPASS, a computational method for inferring the joint phylogeny of SNVs and CNAs from targeted scDNAseq data. We evaluate COMPASS on simulated data and apply it to several datasets including a cohort of 123 patients with acute myeloid leukemia. COMPASS detected clonal CNAs that could be orthogonally validated with bulk data, in addition to subclonal ones that require single-cell resolution, some of which point toward convergent evolution. Nature Publishing Group UK 2023-08-15 /pmc/articles/PMC10427627/ /pubmed/37582954 http://dx.doi.org/10.1038/s41467-023-40378-8 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Sollier, Etienne
Kuipers, Jack
Takahashi, Koichi
Beerenwinkel, Niko
Jahn, Katharina
COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data
title COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data
title_full COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data
title_fullStr COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data
title_full_unstemmed COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data
title_short COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data
title_sort compass: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10427627/
https://www.ncbi.nlm.nih.gov/pubmed/37582954
http://dx.doi.org/10.1038/s41467-023-40378-8
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