A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones

Abstract Background All diseases containing genetic material undergo genetic evolution and give rise to heterogeneity including cancer and infection. Although these illnesses are biologically very different, the ability for phylogenetic retrodiction based on the genomic reads is common between them...

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Autores principales:	Filippo Utro, Chaya Levovitz, Kahn Rhrissorrakrai, Laxmi Parida
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Tumor evolution Clonal evolution Phylogeny COVID-19 Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/139dda9521494055830a756d94608682
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spelling	oai:doaj.org-article:139dda9521494055830a756d946086822021-11-21T12:26:22ZA common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones10.1186/s12864-021-07660-91471-2164https://doaj.org/article/139dda9521494055830a756d946086822021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-07660-9https://doaj.org/toc/1471-2164Abstract Background All diseases containing genetic material undergo genetic evolution and give rise to heterogeneity including cancer and infection. Although these illnesses are biologically very different, the ability for phylogenetic retrodiction based on the genomic reads is common between them and thus tree-based principles and assumptions are shared. Just as the different frequencies of tumor genomic variants presupposes the existence of multiple tumor clones and provides a handle to computationally infer them, we postulate that the different variant frequencies in viral reads offers the means to infer multiple co-infecting sublineages. Results We present a common methodological framework to infer the phylogenomics from genomic data, be it reads of SARS-CoV-2 of multiple COVID-19 patients or bulk DNAseq of the tumor of a cancer patient. We describe the Concerti computational framework for inferring phylogenies in each of the two scenarios.To demonstrate the accuracy of the method, we reproduce some known results in both scenarios. We also make some additional discoveries. Conclusions Concerti successfully extracts and integrates information from multi-point samples, enabling the discovery of clinically plausible phylogenetic trees that capture the heterogeneity known to exist both spatially and temporally. These models can have direct therapeutic implications by highlighting “birth” of clones that may harbor resistance mechanisms to treatment, “death” of subclones with drug targets, and acquisition of functionally pertinent mutations in clones that may have seemed clinically irrelevant. Specifically in this paper we uncover new potential parallel mutations in the evolution of the SARS-CoV-2 virus. In the context of cancer, we identify new clones harboring resistant mutations to therapy.Filippo UtroChaya LevovitzKahn RhrissorrakraiLaxmi ParidaBMCarticleTumor evolutionClonal evolutionPhylogenyCOVID-19BiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss S5, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Tumor evolution Clonal evolution Phylogeny COVID-19 Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Tumor evolution Clonal evolution Phylogeny COVID-19 Biotechnology TP248.13-248.65 Genetics QH426-470 Filippo Utro Chaya Levovitz Kahn Rhrissorrakrai Laxmi Parida A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones
description	Abstract Background All diseases containing genetic material undergo genetic evolution and give rise to heterogeneity including cancer and infection. Although these illnesses are biologically very different, the ability for phylogenetic retrodiction based on the genomic reads is common between them and thus tree-based principles and assumptions are shared. Just as the different frequencies of tumor genomic variants presupposes the existence of multiple tumor clones and provides a handle to computationally infer them, we postulate that the different variant frequencies in viral reads offers the means to infer multiple co-infecting sublineages. Results We present a common methodological framework to infer the phylogenomics from genomic data, be it reads of SARS-CoV-2 of multiple COVID-19 patients or bulk DNAseq of the tumor of a cancer patient. We describe the Concerti computational framework for inferring phylogenies in each of the two scenarios.To demonstrate the accuracy of the method, we reproduce some known results in both scenarios. We also make some additional discoveries. Conclusions Concerti successfully extracts and integrates information from multi-point samples, enabling the discovery of clinically plausible phylogenetic trees that capture the heterogeneity known to exist both spatially and temporally. These models can have direct therapeutic implications by highlighting “birth” of clones that may harbor resistance mechanisms to treatment, “death” of subclones with drug targets, and acquisition of functionally pertinent mutations in clones that may have seemed clinically irrelevant. Specifically in this paper we uncover new potential parallel mutations in the evolution of the SARS-CoV-2 virus. In the context of cancer, we identify new clones harboring resistant mutations to therapy.
format	article
author	Filippo Utro Chaya Levovitz Kahn Rhrissorrakrai Laxmi Parida
author_facet	Filippo Utro Chaya Levovitz Kahn Rhrissorrakrai Laxmi Parida
author_sort	Filippo Utro
title	A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones
title_short	A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones
title_full	A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones
title_fullStr	A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones
title_full_unstemmed	A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones
title_sort	common methodological phylogenomics framework for intra-patient heteroplasmies to infer sars-cov-2 sublineages and tumor clones
publisher	BMC
publishDate	2021
url	https://doaj.org/article/139dda9521494055830a756d94608682
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A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones

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