Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm

Pairtree is a clone tree reconstruction algorithm that uses somatic point mutations to build clone trees describing the evolutionary history of individual cancers. Using the Pairtree software package, we describe steps to preprocess somatic mutation data, cluster mutations into subclones, search for...

Descripción completa

Detalles Bibliográficos
Autores principales: Kulman, Ethan, Wintersinger, Jeff, Morris, Quaid
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9494285/
https://www.ncbi.nlm.nih.gov/pubmed/36129821
http://dx.doi.org/10.1016/j.xpro.2022.101706
_version_ 1784793778939232256
author Kulman, Ethan
Wintersinger, Jeff
Morris, Quaid
author_facet Kulman, Ethan
Wintersinger, Jeff
Morris, Quaid
author_sort Kulman, Ethan
collection PubMed
description Pairtree is a clone tree reconstruction algorithm that uses somatic point mutations to build clone trees describing the evolutionary history of individual cancers. Using the Pairtree software package, we describe steps to preprocess somatic mutation data, cluster mutations into subclones, search for clone trees, and visualize clone trees. Pairtree builds clone trees using up to 100 samples from a single cancer with at least 30 subclonal populations. For complete details on the use and execution of this protocol, please refer to Wintersinger et al. (2022).
format Online
Article
Text
id pubmed-9494285
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Elsevier
record_format MEDLINE/PubMed
spelling pubmed-94942852022-09-23 Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm Kulman, Ethan Wintersinger, Jeff Morris, Quaid STAR Protoc Protocol Pairtree is a clone tree reconstruction algorithm that uses somatic point mutations to build clone trees describing the evolutionary history of individual cancers. Using the Pairtree software package, we describe steps to preprocess somatic mutation data, cluster mutations into subclones, search for clone trees, and visualize clone trees. Pairtree builds clone trees using up to 100 samples from a single cancer with at least 30 subclonal populations. For complete details on the use and execution of this protocol, please refer to Wintersinger et al. (2022). Elsevier 2022-09-20 /pmc/articles/PMC9494285/ /pubmed/36129821 http://dx.doi.org/10.1016/j.xpro.2022.101706 Text en © 2022 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 Protocol
Kulman, Ethan
Wintersinger, Jeff
Morris, Quaid
Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm
title Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm
title_full Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm
title_fullStr Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm
title_full_unstemmed Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm
title_short Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm
title_sort reconstructing cancer phylogenies using pairtree, a clone tree reconstruction algorithm
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9494285/
https://www.ncbi.nlm.nih.gov/pubmed/36129821
http://dx.doi.org/10.1016/j.xpro.2022.101706
work_keys_str_mv AT kulmanethan reconstructingcancerphylogeniesusingpairtreeaclonetreereconstructionalgorithm
AT wintersingerjeff reconstructingcancerphylogeniesusingpairtreeaclonetreereconstructionalgorithm
AT morrisquaid reconstructingcancerphylogeniesusingpairtreeaclonetreereconstructionalgorithm

Ejemplares similares