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DEVOLUTION—A method for phylogenetic reconstruction of aneuploid cancers based on multiregional genotyping data

Andersson, Natalie LU orcid ; Chattopadhyay, Subhayan LU orcid ; Valind, Anders LU orcid ; Karlsson, Jenny LU and Gisselsson Nord, David LU (2021) In Communications Biology 4.
Abstract
Phylogenetic reconstruction of cancer cell populations remains challenging. There is a particular lack of tools that deconvolve clones based on copy number aberration analyses of multiple tumor biopsies separated in time and space from the same patient. This has hampered investigations of tumors rich in aneuploidy but few point mutations, as in many childhood cancers and high-risk adult cancer. Here, we present DEVOLUTION, an algorithm for subclonal deconvolution followed by phylogenetic reconstruction from bulk genotyping data. It integrates copy number and sequencing information across multiple tumor regions throughout the inference process, provided that the mutated clone fraction for each mutation is known. We validate DEVOLUTION on... (More)
Phylogenetic reconstruction of cancer cell populations remains challenging. There is a particular lack of tools that deconvolve clones based on copy number aberration analyses of multiple tumor biopsies separated in time and space from the same patient. This has hampered investigations of tumors rich in aneuploidy but few point mutations, as in many childhood cancers and high-risk adult cancer. Here, we present DEVOLUTION, an algorithm for subclonal deconvolution followed by phylogenetic reconstruction from bulk genotyping data. It integrates copy number and sequencing information across multiple tumor regions throughout the inference process, provided that the mutated clone fraction for each mutation is known. We validate DEVOLUTION on data from 56 pediatric tumors comprising 253 tumor biopsies and show a robust performance on simulations of bulk genotyping data. We also benchmark DEVOLUTION to similar bioinformatic tools using an external dataset. DEVOLUTION holds the potential to facilitate insights into the development, progression, and response to treatment, particularly in tumors with high burden of chromosomal copy number alterations. (Less)
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author
; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Communications Biology
volume
4
article number
1103
publisher
Nature Publishing Group
external identifiers
  • scopus:85115428336
  • pmid:34545199
ISSN
2399-3642
DOI
10.1038/s42003-021-02637-6
language
English
LU publication?
yes
id
10482969-8e9b-4c08-b5f9-778e1e3e4899
date added to LUP
2021-09-21 09:08:47
date last changed
2024-04-20 11:36:38
@article{10482969-8e9b-4c08-b5f9-778e1e3e4899,
  abstract     = {{Phylogenetic reconstruction of cancer cell populations remains challenging. There is a particular lack of tools that deconvolve clones based on copy number aberration analyses of multiple tumor biopsies separated in time and space from the same patient. This has hampered investigations of tumors rich in aneuploidy but few point mutations, as in many childhood cancers and high-risk adult cancer. Here, we present DEVOLUTION, an algorithm for subclonal deconvolution followed by phylogenetic reconstruction from bulk genotyping data. It integrates copy number and sequencing information across multiple tumor regions throughout the inference process, provided that the mutated clone fraction for each mutation is known. We validate DEVOLUTION on data from 56 pediatric tumors comprising 253 tumor biopsies and show a robust performance on simulations of bulk genotyping data. We also benchmark DEVOLUTION to similar bioinformatic tools using an external dataset. DEVOLUTION holds the potential to facilitate insights into the development, progression, and response to treatment, particularly in tumors with high burden of chromosomal copy number alterations.}},
  author       = {{Andersson, Natalie and Chattopadhyay, Subhayan and Valind, Anders and Karlsson, Jenny and Gisselsson Nord, David}},
  issn         = {{2399-3642}},
  language     = {{eng}},
  month        = {{09}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Communications Biology}},
  title        = {{DEVOLUTION—A method for phylogenetic reconstruction of aneuploid cancers based on multiregional genotyping data}},
  url          = {{http://dx.doi.org/10.1038/s42003-021-02637-6}},
  doi          = {{10.1038/s42003-021-02637-6}},
  volume       = {{4}},
  year         = {{2021}},
}