Methods for copy number aberration detection from single-cell DNA-sequencing data

Copy number aberrations (CNAs), which are pathogenic copy number variations (CNVs), play an important role in the initiation and progression of cancer. Single-cell DNA-sequencing (scDNAseq) technologies produce data that is ideal for inferring CNAs. In this review, we review eight methods that have...

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Autores principales: Mallory, Xian F., Edrisi, Mohammadamin, Navin, Nicholas, Nakhleh, Luay
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Review
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7433197/
https://www.ncbi.nlm.nih.gov/pubmed/32807205
http://dx.doi.org/10.1186/s13059-020-02119-8
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author Mallory, Xian F.
Edrisi, Mohammadamin
Navin, Nicholas
Nakhleh, Luay
author_facet Mallory, Xian F.
Edrisi, Mohammadamin
Navin, Nicholas
Nakhleh, Luay
author_sort Mallory, Xian F.
collection PubMed
description Copy number aberrations (CNAs), which are pathogenic copy number variations (CNVs), play an important role in the initiation and progression of cancer. Single-cell DNA-sequencing (scDNAseq) technologies produce data that is ideal for inferring CNAs. In this review, we review eight methods that have been developed for detecting CNAs in scDNAseq data, and categorize them according to the steps of a seven-step pipeline that they employ. Furthermore, we review models and methods for evolutionary analyses of CNAs from scDNAseq data and highlight advances and future research directions for computational methods for CNA detection from scDNAseq data.
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spelling pubmed-74331972020-08-19 Methods for copy number aberration detection from single-cell DNA-sequencing data Mallory, Xian F. Edrisi, Mohammadamin Navin, Nicholas Nakhleh, Luay Genome Biol Review Copy number aberrations (CNAs), which are pathogenic copy number variations (CNVs), play an important role in the initiation and progression of cancer. Single-cell DNA-sequencing (scDNAseq) technologies produce data that is ideal for inferring CNAs. In this review, we review eight methods that have been developed for detecting CNAs in scDNAseq data, and categorize them according to the steps of a seven-step pipeline that they employ. Furthermore, we review models and methods for evolutionary analyses of CNAs from scDNAseq data and highlight advances and future research directions for computational methods for CNA detection from scDNAseq data. BioMed Central 2020-08-17 /pmc/articles/PMC7433197/ /pubmed/32807205 http://dx.doi.org/10.1186/s13059-020-02119-8 Text en © The Author(s) 2020 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Review
Mallory, Xian F.
Edrisi, Mohammadamin
Navin, Nicholas
Nakhleh, Luay
Methods for copy number aberration detection from single-cell DNA-sequencing data
title Methods for copy number aberration detection from single-cell DNA-sequencing data
title_full Methods for copy number aberration detection from single-cell DNA-sequencing data
title_fullStr Methods for copy number aberration detection from single-cell DNA-sequencing data
title_full_unstemmed Methods for copy number aberration detection from single-cell DNA-sequencing data
title_short Methods for copy number aberration detection from single-cell DNA-sequencing data
title_sort methods for copy number aberration detection from single-cell dna-sequencing data
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7433197/
https://www.ncbi.nlm.nih.gov/pubmed/32807205
http://dx.doi.org/10.1186/s13059-020-02119-8
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