Allele-specific multi-sample copy number segmentation in ASCAT.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
27 07 2021
27 07 2021
Historique:
received:
09
09
2019
revised:
08
04
2020
accepted:
19
05
2020
pubmed:
26
5
2020
medline:
10
8
2021
entrez:
26
5
2020
Statut:
ppublish
Résumé
Allele-specific copy number alterations are commonly used to trace the evolution of tumours. A key step of the analysis is to segment genomic data into regions of constant copy number. For precise phylogenetic inference, breakpoints shared between samples need to be aligned to each other. Here, we present asmultipcf, an algorithm for allele-specific segmentation of multiple samples that infers private and shared segment boundaries of phylogenetically related samples. The output of this algorithm can directly be used for allele-specific copy number calling using ASCAT. asmultipcf is available as part of the ASCAT R package (version ≥2.5) from github.com/Crick-CancerGenomics/ascat/.
Identifiants
pubmed: 32449758
pii: 5843787
doi: 10.1093/bioinformatics/btaa538
pmc: PMC8317109
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1909-1911Subventions
Organisme : Winton Group Leader
Organisme : Wellcome Trust
ID : FC001202
Pays : United Kingdom
Organisme : Arthritis Research UK
ID : FC001202
Pays : United Kingdom
Organisme : Cancer Research UK Cambridge Institute
ID : C14303/A17197
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Royal Society Wolfson Research Merit
Organisme : Medical Research Council
ID : FC001202
Pays : United Kingdom
Organisme : Cancer Research UK
ID : FC001202
Pays : United Kingdom
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press.
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