Allele-specific multi-sample copy number segmentation in ASCAT.
Accepted version
Peer-reviewed
Repository URI
Repository DOI
Change log
Authors
Ross, Edith M
Haase, Kerstin
Van Loo, Peter
Markowetz, Florian https://orcid.org/0000-0002-2784-5308
Abstract
MOTIVATION: 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. RESULTS: 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. AVAILABILITY AND IMPLEMENTATION: asmultipcf is available as part of the ASCAT R package (version ≥2.5) from github.com/Crick-CancerGenomics/ascat/.
Description
Keywords
Algorithms, Alleles, DNA Copy Number Variations, Humans, Neoplasms, Phylogeny
Journal Title
Bioinformatics
Conference Name
Journal ISSN
1367-4803
1367-4811
1367-4811
Volume Title
37
Publisher
Oxford University Press (OUP)
Publisher DOI
Rights
All rights reserved
Sponsorship
Cancer Research UK (C14303/A17197)
Cancer Research UK (19274)
Cancer Research UK (28290)
Cancer Research UK (19274)
Cancer Research UK (28290)