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Allele-specific multi-sample copy number segmentation in ASCAT.

Accepted version
Peer-reviewed

Type

Article

Change log

Authors

Ross, Edith M 
Haase, Kerstin 
Van Loo, Peter 

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

Volume Title

37

Publisher

Oxford University Press (OUP)

Rights

All rights reserved
Sponsorship
Cancer Research UK (C14303/A17197)
Cancer Research UK (19274)
Cancer Research UK (28290)