Allele-specific multi-sample copy number segmentation in ASCAT

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...

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Detalles Bibliográficos
Autores principales: Ross, Edith M., Haase, Kerstin, Van Loo, Peter, Markowetz, Florian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317109/
https://www.ncbi.nlm.nih.gov/pubmed/32449758
http://dx.doi.org/10.1093/bioinformatics/btaa538
Descripción
Sumario: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 [Formula: see text]) from github.com/Crick-CancerGenomics/ascat/.

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