Allele-specific multi-sample copy number segmentation in ASCAT

Edith M. Ross; Kerstin Haase; Peter Van Loo; Florian Markowetz

doi:10.1093/bioinformatics/btaa538

Allele-specific multi-sample copy number segmentation in ASCAT

Edith M. Ross, Kerstin Haase, Peter Van Loo, Florian Markowetz

Research output: Contribution to journal › Article › peer-review

12 Scopus citations

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/.

Original language	English (US)
Pages (from-to)	1909-1911
Number of pages	3
Journal	Bioinformatics
Volume	37
Issue number	13
DOIs	https://doi.org/10.1093/bioinformatics/btaa538
State	Published - Jul 1 2021
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btaa538

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title = "Allele-specific multi-sample copy number segmentation in ASCAT",

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/.",

author = "Ross, {Edith M.} and Kerstin Haase and {Van Loo}, Peter and Florian Markowetz",

note = "Funding Information: This research was supported by the Cancer Research UK Cambridge Institute with core grant C14303/A17197 and the Francis Crick Institute with core funding from Cancer Research UK [FC001202], the UK Medical Research Council [FC001202] and the Wellcome Trust [FC001202]. P.V.L. is a Winton Group Leader, F.M. is a Royal Society Wolfson Research Merit award holder. Publisher Copyright: {\textcopyright} 2021 Oxford University Press. All rights reserved.",

year = "2021",

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doi = "10.1093/bioinformatics/btaa538",

language = "English (US)",

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pages = "1909--1911",

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T1 - Allele-specific multi-sample copy number segmentation in ASCAT

AU - Ross, Edith M.

AU - Haase, Kerstin

AU - Van Loo, Peter

AU - Markowetz, Florian

N1 - Funding Information: This research was supported by the Cancer Research UK Cambridge Institute with core grant C14303/A17197 and the Francis Crick Institute with core funding from Cancer Research UK [FC001202], the UK Medical Research Council [FC001202] and the Wellcome Trust [FC001202]. P.V.L. is a Winton Group Leader, F.M. is a Royal Society Wolfson Research Merit award holder. Publisher Copyright: © 2021 Oxford University Press. All rights reserved.

PY - 2021/7/1

Y1 - 2021/7/1

N2 - 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/.

AB - 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/.

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JF - Bioinformatics

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Allele-specific multi-sample copy number segmentation in ASCAT

Abstract

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