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Type: Journal article
Title: A comparative analysis of algorithms for somatic SNV detection in cancer
Author: Roberts, N.
Kortschak, R.
Parker, W.
Schreiber, A.
Branford, S.
Scott, H.
Glonek, G.
Adelson, D.
Citation: Bioinformatics, 2013; 29(18):2223-2230
Publisher: Oxford Univ Press
Issue Date: 2013
ISSN: 1367-4803
Statement of
Nicola D. Roberts, R. Daniel Kortschak, Wendy T. Parker, Andreas W. Schreiber, Susan Branford, Hamish S. Scott, Garique Glonek and David L. Adelson
Abstract: Motivation: With the advent of relatively affordable high-throughput technologies, DNA sequencing of cancers is now common practice in cancer research projects and will be increasingly used in clinical practice to inform diagnosis and treatment. Somatic (cancer-only) single nucleotide variants (SNVs) are the simplest class of mutation, yet their identification in DNA sequencing data is confounded by germline polymorphisms, tumour heterogeneity and sequencing and analysis errors. Four recently published algorithms for the detection of somatic SNV sites in matched cancer–normal sequencing datasets are VarScan, SomaticSniper, JointSNVMix and Strelka. In this analysis, we apply these four SNV calling algorithms to cancer–normal Illumina exome sequencing of a chronic myeloid leukaemia (CML) patient. The candidate SNV sites returned by each algorithm are filtered to remove likely false positives, then characterized and compared to investigate the strengths and weaknesses of each SNV calling algorithm. Results: Comparing the candidate SNV sets returned by VarScan, SomaticSniper, JointSNVMix2 and Strelka revealed substantial differences with respect to the number and character of sites returned; the somatic probability scores assigned to the same sites; their susceptibility to various sources of noise; and their sensitivities to low-allelic-fraction candidates.
Keywords: Humans; Neoplasms; Sequence Analysis, DNA; Mutation; Algorithms; Software; Genotyping Techniques; Exome
Rights: © The Author 2013. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
RMID: 0020130214
DOI: 10.1093/bioinformatics/btt375
Appears in Collections:Molecular and Biomedical Science publications
Environment Institute publications

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