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Studying Cancer Genomics Through Next-Generation DNA Sequencing and Bioinformatics

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Clinical Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1168))

Abstract

Cancer is a complex disease driven by multiple mutations acquired over the lifetime of the cancer cells. These alterations, termed somatic mutations to distinguish them from inherited germline mutations, can include single-nucleotide substitutions, insertions, deletions, copy number alterations, and structural rearrangements. A patient’s cancer can contain a combination of these aberrations, and the ability to generate a comprehensive genetic profile should greatly improve patient diagnosis and treatment. Next-generation sequencing has become the tool of choice to uncover multiple cancer mutations from a single tumor source, and the falling costs of this rapid high-throughput technology are encouraging its transition from basic research into a clinical setting. However, the detection of mutations in sequencing data is still an evolving area and cancer genomic data requires some special considerations. This chapter discusses these aspects and gives an overview of current bioinformatics methods for the detection of somatic mutations in cancer sequencing data.

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Abbreviations

CNA:

Copy number alterations

CNV:

Copy number variants

SNV:

Single-nucleotide variants

SR:

Structural rearrangements

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Author information

Authors and Affiliations

  1. Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia

    Maria A. Doyle, Jason Li, Ken Doig, Andrew Fellowes & Stephen Q. Wong

Authors
  1. Maria A. Doyle
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  2. Jason Li
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  3. Ken Doig
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  4. Andrew Fellowes
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  5. Stephen Q. Wong
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Corresponding author

Correspondence to Maria A. Doyle .

Editor information

Editors and Affiliations

  1. Department of Medical Genomics, Royal Prince Alfred Hospital and Sydney Medical School, University of Sydney, Camperdown, Australia

    Ronald Trent

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Doyle, M.A., Li, J., Doig, K., Fellowes, A., Wong, S.Q. (2014). Studying Cancer Genomics Through Next-Generation DNA Sequencing and Bioinformatics. In: Trent, R. (eds) Clinical Bioinformatics. Methods in Molecular Biology, vol 1168. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0847-9_6

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  • DOI: https://doi.org/10.1007/978-1-4939-0847-9_6

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0846-2

  • Online ISBN: 978-1-4939-0847-9

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