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Impact and Challenges in Assessing Tumor Purity by Next-Generation Sequencing

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Next Generation Sequencing in Cancer Research

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Abstract

Cancer research is receiving a tremendous boost from the technological advancements known as next-generation sequencing, which have enabled researchers to identify gene mutations that are highly recurrent in several different subtypes of cancer and to discover new subtypes of cancer based on a profile of gene mutations. The ability to identify and then target the specific genetic profile of each tumor is the promise of developing personalized cancer treatments. Much research effort is needed before that promise can be realized. One area of research supporting this effort is estimating tumor purity and heterogeneity. Tumors removed from patients contain a mixture of normal and tumor cells. As a result, analyses of mutations related to cancer must include a determination of how much the tumor’s genome sequence differs from that of the normal matched tissue as a result of mutation. We explore tumor purity estimation in this chapter and discuss a new software named PurityEst that uses the major tumor clones as estimation of tumor purity.

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Author information

Authors and Affiliations

  1. Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Unit 1410, Houston, TX, 77230-1402, USA

    Xiaoping Su Ph.D.

  2. Department of Medical Oncology, Groupe Hospitalier Pitie-Salpetriere University Pierre and Marie Curie (Paris VI), Paris, France

    Gabriel G. Malouf M.D., M.Sc.

  3. Division of Cancer Medicine, Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA

    Francisco J. Esteva M.D., Ph.D.

Authors
  1. Xiaoping Su Ph.D.
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  2. Gabriel G. Malouf M.D., M.Sc.
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  3. Francisco J. Esteva M.D., Ph.D.
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Correspondence to Xiaoping Su Ph.D. .

Editor information

Editors and Affiliations

  1. Dept. Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada

    Wei Wu

  2. The Wellcome Trust Centre for Human Gene, University of Oxford, Oxford, United Kingdom

    Hani Choudhry

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Su, X., Malouf, G.G., Esteva, F.J. (2013). Impact and Challenges in Assessing Tumor Purity by Next-Generation Sequencing. In: Wu, W., Choudhry, H. (eds) Next Generation Sequencing in Cancer Research. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7645-0_18

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