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Next Generation Sequencing in Cancer Research

Volume 1: Decoding the Cancer Genome

  • Book
  • © 2013

Overview

Editors:
  1. Wei Wu

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

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  2. Hani Choudhry

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

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    You can also search for this editor in PubMed   Google Scholar

  • Applies the Next Generation Sequencing (NGS) technology to practical and real cancer research projects?

  • Each chapter will briefly cover the outline for bioinformatic analysis

  • The primary audience are researchers and scientists in cancer biology, molecular biology, and other related areas in biomedical research

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Table of contents (18 chapters)

  1. Front Matter

    Pages i-xii
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  2. The Evolution of High-Throughput Sequencing Technologies: From Sanger to Single-Molecule Sequencing

    • Chee-Seng Ku, Yudi Pawitan, Mengchu Wu, Dimitrios H. Roukos, David N. Cooper
    Pages 1-30

  3. Next-Generation Sequencing in Cancer Epigenomics and Potential Clinical Applications

    • Hong Kiat Ng, Dimitrios H. Roukos, Barry Iacopetta, Chee-Seng Ku
    Pages 31-53

  4. Next-Generation Sequencing for Cancer Genomics

    • Aarti N. Desai, Abhay Jere
    Pages 55-74

  5. Genomic Landscape of Cancer Metastasis

    • Arvind K. Singla, Chandini Thirukkumaran, Rajiv Dixit, Wei Wu
    Pages 75-90

  6. Mapping the HIF Transcription Factor in Cancer by ChIP-Seq Technology

    • Johannes Schödel, David R. Mole
    Pages 91-117

  7. Application of Next-Generation Sequencing to Analysis of TGFβ/SMAD4 Targets in Ovarian Cancer

    • Russell Bonneville, Kenneth Nephew, Victor X. Jin
    Pages 119-135

  8. Targeted Sequencing Strategies in Cancer Research

    • HoJoon Lee, Billy T. Lau, Hanlee P. Ji
    Pages 137-163

  9. Comprehensive Genomic Alterations in Common Cancer Cell Lines Revealed by Exome Sequencing

    • Han Chang, Donald G. Jackson, Paul S. Kayne, Petra B. Ross-Macdonald, Rolf-Peter Ryseck, Nathan O. Siemers
    Pages 165-182

  10. Application of Next-Generation Sequencing in RNA Biomarker Discovery in Cancer Research

    • Stephen P. Fink, Kishore Guda
    Pages 183-197

  11. Understanding the Role of Long Noncoding RNAs in the Cancer Genome

    • Wei Wu, Jennifer A. Chan
    Pages 199-215

  12. Identification of piRNAs in HeLa Cells by Massive Parallel Sequencing

    • Yilu Lu, Yongxin Ma
    Pages 217-231

  13. MicroRNA Expression in Breast Cancer Revealed by Deep Sequencing Technology

    • Thalia A. Farazi, Carl S. Leonhardt, Thomas Tuschl
    Pages 233-261

  14. RNA-Seq in Prostate Cancer Research

    • ShanCheng Ren, Min Qu, Yinghao Sun
    Pages 263-286

  15. Next-Generation Sequencing for High-Throughput RNA Interference Screens

    • Toby M. Ward, Anna-Maria Jegg, Elizabeth Iorns
    Pages 287-299

  16. Assessment of Mapping and SNP-Detection Algorithms for Next-Generation Sequencing Data in Cancer Genomics

    • Weixin Wang, Feng Xu, Junwen Wang
    Pages 301-317

  17. Applications of Very Low-Coverage Sequencing in Cancer Genomics: Copy Number, Virus Detection and Survival

    • Henry M. Wood
    Pages 319-333

  18. Tumor Phylogenetics in the NGS Era: Strategies, Challenges, and Future Prospects

    • Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz
    Pages 335-357

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

    • Xiaoping Su, Gabriel G. Malouf, Francisco J. Esteva
    Pages 359-371

  20. Back Matter

    Pages 373-383
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Keywords

About this book

​​​​This volume provides an interdisciplinary perspective of applying Next Generation Sequencing (NGS) technology to cancer research. It aims to systematically introduce the concept of NGS, a variety of NGS platforms and their practical implications in cancer biology.This unique and comprehensive text will integrate the unprecedented NGS technology into various cancer research projects as opposed to most books which offer a detailed description of the technology. This volume will present true experimental results with concrete data processing pipelines, discuss the bottleneck of each platform for real project in cancer research. In additional, single cancer cell sequencing as the proof of concept will be introduced in this book, along with cutting-edge information provided will help the intended audience to develop a comprehensive understanding of the NGS technology and practical whole genome sequencing data analysis and rapidly translate into their own research, specifically in the field of cancer biology. 

Editors and Affiliations

  • Dept. Pathology & Laboratory Medicine, University of Calgary, Calgary, Canada

    Wei Wu

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

    Hani Choudhry

Bibliographic Information

  • Book Title: Next Generation Sequencing in Cancer Research

  • Book Subtitle: Volume 1: Decoding the Cancer Genome

  • Editors: Wei Wu, Hani Choudhry

  • DOI: https://doi.org/10.1007/978-1-4614-7645-0

  • Publisher: Springer New York, NY

  • eBook Packages: Biomedical and Life Sciences, Biomedical and Life Sciences (R0)

  • Copyright Information: Springer Science+Business Media New York 2013

  • Hardcover ISBN: 978-1-4614-7644-3Published: 05 August 2013

  • Softcover ISBN: 978-1-4899-8808-9Published: 25 August 2015

  • eBook ISBN: 978-1-4614-7645-0Published: 04 August 2013

  • Edition Number: 1

  • Number of Pages: XII, 383

  • Topics: Cancer Research, Bioinformatics, Human Genetics, Biomedicine general

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