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Computational Analysis of DNA and RNA Sequencing Data Obtained from Liquid Biopsies

  • Francesco Marass
  • Francesc Castro-Giner
  • Barbara Maria Szczerba
  • Katharina Jahn
  • Jack Kuipers
  • Nicola AcetoEmail author
  • Niko BeerenwinkelEmail author
Chapter
Part of the Recent Results in Cancer Research book series (RECENTCANCER, volume 215)

Abstract

Next-generation sequencing of DNA and RNA obtained from liquid biopsies of cancer patients may reveal important insights into disease progression and metastasis formation, and it holds the promise to enable new methods for noninvasive screening and clinical decision support. However, implementing liquid biopsy sequencing protocols is challenged by capturing circulating tumor cells or cell-free tumor DNA from blood samples, by amplifying genomic DNA and RNA in a reliable and unbiased manner, and by extracting biologically meaningful signals from the noisy sequencing data. In this chapter, we discuss computational methods for the analysis of DNA and RNA sequencing data obtained from liquid biopsies, addressing these challenges.

Keywords

Liquid biopsy Noninvasive cancer genomics Circulating tumor cell Circulating tumor DNA Mutation calling Copy-number profiling Gene expression analysis Tumor phylogeny 

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Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Francesco Marass
    • 1
    • 2
  • Francesc Castro-Giner
    • 2
    • 3
  • Barbara Maria Szczerba
    • 3
  • Katharina Jahn
    • 1
    • 2
  • Jack Kuipers
    • 1
    • 2
  • Nicola Aceto
    • 3
    Email author
  • Niko Beerenwinkel
    • 1
    • 2
    Email author
  1. 1.Department of Biosystems Science and EngineeringETH ZurichBaselSwitzerland
  2. 2.Swiss Institute of BioinformaticsBaselSwitzerland
  3. 3.Faculty of Medicine, Department of BiomedicineUniversity of Basel and University Hospital BaselBaselSwitzerland

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