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Tumor Profiling pp 169–184Cite as

Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: Overview of Library Preparation Methods

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1908))

Abstract

RNA sequencing (RNA-seq) is revolutionizing the study of cancer by providing a highly sensitive and robust tool to interrogate the transcriptome. It leverages the power of deep sequencing technology and provides global and multidimensional views of transcriptional landscapes in healthy and tumor tissues. Such information is contributing innovative insights to our understanding of the genetic basis of cancer and the progression of the disease. RNA-seq is a superior technology to DNA microarrays in that it provides digital rather than analog information on transcripts and their isoforms. The front end (sequencing library preparation and validation) is technically complex and time intensive. The primary objective in preparing a sequencing library is to eliminate or minimize bias, so that the library is reflective of the input RNA sample in terms of both sequence content and transcript abundance. This chapter describes the RNA-seq approach, and reviews methods and good practices for library preparation and sequencing.

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Acknowledgments

This work was conducted with support from start-up funds from the MUSC COM to GH and an award from SC EPSCoR. The content is solely the responsibility of the authors and does not necessarily represent the official views of the Medical University of South Carolina. Sean M. Courtney and Willian A. da Silveira contributed equally to this work.

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Author notes

  1. Sean M. Courtney and Willian A. da Silveira contributed equally to this work.

Authors and Affiliations

  1. MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA

    Sean M. Courtney, Willian A. da Silveira, E. Starr Hazard & Gary Hardiman

  2. Institute for Global Food Security, Queens University Belfast, Belfast, UK

    Willian A. da Silveira

  3. Library Science and Informatics, Medical University of South Carolina (MUSC), Charleston, SC, USA

    E. Starr Hazard

  4. Department of Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA

    Gary Hardiman

  5. Department of Public Health Sciences, Medical University of South Carolina (MUSC), Charleston, SC, USA

    Gary Hardiman

  6. School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Stranmillis Road, Belfast, BT9 5AG, UK

    Gary Hardiman

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  1. Sean M. Courtney
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  2. Willian A. da Silveira
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  3. E. Starr Hazard
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  4. Gary Hardiman
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Corresponding author

Correspondence to Gary Hardiman .

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Editors and Affiliations

  1. Department of Pathology, University of California San Diego, La Jolla, CA, USA

    Sarah S. Murray

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Courtney, S.M., da Silveira, W.A., Hazard, E.S., Hardiman, G. (2019). Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: Overview of Library Preparation Methods. In: Murray, S. (eds) Tumor Profiling. Methods in Molecular Biology, vol 1908. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9004-7_12

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  • DOI: https://doi.org/10.1007/978-1-4939-9004-7_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9002-3

  • Online ISBN: 978-1-4939-9004-7

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