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Transcriptome Sequencing (RNA-Seq)

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Genomic Applications in Pathology

Abstract

The transcriptome is the entire assembly of RNA transcripts in a given cell type, including protein-coding and noncoding transcripts. Transcriptome sequencing (RNA-Seq) is a recently developed technology that uses high-throughput sequencing approaches (next-generation sequencing or NGS) to determine the sequence of all RNA transcripts in a given specimen. This chapter provides an overview of the development and technical background of transcriptomics and the advantages and limitations of RNA-Seq. This technology has rapidly increased our understanding of gene expression profiles of various cells and tissues and is allowing us to better understand alternative splicing and the functional elements of the genome and to identify single-nucleotide variants and new fusion transcripts in cancer. We also review current and potential clinical applications of RNA-Seq technology in inherited, chronic, neoplastic, and infectious diseases.

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Acknowledgments

The authors would like to thank Karen Prince of Texas Children’s Hospital for her help with the design of the figures for this chapter.

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Authors and Affiliations

  1. Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA

    Jacquelyn Reuther & Federico A. Monzon

  2. Department of Pathology and Immunology and Pediatrics, Baylor College of Medicine, Houston, TX, USA

    Angshumoy Roy

  3. Castle Biosciences, Friendswood, TX, USA

    Federico A. Monzon

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  1. Jacquelyn Reuther
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  2. Angshumoy Roy
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  3. Federico A. Monzon
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Correspondence to Federico A. Monzon .

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  1. Professor and Chair of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA

    George Jabboure Netto

  2. Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Clinical Professor of Pathology, University of Chicago Pritzker School of Medicine, Evanston, IL, USA

    Karen L. Kaul

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Reuther, J., Roy, A., Monzon, F.A. (2019). Transcriptome Sequencing (RNA-Seq). In: Netto, G., Kaul, K. (eds) Genomic Applications in Pathology. Springer, Cham. https://doi.org/10.1007/978-3-319-96830-8_4

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