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

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

Research output: Contribution to journalArticle

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.

Original languageEnglish
Pages (from-to)169-184
JournalMethods in Molecular Biology
Volume1908
DOIs
Publication statusPublished - 17 Jan 2019

Keywords

  • Alternative Splicing
  • Gene Expression Profiling/methods
  • Gene Expression Regulation, Neoplastic
  • Gene Library
  • High-Throughput Nucleotide Sequencing/methods
  • Humans
  • Neoplasms/genetics
  • RNA, Neoplasm
  • Sequence Analysis, RNA/methods

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