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Lymphoma pp 295-312 | Cite as

High-Throughput RNA Sequencing in B-Cell Lymphomas

  • Wenming Xiao
  • Bao Tran
  • Louis M. Staudt
  • Roland SchmitzEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 971)

Abstract

High-throughput mRNA sequencing (RNA-seq) uses massively parallel sequencing to allow an unbiased analysis of both genome-wide transcription levels and mutation status of a tumor. In the RNA-seq method, complementary DNA (cDNA) is used to generate short sequence reads by immobilizing millions of amplified DNA fragments onto a solid surface and performing the sequence reaction. The resulting sequences are aligned to a reference genome or transcript database to create a comprehensive description of the analyzed transcriptome. This chapter describes a protocol to perform RNA-seq using the Illumina sequencing platform, presents sequencing data quality metrics and outlines a bioinformatic pipeline for sequence alignment, digital gene expression, and mutation discovery.

Key words

Next-generation sequencing Transcriptome Gene expression B cell B-cell lymphoma Immunoglobulin genes Mutation 

Notes

Acknowledgments

This work was supported by the by the Dr. Mildred Scheel Stiftung für Krebsforschung (Deutsche Krebshilfe). We are grateful to Yuliya Kriga, Jyoti Shetty, Yongmei Zhao, John Powell, and George Wright who were instrumental in establishing the protocols described here.

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Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Wenming Xiao
    • 1
  • Bao Tran
    • 2
  • Louis M. Staudt
    • 3
  • Roland Schmitz
    • 3
    Email author
  1. 1.Bioinformatics and Molecular Analysis Section, Division of Computational Bioscience, Center for Information TechnologyNational Institutes of HealthBethesdaUSA
  2. 2.Center for Cancer Research Sequencing Facility, SAIC-F Advanced Technology ProgramNational Cancer Institute, NIHFrederickUSA
  3. 3.Metabolism Branch, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaUSA

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