Clinical applications of next-generation sequencing of formalin-fixed paraffin-embedded tumors

Cheryl L. Thompson, Vinay Varadan

Research output: Chapter in Book/Report/Conference proceedingChapter


Significant progress has been made in next-generation sequencing (NGS) of tumors from formalin-fixed paraffin-embedded (FFPE) tumors. In this chapter, we review some of therecent developments in RNA and DNA sequencing from FFPE. We highlight some of the current challenges and considerations that mustbe in place before using NGS in a clinical setting. We begin with a discussion of the technical challenges in dealing with FFPE tumors, including nucleic acid degradation and the potential utility of adding in dissection methods to the tumors. We then discuss bioinformatical and statistical considerations that must be employed when analyzing data obtained from FFPE tissues. We end with a brief discussion of ethical implications and other issues that will need to be addressed before translating discoveries into the clinic.

Original languageEnglish (US)
Title of host publicationNext Generation Sequencing in Cancer Research, Volume 2
Subtitle of host publicationFrom Basepairs to Bedsides
PublisherSpringer International Publishing
Number of pages14
ISBN (Electronic)9783319158112
ISBN (Print)9783319158105
StatePublished - Jan 1 2015

All Science Journal Classification (ASJC) codes

  • General Medicine
  • General Biochemistry, Genetics and Molecular Biology


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