Using FFPE Tissue in Genomic Analyses: Advantages, Disadvantages and the Role of Biospecimen Science

William Mathieson*, Gerry Thomas

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

8 Citations (Scopus)

Abstract

Purpose of Review: Formalin-fixed, paraffin-embedded (FFPE) tissue blocks are considered by some to be suboptimal for Next Generation Sequencing (NGS) because, compared with fresh-frozen (FF) biospecimens, the nucleic acid obtained from them is fragmented and low in quantity, containing formalin-induced modifications and mutations. However, clinical workflows do not typically have the capability to collect FF tissue, so there is an inherent necessity to perform NGS using FFPE tissue. We review relevant literature that addresses the issue of extracting DNA from FFPE tissue biospecimens then applying it to NGS. Recent Findings: Practical and straightforward optimisation experiments and quality control assays can be performed by laboratories who extract DNA from FFPE biospecimens to maximise its amenability to NGS. Summary: FFPE biospecimens can be used in genomic medicine with confidence because the disadvantages associated with DNA quality are outweighed by the ease of sample collection and can be addressed by protocol optimisation.

Original languageEnglish
Pages (from-to)35-40
Number of pages6
JournalCurrent Pathobiology Reports
Volume7
Issue number3
DOIs
Publication statusPublished - 15 Sep 2019
Externally publishedYes

Keywords

  • DNA sequening
  • FFPE
  • Fixation time
  • Ischemia
  • Whole genome sequencing

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