Mitigating the challenges of nucleic acid extraction from FFPE samples

Extensive archives of formalin-fixed, paraffin-embedded (FFPE) tissues combined with recent innovations in next generation sequencing (NGS) techniques provide a rich resource for identifying and validating new biomarkers in a... [ view full abstract ]

Extensive archives of formalin-fixed, paraffin-embedded (FFPE) tissues combined with recent innovations in next generation sequencing (NGS) techniques provide a rich resource for identifying and validating new biomarkers in a variety of disease research areas. The ability to isolate both DNA and RNA from a single FFPE sample allows for retrospective studies of diseased tissues at both the genomic and transcriptomic levels. However, an abundance of protein-nucleic acid and nucleic acid-nucleic acid crosslinks present significant challenges to extracting reliable genetic material from FFPE-preserved samples. Additionally, isolated nucleic acids are commonly fragmented and chemically modified to such a degree that renders them useless in many downstream molecular analyses. The poor quality of FFPE isolates is typically worsened by extraction methods that are complex and cumbersome to perform. Here we describe a highly efficient and robust process for isolating high quality DNA and RNA from FFPE materials using Beckman Coulter’s Biomek i7 liquid handling system and FormaPure DNA reagent. Furthermore, these FFPE-derived nucleic acids are shown to produce superior data in both PCR-based and NGS applications