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

Abstract

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. 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. 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.