Formalin fixation delivers quality biomarker results by NGS and IHC

In cancer research, there currently exists an age-old quandary: the large demand for high-quality tissue samples and a low supply of readily available fresh or frozen tissue samples. These ‘live’ tissue samples, which are known to achieve the highest quality results when determining tissue biomarker correlation, are both expensive and in short supply for researchers due to the difficulty they pose for handling, transporting and storing. It was obvious for researchers early on in developing and utilising next-generation sequencing (NGS) analysis that finding a way to use formalin-fixed, paraffin wax-embedded (FFPE) tissue samples would not only alleviate the challenges posed by fresh or frozen samples, but also open up the floodgates for researchers to access the vast banks and archives of FFPE tissue samples globally.

Long used as the standard for haematoxylin and eosin (H&E) staining and immunohistochemistry (IHC) analysis, FFPE samples have been used to correlate biomarkers within the cell structure. Biomarkers exist at the DNA, RNA and protein levels, and the ability to trace one biomarker type through its various moieties helps to elucidate the workings of normal and neoplastic cells.^1–3 Immunohistochemistry continues to be a popular method to study the protein expression of target biomolecules in tissue sections in clinical settings and in diagnostic research.^4–9 Genomic testing of RNA and DNA, such as with NGS, is now a leading technology to pinpoint actionable mutations accurately. Both methods help to characterise a tumour, and, in some cases, guide therapy decisions. And while FFPE tissues are the most plentiful biospecimen archive available, often well-annotated and linked with clinical information and outcomes, they have up until recently posed a problem when undergoing NGS analysis. The results of many studies using FFPE samples for nucleic acid analysis showed significant variance in biomarker expression and quality depending on the exact formulations and preparation of the FFPE sample.^10–12

In a recent white paper authored by Epredia, it was demonstrated that FFPE tissue can be used to produce well-correlated biomarker data from NGS and IHC analysis through proper biospecimen preservation, processing and handling prior to undergoing NGS. Epredia is a global company with a long history of partnering with clinicians and researchers to enhance precision cancer diagnostics. “Our NGS colleagues reached out to us inquiring about some recent, repeated test failures to see if sample preparation might be a contributing factor,” stated Jennifer Freeland, one of the key authors of the study, and Global Market Development Manager for Immunohistochemistry at Epredia.