Formalin-Fixed Paraffin-Embedded Tissue (FFPET) Sections for Nucleic Acid-Based Analysis in Biomarker Discovery and Early Drug Development

Formalin-fixed paraffin-embedded tissue (FFPET) samples represent the clinical standard of tissue fixation, and huge archives of this material offer a valuable source for biomarker identification and validation. For this reason, techniques for efficient and reliable analysis of FFPET are important for rapid advances in personalized health care (PHC). This chapter focuses on the use of FFPET for nucleic acid biomarker verification by RNA and DNA analysis in clinical FFPET samples, describes in particular the workflow applied for hypothesis testing to determine quantitative expression levels of putative transcriptional biomarkers in different tumor FFPET samples, and gives an overview of current major applications for nucleic acid analyses from FFPET. Due to formalin fixation-caused modification and degradation of RNA and DNA, special attention is paid to the methods for nucleic acid isolation, because yield and quality of extracted nucleic acids are crucial for successful downstream applications. The described procedures usually achieve yields of several μg of high-quality RNA and DNA obtained from standard 5–10 μm FFPET sections; however, amounts significantly depend on factors like sample size, number of well-preserved cells, and tumor entity. A major application for isolated RNA is its use for reliable quantitative gene expression analysis by reverse transcription quantitative real-time PCR (RT-qPCR) assays based on optimized cDNA synthesis and quantitative real-time PCR (qPCR). In cases of very low starting material, an optimized pre-amplification protocol achieves an up to 4,000-fold increase in cDNA yields, thereby significantly improving the sensitivity of downstream applications. Pre-amplification is also implemented in a workflow for RT-qPCR analysis of microdissected material from immunohistochemically stained FFPET sections. This procedure permits capture of defined cell types in order to enhance specificity of gene expression profiling. Further applications for RNA analysis relate to expression profiling by microarrays and to a combination of genetic and transcriptional analysis by advanced RNA-Seq technology utilizing next-generation sequencing (NGS). The major applications described for DNA isolated from FFPET relate to qPCR and various approaches for mutation analysis. The overview comprises sequencing techniques including NGS as well as highresolution melting (HRM) and allele-specific qPCR (AS qPCR). Additionally the use of FFPET for the analysis of epigenetic methylation patterns by methylationsensitive HRM (MS-HRM) is addressed. The final chapter refers to the application of FFPET in clinical diagnostics of different cancer types. To date first approved IVD kits are available to analyze mutations as well as expression patterns of related marker genes and thus represent an essential precondition for prognosis, treatment decisions, and therapy in PHC. List of Abbreviations AS qPCR Allele-Specific qPCR CGH Comparative Genomic Hybridization Cq Quantification Cycle CRC Colorectal Cancer 188 S. Lohmann et al.