The assessment by NGS of FFPE derived tumour DNA using an ovarian cancer and a custom solid tumour hybridisation-based enrichment panel approach

Contributors

Jacqueline Chan, Juliette Forster, William Wright, Graham Speight

Introduction

• One of the challenges in cancer research is the high level of genetic complexity and tumour heterogeneity. 
• Research that generates detailed information about the genetic profile of each individual tumour will further our understanding and may be used in the future to guide treatment strategies¹. 
• Next Generation Sequencing (NGS) has enabled the simultaneous study of multiple mutations in high-penetrance cancer predisposition genes. However, tissue biopsies are typically archived as formalin-fixed, paraffin embedded (FFPE) blocks which can significantly compromise the quality and amount of nucleic acids available for genomics research.

To overcome these issues, we have used the SureSeq™ FFPE DNA Repair Mix*, in combination with a hybridisation-based NGS custom enrichment panel, the SureSeq Ovarian Cancer Panel (Figure 1) to identify somatic variation in key DNA repair genes associated with ovarian cancer.

Table 1: Key ovarian cancer-related genes in the SureSeq Ovarian Cancer Panel.

To evaluate the application of a hybridisation-based approach we:

• Compared the uniformity of coverage between PCR-based and hybridisation-based enrichment approaches for the analysis of BRCA1and BRCA2 in solid tumour samples^a . 
• Identified important somatic variants in TP53 from DNA extracted from FFPE blocks of type II epithelial ovarian cancer (EOC) samples^b. 
• Assessed the performance of a 4.5 kb custom panel from the SureSeq myPanel™ NGS Custom Cancer Panel range using the formalin-compromised Quantitative Multiplex Reference Standard from Horizon Diagnostics.