The analysis of FFPE samples by NGS of key genes for research into breast and ovarian cancer

Contributors

Jacqueline Chan, Sabine Eckert, Lyudmila Georgieva and Graham Speight

OGT, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxford, UK

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 .

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 (Table 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 a PCR-based and a hybridisation-based enrichment approach for the analysis of BRCA1 and BRCA2 in solid tumour samples^a
• Identified potentially important variants in TP53 and BRCA1 genes from DNA extracted from FFPE blocks of type II epithelial ovarian cancer (EOC) samples^b