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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.

Figure 1: Key ovarian cancer-related genes in the SureSeq Ovarian Cancer PanelTable 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 samplesa . 
  • Identified important somatic variants in TP53 from DNA extracted from FFPE blocks of type II epithelial ovarian cancer (EOC) samplesb
  • 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.

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