NGS Banner
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.

Register with us to read the full article

Once you have registered with us for free you will be able to read all our supportive literature, video tutorials and webinars.

CTA Icon

Stay up-to-date with the latest news from OGT, including new products, support resources, and our DNA Dispatch newsletter