The application of a hybridisation-based next-generation sequencing (NGS) enrichment panel for the analysis of key genes involved in ovarian and breast tumours using DNA from FFPE samples
Jacqueline Chan, Sabine Eckert, Lyudmila Georgieva and Graham Speight
Presented at the 2017 Cancer Genomics Consortium (CGC) annual summer meeting in Denver, USA, this poster illustrates the SureSeq™ hybridisation-based approach as a robust method for the identification of germline and somatic mutations in TP53, BRCA1, and BRCA2 and how it is possible to obtain important sequence information from as little as 50 ng of formalin-compromised DNA.
One of the challenges in cancer research is the high level of genetic complexity and tumour heterogeneity. Detailed information about the genetic profile of each individual tumour may help 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.
- Identified potentially damaging variants in TP53, BRCA1 and BRCA2 genes from DNA extracted from FFPE blocks of type II epithelial ovarian cancer (EOC) samples.
- Ross, J.S. and Cronin, M., 2011. Whole cancer genome sequencing by next-generation methods. American journal of clinical pathology, 136(4), pp.527- 539.
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