The use of a hybridisation-based NGS enrichment panel for the confident identification of a broad range of low frequency variants from as little as 50ng of challenging clinical research FFPE samples
Graham Speight, Ephrem Chin, Jacqueline Chan, Robert Zeillinger, Nicole Concin, David Cook
Presented at the Association For Molecular Pathology (AMP) 2016 annual meeting in Charlotte, NC, USA in November 2016, this poster outlines how the SureSeq™ FFPE DNA Repair Mix significantly improves NGS library yields, with an increase of mean target coverage (increased by >2.2 fold), resulting in more meaningful data and therefore confident variant calling from this challenging sample type.
One of the challenges in the treatment of cancer is the high level of genetic complexity and tumour heterogeneity. Detailed information about the genetic profile of each individual tumour can help guide treatment strategies1. Epithelial ovarian cancer (EOC) is the most lethal gynaecological malignancy2 , and the type II tumours accounting for approximately 75% of all EOCs, are nearly always detected in advanced stages. These highly aggressive tumours are characterised by their morphological and molecular homogeneity and often (>80% of cases) contain TP53 mutations. The GANNET53 (Ganetespib in metastatic, p53 mutant, platinum-resistant ovarian cancer) trial started in October 2015 and aims to improve the prognosis and quality of life in platinum-resistant EOC patients (www.gannet53.eu). This European multi-centre clinical trial is currently in stage II during which biomaterials have been collected and analysed using a SureSeq hybridisation-based enrichment panel for targeted next-generation sequencing (NGS), to determine the TP53 mutation status of the 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.
- Kurman, R.J. and Ie-Ming, S., 2010. The origin and pathogenesis of epithelial ovarian cancer: a proposed unifying theory. The American journal of surgical pathology, 34(3), pp.433-443.
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