A recent publication in Nature Genetics1 analyzed TCGA data, and classified solid tumors into two mutually exclusive classes: C class tumors, driven by copy number alterations; and M class tumors, driven by somatic mutations. The C class tumors were ovarian cancer, breast cancer, squamous cell lung cancer and head and neck cancers. Prostate cancer is also believed to be a C class tumor. The publication also listed 23 actionable copy number alterations that are targetable based on currently available therapies.
NGS based technologies are not cost effective for the detection copy number changes in heterogeneous, solid tumor FFPE samples owing to the high depth of sequencing required to detect CNV in this sample type.
In this talk, the presenter will describe the Molecular Inversion Probes (MIP) technology, for the detection of genome wide copy number changes, with high resolution in ~900 cancer genes, using less 80ng of DNA from formalin fixed paraffin embedded (FFPE) samples such as those from biopsies, ,There have been over 100 publications in the last two years using the MIP based OncoScan Assay. She will present on some key publications using the platform.
She will also share case studies across several solid tumors, where actionable copy number alterations were observed in patients who had no actionable somatic mutations, and thus emphasize the need for a reliable copy number platform for solid tumors to complement next generation sequencing based somatic mutations panels offered by many CLIA certified laboratories.
1. Ciriello G., et al. Emerging landscape of oncogenic signatures across human cancers. Nature Genetics 45(10):1127−1133 (2013). doi: 10.1038/ng.2762.
2. Huw L., et al. Acquired PIK3CA amplification causes resistance to selective phosphoinositide 3-kinase inhibitors in breast cancer. Oncogenesis 2:e83 (2013). doi: 10.1038/oncsis.2013.46.