AUG 20, 2014 10:45 AM PDT

OncoScan Assay for copy number from FFPE. Publications & cases on actionable CNV detection

  • Director of OncoScan Product Marketing Strategy, Affymetrix
      Padma led the design, development and commercialization of the OncoScan Assay kit, a whole genome copy number platform with high resolution in ~900 cancer genes, that requires  80ng of input DNA from formalin fixed paraffin embedded (FFPE) samples such as those from biopsies. .  The OncoScan Assay has been used extensively for Translational research  in the Academic and Pharma settings,  resulting in over 100 publications in the last two years.. Several labs including the Memorial Sloan Kettering Cancer Center, Fox Chase Cancer Center, ARUP labs and Seattle Cancer Care have launched the OncoScan Assay as a CLIA validated testWorking closely with researchers at leading cancer hospitals worldwide such as at the MD Anderson Cancer Center, Washington Unoversity, and the Hunstsman Cancer Institute,, Padma has designed clinical studies that have successfully demonstrated the clinical utility of the OncoScan Assay in identifying actionable copy number alterations in solid tumor samples. These studies have been presented at  webinars hosted by Science, The European College of Pathology, the Cancer Genomic Consortium, The American Society of Human Genetics among others.    In partnership with CollabRx, a cloud based data analytics company, Padma helped develop a copy number annotation service that  delivers concise, real time information on therapeutics targeting CNVs in cancer patients, with a 24 hour turnaround. This report can be integrated with somatic mutations, such as those from Next generation sequencing panels, Prior to joining Affymetrix, Padma Sundar worked for over 13 years in the Life Sciences industry in Business development roles  at Johnson and Johnson,  Medical Device and Diagnostics Division, and has served various Pharmaceutical clients as a management consultant with McKinsey & Company.She has a Bachelors in Chemistry from the University of Delhi, India and an MBA and a Masters in Public Health from University of California at Berkeley


    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.

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