OCT 30, 2014 09:00 AM PDT

A head-to-head comparison of whole blood derived samples (cfDNA vs CTC DNA) for cancer research using next-generation sequencing

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  • Chief Science Officer, Cynvenio
      Dr. Dempsey is an immunologist by training with more than 25 years of experience in biomedical research. Before joining Cynvenio, Dr. Dempsey was an Assistant Research Professor in the Department of Microbiology, Immunology and Molecular Genetics at the University of California, Los Angeles. He brings extensive hands-on research experience in life sciences, molecular biology, and reagent development.
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      <br />Dr. Dempsey was a Leukemia and Lymphoma Society Fellow from 2000 to 2003, has published 20 scientific articles and abstracts, and holds patents in technologies designed to amplify the immunogenicity of vaccines and rare-cell recovery.
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      <br />Dr. Dempsey holds a BS in Microbiology and Virology from the University of Warwick in Coventry, UK, and a PhD from Johns Hopkins University School of Medicine.
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    Both cell free DNA (cfDNA) and circulating tumor cells (CTC) represent important possible templates for mutation analysis of clinical samples. Each template has different theoretical advantages for a clinical test. cfDNA is very easy to access and isolate, while CTC can provide both DNA as well as RNA for clinical testing. In addition, the templates may reflect different aspects of cancer biology. Cynvenio has tested head-to-head cfDNA and CTC DNA using LiquidBiopsyTM coupled with Ion TorrentTM next-generation sequencing of normal and tumor samples. Both cfDNA and CTC samples provided sufficient quantity and purity of the limited number of tumor genomes for a direct sequencing clinical research test. No whole genome amplification was involved. The test for comparison purposes consisted of coupling these CTC and cfDNA purification technologies to an amplicon re-sequencing panel of 50 cancer-associated genes using a CLIA-validated sequencing pipeline for SNV mutations with a sensitivity of 1%. Typically, this pipeline can isolate, extract, sequence and analyze blood borne cancer cells in 7 days. In the CLIA setting, the validated DNA sequencing process, when applied to breast cancer tumor samples, has demonstrated useful data. The data suggest that cfDNA and DNA recovered from tumor-derived blood cells are complementary and may represent different aspects of cancer biology.

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