FEB 22, 2017 06:00 AM PST
Mate-pair next generation sequencing as a powerful clinical tool for the characterization of cancer
Presented at the Precision Medicine 2017 Virtual Event
CONTINUING EDUCATION (CME/CE/CEU) CREDITS: CME | P.A.C.E. CE | Florida CE
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Speakers:
  • Professor and Consultant at Mayo Clinic
    Biography
      David I Smith received his B.S. in Mathematics and Molecular Biology from the University of Wisconsin in Madison. He then received his Ph.D. for the Department of Biochemistry also at the University of Wisconsin in Madison. After several postdoctoral positions he got his first academic appointment at Wayne State University. In 1996 he joined the Mayo Clinic in the Department of Laboratory Medicine and Pathology as Professor and Consultant. He was also appointed as the head of the Cancer Genetics Program for the Mayo Clinic Cancer Center. His research focuses on the role that the common fragile sties play in cancer development. His laboratory also works on the various roles that human papillomavirus plays in the development of different cancers. Dr. Smith is also the Chairman of the Technology Assessment Group for the Mayo Clinic Center for Individualized Medicine. The responsibility of this group is to evaluate new technologies for their potential impact on research and its' clinical translation. His laboratory utilizes next generation sequencing to characterize the molecular alterations that occur during the development of cancer. They also have been using the powerful technique of mate-pair next generation sequencing (MP-Seq) to characterize the physical status of HPV in different HPV-driven cancers.

    Abstract:

    Recent advances in DNA sequencing have now made it possible to characterize genomes, transcriptomes and even methylomes which is transforming both basic research and clinical practice. Whole genome sequencing (WGS) is a powerful tool to analyze molecular alterations that occur during the development of cancer, but there are a number of challenges to using WGS as a clinical tool. A practical alternative to WGS is the utilization of mate-pair next generation sequencing (MP-Seq) which can be done for a fraction of the cost of WGS. We have been using MP-Seq to characterize the different roles that human papillomavirus (HPV) plays in the development of different cancers. The cancer that we have been studying is oropharyngeal squamous cell carcinoma (OPSCC) as this cancer is increasingly caused by infection with HPV and there has been an epidemic increase in the incidence of this cancer. We utilized MP-Seq to analyze a group of HPV-positive OPSCCs. What we have found is that HPV is integrated into the genome of OPSCCs in only 30% of these cancers, which is quite distinct from what is observed in cervical cancer. In addition, we have found that the highly unstable common fragile sites and the large genes contained within these regions are hot-spots both for viral integrations and for other alterations in these cancers. Several large common fragile site genes are consistently altered in these cancers. MP-Seq can also determine genome-wide molecular alterations and these alterations can be utilized as cancer-specific markers for the detection of circulating tumor-free DNA from the blood of these patients. This could provide a powerful tool for the development of the liquid biopsy to monitor cancer-treatment of these patients. We will discuss how MP-Seq could thus become a powerful clinical tool for the characterization of genomic alterations in cancer and the development of the liquid biopsy.

    Learning Objective 1: Understand how MP-Seq can provide important information about genomic alterations in cancer

    Learning Objective 2: Learn about how HPV is involved in the development of different cancers

    Learning Objective 3: Learn about how MP-Seq can be a powerful tool to aid in the development of the liquid biopsy

     


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