OCT 23, 2018 10:00 AM PDT
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Pediatric Cancer Genomics: Accessing Data, Tools and Visualizations in St. Jude Cloud

SPONSORED BY: DNAnexus
C.E. CREDITS: P.A.C.E. CE | Florida CE
Speakers
  • Group Lead-Bioinformatics Analysis, St. Jude Children's Research Hospital
    Biography
      After working for several years with adult cancer patients and following the work of the St. Jude Washington University Pediatric Cancer Genome Project, Scott Newman, Ph.D., joined the St. Jude Department of Computational Biology almost three years ago.
      As leader of the clinical bioinformatics analysis team, Dr. Newman's group analyzes the whole genome and transcriptions sequence data generated for every St. Jude patient's tumor. The team's job, in his words, is to "make sense of a vast amount of data and use it to guide patient care".
      In addition to that work, Dr. Newman's team is also leading the biological efforts of the St. Jude Cloud team. St. Jude Cloud currently hosts more than 5,000 whole genome sequences (which comprise half a petabyte of data). That number is expected to double by the first quarter of 2019, making St. Jude Cloud one of the largest public whole genome sequencing sets in the world. Researchers are able to access data on pediatric cancer and other diseases treated and studied at St. Jude at no charge.
      The collaboration, either direct or indirectly between St. Jude researchers and external researchers who use St. Jude Cloud could result in new biological discoveries and, eventually, new treatment options not only in the U.S., but in other countries where cancer cure rates may not be as high.
      And those discoveries aren't just limited to pediatric cancer. In some cases, novel genetic mutations discovered in pediatric cancers are also found in adult cancer patients. Thanks to St. Jude Cloud, collaborations that may have historically taken years to yield results can happen in a fraction of that time.
      "Collaboration would be happening, but it would happen very slowly if we weren't doing this," Dr. Newman says.
    • Manager of Bio Info Software Development, St. Jude Children's Research Hospital
      Biography
        Growing up in Memphis, Clay McLeod was familiar with the work being done at St. Jude, but because he specialized in computer science, his job prospects were originally thought to be more tailored for a career in New York, Chicago or Silicon Valley. After one of his college professors told him St. Jude was interested in sharing their genomics data with the world, those options included staying in Memphis to work at the hospital.
        Clay joined St. Jude in 2016 as a senior software engineer, and is now manager of the development team for St. Jude Cloud, which involves putting genomic data, analysis tools and visualization into the cloud. That work also includes working closely with internal and external researchers to make sure the data is accurate and accessible when needed. That proximity to researchers allows for quick changes that will make St. Jude Cloud a revolutionary tool in cancer research.
        The cloud currently includes more than 5,000 whole genome sequences (which comprise half a petabyte of data). Clay co-authored the Rapid RNA-Seq pipeline for St. Jude Cloud.
        While the work is complex and challenging, Clay embraces it because it is putting St. Jude in one-of-a-kind territory of providing some of the most cutting-edge biology in the world to peer researchers at no charge.
        "What we aim to do is enable scientists around the world to do research at their own pace," Clay says. "If you just give them the tools to make the world-changing discoveries, they'll take it from there."
        Clay earned his degree in Computer Science from the University of Mississippi.

      Abstract:
      DATE: October 23, 2018
      TIME: 10:00am PDT, 1:00pm EDT
       

      Next-generation genomic sequencing is transforming what is known about pediatric cancer and how we treat patients. But even with new technologies, challenges remain. In the past, the sheer size of genomics data has made sharing across the global scientific community a challenge. St. Jude Cloud is a new data ecosystem developed to advance cures by reducing the technological barriers to data sharing and analysis. Developed by St. Jude Children’s Research Hospital in partnership with Microsoft and DNAnexus, St. Jude Cloud is the world’s largest public repository of pediatric cancer genomics data and offers unique analysis tools and visualizations in a secure cloud-based environment. Access to data is simple, fast and does not require downloading prior to exploration. Researchers can also upload their own data in a private, password-protected environment to use the St. Jude Cloud visualization and analysis tools.

      In this webinar, Scott Newman, PhD, biological lead and Clay McLeod, lead developer of St. Jude Cloud, will provide an overview of this growing data-sharing platform that includes more than 5,000 whole-genome, 5,000 whole-exome and 1,200 RNA-Seq datasets from more than 5,000 pediatric cancer patients and survivors. They will also demonstrate the collection of bioinformatics tools and unique visualizations to help both experts and non-specialists gain novel insights from genomics data.

      Specific use cases will be covered. For example, the team discovered mutations connected to UV damage in a B-cell leukemia in work that was recently published in Nature. The finding led the team to use the rapid computing capabilities of the St. Jude Cloud to discover if other leukemia samples not included in the original study might have similar patterns of mutations.

      If desired, participants may explore St. Jude Cloud before the webinar and register as users at https://www.stjude.cloud.

      Learning objectives:

      • Explore data, tools and visualizations that are available in St. Jude Cloud.
      • Understand how to use St. Jude Cloud to request, access and visualize St. Jude genomics data
      • Understand how to use St. Jude Cloud to upload and analyze user-generated data

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