Session Synopsis: Genomic medicine, will change the way we prevent, manage and treat disease. Optimizing platform components to manage, access, and store genomics data, as well as various computational tools are important to make this a reality for successful genome characterization and population scale projects for precision medicine to be discussed in this session.
Session Chair Profile
Sequencing Technologies Visionary and Leader in Genomics and Cancer Genomics
Ph.D., Co-Director, Genomics Institute, Nationwide Children’s Hospital, Columbus, OH
Dr. Mardis is an internationally recognized expert in genomics,cancer genomics and sequencing technologies whose research interests are in the application of next generation sequencing to characterize cancer genomes and transcriptomes as well as translation of basic science discoveries about human disease to support therapeutic decision-making. Prior to being named Co-Director of the Genomics Institute at Nationwide Children’s Hospital in 2016, Dr. Mardis served as Co-director of the McDonnell Genome Institute at Washington University in St. Louis since its inception in 1993. As Co-Director and Director of Technology Development at one of four genomics centers funded by the National Human Genome Research Institute, Dr. Mardis played a pivotal role in the completion of the Human Genome project by helping to create methods and automation pipelines. She then orchestrated the Center’s efforts to explore massively parallel sequencing technologies and transition them into production sequencing capabilities as well as new applications. The Institute was among the first to use DNA sequencing technology to explore cancer tumor growth, resulting in the international effort to explore the genomics of cancer. Her team was also integral to the St. Jude-Washington University Pediatric Cancer Genome Project, which sequenced the genomes of cancerous and normal cells of nearly 1000 children. Dr. Mardis is a member of the Board of Directors for the American Association for Cancer Research and a member of the Supervisory Board of Qiagen N.V. She is editor-in-chief of Molecular Case Studies and a senior editor of Molecular Cancer Research, a monitoring editor of Disease Models and Mechanisms and Associate Editor of Annals of Oncology. Dr. Mardis also serves on several NIH study sections. Among numerous awards, Dr. Mardis has received the 2016 Morton K. Schwartz award from the American Association for Clinical Chemistry and the Scripps Translational Research award for her work on cancer genomics in 2010. She was included on the 2013 Thomson Reuters’ list of most cited researchers, one of only two women listed. Dr. Elaine Mardis graduated Phi Beta Kappa from the University of Oklahoma with a BS degree in zoology and then completed her PhD in Chemistry and Biochemistry in 1989, also at Oklahoma.
Precision Cancer Genomics
Genomic characterization of cancers provides a unique opportunity for precision medicine. My talk will outline various computational tools used to interpret cancer genomics data in the context of targeted therapies. I also will illustrate the cancer “immunome” that can be elucidated through genomic profiling to identify neoantigens that may have therapeutic benefit.
Ph.D., Director of the Genomics Platform, Broad Institute of MIT and Harvard
Under Gabriel’s guidance, the Genomics Platform explores, validates, optimizes, and implements new technologies, methods, and analysis tools to meet the needs of the Broad community. Gabriel and the members of her team are committed to pushing the boundaries of the genomic frontier through the application of operational excellence, advanced process design, data analysis and visualization, and technology development capabilities. In addition to her activities with the Genomics Platform, Gabriel’s research interests lie in using genomic techniques to understand the genetic component of common disease. She has represented the Broad in many large national projects, including providing foundational research for the International HapMap Project; serving on the steering committee for the 1000 Genomes Project, as well as co-chairing the project’s production group; serving on the steering committee for The Cancer Genome Atlas; serving as principal investigator on the National Heart, Lung and Blood Institute’s Exome Sequencing Project; and co-principal investigator (with Eric Lander) of the National Human Genome Research Institute’s large-scale sequencing center at the Broad Institute. She has also served as principal investigator on eight NIH grants, totaling over $200 M, related to large-scale genotyping, sequence production, and analysis.
To the Cloud(s): Keeping up with DNA Sequencing
Recent advances in genomics technology have created vast opportunity in the breadth (scale of data collection, type of nucleic acid, type of event) and the resolution (rare somatic mutations, single cells, cfDNA) at which human biology can be studied. In particular, implementation of the HiSeqX platform has opened the door to human whole genome sequencing in an unprecedented way, enabling projects that would now have been undertaken previously and setting the stage for bold new directions at the population scale. Along with this we experience a divergence in the growth of DNA sequencing versus cost and scalability of compute as well as ease of data sharing and aggregation. In order to keep up with sequencing at population scale we require scalable, efficient, and cost effective analysis approaches to eliminate computation as the gating factor in the progress of scientific discovery. We will discuss challenges and findings from our experience, and an approach to empower other researchers to leverage our cloud-based best practice analysis pipelines capable of processing a whole genome every 4 minutes.