Latest webinar

Viewing cancer genomes at high resolution

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Large-scale cancer genomics studies have established an extensive and unprecedented catalog of somatic mutations in multiple cancer types. This landscape was determined using mostly highly cellular, untreated primary tumors and is mostly static with limited implications to understand cancer progression and drug response in the clinic. Tumors are composed of multiple cell types: stromal, immune or malignant cells. Malignant cells can also show sub-clonal heterogeneity, where different clones carry various somatic mutations and show variable oncogenic potential or drug sensitivity. Finally this sub-clonal population can change during the progression of cancer or as a consequence of the treatment. Additional genomic heterogeneity arises through the characteristic signatures of the various mutational processes that drive genome disruption during tumorigenesis, which highly powered technologies are beginning to resolve. In a webinar presented by Bio-Rad and Genome Biology, Elaine Mardis (Washington University in St Louis), a world leader in the field of cancer genomics, and Olivier Harismendy (University of California San Diego), who is developing clinical assays in which next-generation sequencing is combined with digital PCR, discuss the latest developments and outstanding questions that relate to viewing cancer genomes at high resolution. The webinar will be open for audience discussion.    

Speakers and Moderators

Moderator:

Clare Garvey: Editor Genome Biology, BioMed Central, UK

Dr Clare Garvey joined the Genome Biology team in 2007 after working as an Assistant Editor at Nature Publishing Group. At BioMed Central, Clare and her team manages the peer-review of manuscripts in addition to commissioning reviews and other interesting articles for publication. Dr Garvey’s background is Drosophila developmental genetics. Before moving into publishing Clare undertook two postdocs in Cambridge, UK 

Speakers

Elaine R. Mardis, Ph.D. : Professor of Genetics and Molecular Microbiology. Co-director, The Genome Institute at Washington University School of Medicine

Dr. Elaine Mardis graduated Phi Beta Kappa from the University of Oklahoma with a B.S. degree in zoology.  She then completed her Ph.D. in Chemistry and Biochemistry in 1989, also at Oklahoma.   Following graduation, Dr. Mardis was a senior research scientist for four years at BioRad Laboratories in Hercules, CA.

In 1993, Dr. Mardis joined The Genome Institute at Washington University School of Medicine. As Director of Technology Development, she helped create methods and automation pipelines for sequencing the Human Genome.  She currently orchestrates the Center’s efforts to explore massively parallel sequencing technologies and to transition them into production sequencing capabilities as well as new applications.

Dr. Mardis has research interests in the application of DNA sequencing to characterize cancer genomes and transcriptomes, and using these data to support therapeutic decision-making.   She also is interested in facilitating the translation of basic science discoveries about human disease into the clinical setting.

Dr. Mardis serves as an editorial board member of Molecular Cancer Research, Genome Research and Molecular Oncology, and acts as a reviewer for Nature, the New England Journal of Medicine, Cell and Genome Research.   She serves on the scientific advisory boards of Pacific Biosciences, Inc., DNA Nexus, and ZS Genetics.  Dr. Mardis received the Scripps Translational Research award for her work on cancer genomics in 2010, and was named a Distinguished Alumni of the University of Oklahoma College of Arts and Sciences for 2011.  She is the former chair of Basic and Translational Sciences for the American College of Surgeons Oncology Group (ACOSOG).

Dr. Olivier Harismendy, Ph.D. : Assistant Professor at UC San Diego

Dr. Harismendy graduated with an M.S. in Process Engineering from ENSTA-ParisTech (France) and a joint MS in Microbiology from the Pasteur Institute and Paris 7 University. He obtained his PhD in Microbiology from the same university after studying RNA polymerase III transcriptional regulation in yeast using ChIP-chip at Dr. Sentenac’s laboratory (CEA-Saclay, France). He then joined Dr. Edelman’s Department of Neurobiology at The Scripps Research Institute (La Jolla, CA), where he developed ChIP-Seq approaches to study Neuron Restrictive Silencing Factor DNA binding in mouse developing brains.

Since 2007, Dr. Harismendy has been working in translational genomics, evaluating methods for targeted sequencing, exploring the role of regulatory variants in common diseases, and detecting and studying the role of somatic mutations in cancer. Currently, Dr. Harismendy is implementing an Ultra Deep Targeted Sequencing assay to detect low-prevalence mutation in clinical samples, with the promise to provide a comprehensive personalized molecular profile of solid tumors. In addition to his functions at the Cancer Center, Dr. Harismendy is the associate director of the BioComputational Center at UCSD’s Clinical and Translational Science Institute, where he advises and supports the analysis of genomic studies initiated by clinicians.

Sponsor

Bio-Rad's unique Droplet Digital™ PCR technology provides absolute quantification of nucleic acids for a wide range of applications including cancer mutation studies, HIV detection, and environmental monitoring. This simple, reliable, and award-winning technology has already led to a robust set of published findings.

The QX200 Droplet Digital PCR (ddPCR™) system provides absolute quantification of target DNA or RNA molecules for EvaGreen or probe-based digital PCR applications.

Benefits of the QX200 Droplet Digital PCR system

Applications of the QX200 Droplet Digital PCR system

Cancer biomarker studies and copy number variation  Measure varying degrees of cancer mutations, detect rare DNA target copies, and resolve copy number variation states with superior sensitivity and resolution. PrimePCR ddPCR assays are now available for mutation and copy number detection. These are predesigned, we-lab validated assays.

Pathogen detection  Employ the extreme precision of the QX200 system to quantify small fold changes in target DNA or RNA molecules in pathogen detection and monitoring.

Next generation sequencing  Perform absolute quantification of a NGS library without the use of a standard curve.

Gene expression analysis  Achieve reliable and reproducible measurements of small fold changes for low abundance of mRNA and miRNA.

Environmental monitoring  Test a wide variety of environmental samples like soil and water using the QX200 system.

Food testing  Perform routine evaluation of genetically modified organisms (GMO) using validated ddPCR methods.