MAY 12, 2016 12:00 PM PDT

Implementation of genomic assays for tumor genome profiling in a clinical laboratory setting

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  • Professor, Department of Pathology, Director, Genomic Technologies, Center for Advanced Laboratory Medicine, University of California San Diego
      Dr. Murray is Director of Genomic Technologies at UC San Diego's Center for Advanced Laboratory Medicine (CALM) and Professor in the Department of Pathology. At the CALM, Dr. Murray is involved with the development of advanced genomic technologies for the clinical lab, and oversees the bioinformatics and analysis of genomic data. Prior to coming to UCSD, she was a founding member of the Scripps Translational Science Institute, serving as the institute's Director of Genetics, as well as Associate Professor of Translational Genomics at The Scripps Research Institute. While at Scripps, Dr. Murray directed a high-throughput genotyping and sequencing laboratory aimed at discovering genetic components of various diseases and health, and determining risk profiles based on combinations of specific risk alleles in large prospective studies. From 2003-2007, Dr. Murray was the chief geneticist at Illumina, a San Diego genomics biotech company, where she played a large role in developing the content and design strategy for numerous whole genome genotyping arrays that enabled large-scale genome-wide genetic studies. Dr. Murray has a long history in both theoretical and applied genetics research. She has published over 90 articles in the human genetics literature that focus on the discovery and analysis of DNA sequence polymorphism. Dr. Murray received her Ph.D. from the University of Pittsburgh's Department of Human Genetics, and was a postdoctoral fellow at Case Western Reserve's Department of Genetics. Dr. Murray also has a M.S. degree in genetic counseling from the University of Pittsburgh.


    In order to realize the benefits of personalized cancer therapy, increasing demands are placed upon clinical laboratories to provide timely, comprehensive, clinically actionable, and analytically valid information regarding the genomic profile of individual patients’ tumor specimens. We have employed both next generation sequencing (NGS) technologies as well as DNA microarrays to comprehensively profile solid tumors for diagnostic, prognostic, and therapeutic indications. We have developed a custom NGS-based panel test to interrogate all exons for 397 genes, as well as most introns for a subset of 28 genes. The NGS panel detects several types of genomic alterations, including coding missense, nonsense, splice variants, insertions/deletions, focal gene amplifications, homozygous deletions, and selected rearrangements. Reportable variants are classified as either clinically significant with in-depth annotation regarding clinical relevance, relevant therapies and clinical trials, or variants of uncertain clinical significance with limited annotation. The DNA microarray complements the NGS assay by assessing genome-wide chromosome structural changes including gains, losses, focal gene amplifications, and copy-neutral events such as loss of heterozygosity (LOH). Direct involvement of clinical lab directors, pathologists, oncologists, and radiologists in our institution’s working tumor conferences via the presentation of in-house laboratory findings enhances both patient care and the educational environment via better informed discussion of unique patient specific findings.

    Learning objectives:

    • Understand technical advantages and limitations for next-generation sequencing and DNA microarrays in a clinical test setting.
    • Understand how next-generation sequencing and DNA microarrays can be used to aid in diagnosis, prognosis and therapeutic decision-making in oncology.

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