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Finer Screens for Circulating Tumor Markers NGS Ready for Clinical Oncology Testing In particular, by making it possible to screen the entire coding sequence of cancer-related genes, NGS overcomes a key problem—cancer predispo- sition cannot be monitored by just a few hotspot mutations. The sensitivity, speed, and potentially decreased cost per sample make NGS a highly attractive tech- nology. In fact, NGS may soon consolidate many other platforms. While some NGS applications, such as whole-genome sequencing, will probably have to wait several years before they spread and enter routine clinical use, other NGS applications are ready now. One NGS application that shows immediate promise for clinical oncology testing is exome sequencing. "We hope that in the near future, se- quencing of the cancer exome will soon provide oncologists with information they need to identify and utilize treatment options based on the patient's genomic profle," says Helen Fernandes, Ph.D., associate professor of pathology and laboratory medicine, Weill Cornell Medical College. Dr. Fer- nandes, however, adds that NGS will become es- tablished in the clinic only after certain challenges are addressed. NGS Assays "We need to understand the role of several mu- tations in the pathogenesis and outcomes of tumors before the information can be used for patient care," explains Dr. Fernandes. see page 34 Personal Genome Diagnostics (PGDx) performs CLIA-validated next- generation sequencing for the identifcation of MET amplifcation in plasma using circulating tumor DNA. Here, clinical libraries generated from cell-free DNA for the MET locus are being enriched in preparation for sequencing. Exome sequencing has promise in oncology testing, particularly in the monitoring of disease progression and the prediction of therapeutic responses. To realize this promise, researchers are developing and validating assays of ever-wider scope. Zmeel/iStock They are increasingly being used for diagnostic and prognostic applications to guide patient care and therapeutic decision making. Advances in the de- tection, isolation, and analysis of CTCs, ctDNA, and exosomes were the focus of several presenters at Se- lectBio's "Circulating Biomarkers" conference held recently in Boston, including Robert McCormack, Ph.D., head of technology innovation and strategy at Janssen Diagnostics, a subsidiary of Johnson & Johnson. It has become apparent that "CTC's refect more the biology of a cancer than the amount of cancer," said Dr. McCormack, and "therein lies their true value." Vicki Glaser Circulating tumor cells (CTCs) and circulating tumor (cell-free) DNA (ctDNA) are valuable research tools for studying the biology, genetic makeup, and activity of metastatic cancer. Kate Marusina, Ph.D. Next-generation sequencing (NGS) not only continues to make steady advances in the molecular diagnosis of cancers, it also seems to ft perfectly with our current knowledge of the oncogenome. see page 12 TO O L S T E C H N O LO G I E S T E C H N I Q U E S August 2014 www.GENengnews.com Sticky Ends... Chimps Find New Homes 6 FDA Gets Social with Biopharmas 8 Real-Time PCR: Yet More Worlds to Conquer 18 Embracing the Innovation Imperative 28 Single-Use Bioreactors Dare to Scale 24