Genetic Engineering & Biotechnology News

NOV15 2017

Genetic Engineering & Biotechnology News (GEN) is the world's most widely read biotech publication. It provides the R&D community with critical information on the tools, technologies, and trends that drive the biotech industry.

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Kathy Liszewski A good bioassay, like a good marriage, joins two part- ners in a bond is mutually beneficial. In the case of bio- assays, optimal design and development and accurate statistical analysis comprise a lasting partnership. At the Cambridge Healthtech Institutes's fifth annual Optimizing Bioassays for Biologics confer- ence, held in October 2017 in Washington DC, experts discussed the many challenges facing this field and weighed in on how to avoid costly mistakes when opti- mizing bioassays for biologics. Solutions suggested include automating workflows to enhance potency bioassays to save time and money, employing carefully selected cell-based assays that will reduce development time and sat- isfy requirements for comparability Avoiding Costly Errors in Bioassay Development Over the years, some of the challenges surrounding cir- culating DNA have revolved around developing meth- ods to allow for its sensitive detection, interrogating its composition, and translating research findings into clinical applications. "Cell-free DNA (cfDNA) is stable, easy to collect, and relatively easy to analyze, but we are still learn- ing about what it contains," says Geoffrey R. Oxnard, M.D., assistant professor of medicine at Harvard Med- ical School. Dr. Oxnard and colleagues have developed a strategy to discriminate germline and cancer-derived variants of the EGFR T790M mutations from cfDNA in patients with non-small cell lung cancer. As part of this work, investigators in Dr. Oxnard's lab interrogated a database of plasma next-generation sequencing (NGS) data originating from over 31,000 patients using a bioinformatics algorithm that they developed and validated—illustrating the possibility of collecting data about germline and somatic cancer mutations and discriminating between the two in a single assay. "The fact that we are finding germline mutations when we study cfDNA reminds us that the vast major- ity of this DNA is germline," says Dr. Oxnard. cfDNA is a complex mixture that contains nucleic acid from benign cells, white blood cells, and viruses, with tu- mor DNA appearing to represent only a fraction. "The most important lesson from our [work] is that we need to remember that we still aren't quite sure yet of what exactly is see page 28 Richard A. Stein, M.D., Ph.D. Ever since the first description of circulating, non- encapsulated DNA in the bloodstream, the detection in body fluids of DNA that originates from malignant tumors has attracted considerable interest for diagnostic and therapeutic purposes. Cell-Free DNA Drives Liquid Biopsy Testing November 15, 2017 CRISPR Tools Grow in Sophistication 14 Unlocking the Potential of CRISPR- Based Gene Editing 18 Cell and Gene Therapies: Industry Faces Potential Capacity Shortages 25 see page 8 Meghaan M. Ferreira Imagine publishing a paper, accepting a research grant, or recruiting patients for a clinical trial only to discover that the esophageal cancer cell line used in your disease model actually came from a different tumor type. It's a scientist's nightmare, but it became an unfortunate real- ity for researchers working with the widely used esoph- ageal cancer cell lines, SEG-1, BIC-1, and SK-GT-5, when an alarming report in the Journal of the National Cancer Institute, published in 2010, ripped away the mask concealing these misidentified cell lines. 1 The really frightening part, however, is that this ex- ample does not represent a single, isolated event, but rather, an insidious recurring issue that has affected the entire biomedical research community and has even received attention from public media outlets. In 2014, NPR broadcasted a report about a misidentified mela- noma cell line, MDA-MB-435, that researchers have used for years as a model for human breast cancer. 2 Now the validity of all that data, which included over a thousand publications, comes into question. In addition to littering scientific literature with po- tentially erroneous conclusions, research studies using contaminated or misidentified cell lines receive an esti- mated $700 million dollars in grant funding every year. 3 To break this cycle, the National Institutes of Health and many Raising the Bar for Cell Line Authentication see page 22 Leading the Way in Life Science Technologies Capturing and identifying circulating DNA could hold the key to rapid, minimally invasive, disease diagnostics— ultimately improving clinical decision making and outcomes. oonal / Getty Images

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