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Plastic or Steel, Bioreactors Aim to Put Quality First Next-generation sequencing (NGS) is emerging as a powerful clinical diagnostic tool expediting molecular stratification, and it is enhancing our knowledge of tumor clonal changes. This article presents feasibility of NGS in the context of tar- geted therapeutic approaches to cancer. "We are entering a promising time in cancer treatment, when the accumulated experience in cancer genome sequencing can be put to practical use in clinical practice," says Shashikant Kulkarni, Ph.D., a professor of molecular and human genet- ics at Baylor College of Medicine, and a senior of- ficer at Baylor Miraca Genetics Laboratories. "In just five years, NGS went from an experimental laboratory technology to clinically validated diag- nostic tool." Dr. Kulkarni points to the recent guidelines de- veloped by the Next-Generation Sequencing: Stan- dardization of Clinical Testing (Nex-StoCT) work- group. Combined with more recent guidelines for bioinformatics, these im- portant principles ensure see page 32 A technician inserts a single-use probe into a 1,000 L Thermo Scientific HyPerforma single-use bioreactor. Theoretically, single-use probes could be used in stainless-steel bioreactors irrespective o f t h e i r m a n u f a c t u r e r s . P r a c t i c a l l y, s u c h interoperability is unlikely until standards efforts resolve connectivity issues such as probe/port dimensions and sterilization-friendly formats. Researchers based at the Mayo Clinic's Biomarker Discovery Program have combined laser capture microdissection and mate -pair sequencing to generate plots that detail large genomic alterations such as breakpoints, rearrangements, and copy-number variations. Such plots can help clinicians distinguish between independent primary tumors and metastasis. In this image, lines indicate bioinformatically associated breakpoints; line widths, numbers of associated mate-pair reads. But familiar distinctions are becoming less relevant, and new developments are changing the stainless/plastic calculus. With single-use systems gaining ground every day, it becomes impossible to ignore plastic in any discussion of bioreactors, even discussions purportedly focused on steel. With the adoption of single-use bioprocess equipment reaching a turning point in terms of acceptance, industry has taken a more neutral—perhaps philosophical is a better Angelo DePalma, Ph.D. Whoever said there's nothing new under the sun was not, evidently, referring to bioreactors. Yes, we may feel as though we have heard everything about the relative benefits and capabilities of both stainless-steel equipment and single-use systems. Kate Marusina, Ph.D. Drug development in oncology continues to experience high failure rate. We now understand that tumors are heterogeneous and dynamic, and we are seeing the importance of stratifying patients as well as continuously monitoring for resistant mutations. These measures may improve response rates to targeted therapies and their survival benefit. see page 24 35 Anniversary! th Leading the Way in Life Science Technologies August 2016 GENengnews.com Sequencing Boosts Standard of Care 6 12 20 27 Evolution Faster When Earth Was Warmer GEN ROUNDUP Context-Enriched Cell-Based Assays Sift, Sort, Seize Transcriptomic Gold Microbial Platforms Set for Rapid Growth 36 Stem Cells and the Frozen Zoo DNY59 / Getty Images