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OMICS Data Analysis: Today's Next-Gen Sequencing Imperative John Russell Without question, next-generation sequencing (NGS) has been immensely successful, even if it hasn't transformed medicine just yet. Sequencing itself has become nearly trivial. Declining costs have made it widely accessible. Recently, the rise of affordable benchtop NGS instruments promises to democratize the technology further, extending it out from large sequencing centers into smaller labs and clinics. Today, the bigger challenge is deciphering the vast NGS datasets of wide-ranging data types—RNA-Seq, ChiP-Seq, exome, etc.—in order to inform biomedical questions ranging from evolutionary heritage to the functioning of cellular molecular machinery. NGS data analysis was among the many topics discussed at last month's "NGX: Applying Next-Generation Sequencing" meeting. Integrating various NGS data into networks that are both manageable in size and likely to be true was the core of a talk from MIT's Ernest Fraenkel, Ph.D., associate professor of biological engineering. Interpreting high-throughput data, he noted, can be like reading "The Hitchhikers' Guide to the Galaxy," in which the meaning of life and the universe turns out to be the number 42. "Suddenly you realize you didn't understand what the question was," Dr. Fraenkel said. "That's often true of high-throughput data. We get different answers and we don't know what they mean. Our integrative approach is to try to discover a biological process that gives rise to the experimental data we detect." Two recent papers describe his approach, which does not rely on published literature or traditional pathway analysis. Rather, the method uses only the physical interactions. The basic idea is to connect those interactions within true biological networks of manageable size. Dr. Fraenkel uses a graph-based Prize-Collecting Steiner Tree (PCST) algo- Next-generation sequencing methods have revealed that foreign RNAs are common in human plasma. Pacifc Northwest Diabetes Research Institute (PNDRI) NEWS Genomics & Proteomics > New England Biolabs Gains Access to Advanced NGS Library Prep Method Population Genetics Technologies (PGT) assigned exclusive rights to U.S. patent 8,420,319 to New England Biolabs (NEB). The patent covers techniques for asymmetric adaptor library construction. As part of next-generation sequencing (NGS) library preparation, this technology enables increased efciency at the adaptor ligation step, resulting in high-yield libraries and minimized adaptor-dimer formation, according to PGT. "Given the incredible expansion of genome sequencing and nucleic acidbased assays, methods that simplify and improve nucleic acid manipulation and analysis are of high value," said Frank Massam, PGT's COO. "We are therefore delighted that some of the methods we have invented and developed can now be made available to a larger customer base via NEB's global distribution network. This partnership fts well with our strategy of engaging with partners to 26 | fully realize the value of our technologies and capabilities." "We are excited to ofer a novel adaptor solution for NGS library preparation to our customers," added Peter Nathan, NEB's executive director of global business development. "The increased efciencies resulting from use of this process further enhance the workfows for our NEBNext library construction kits." associated therapeutic strategies such as drugs and clinical trials. According to CollabRx, this content leverages the company's semantic integration platform, a proprietary technology that enables CollabRx scientists and physicians to dynamically update the company's knowledge base with the latest medical and scientifc data available in the public domain. > CollabRx Launches Service for > Controlled Access to HeLa Data analytics company CollabRx, launched the company's Genetic Variant AnnotationTM (GVA) service. The GVA service is a new product and the company's frst offering for the clinical laboratory market. GVA is intended to provide an automated and scalable medical informatics solution that pairs the results of genetic sequencing tests with clinically actionable and dynamically updated knowledge. Such knowledge includes the clinical impact of specifc genetic profles and The NIH reached an understanding with the family of the late Henrietta Lacks to allow researchers controlled access to the full genome sequence data from cells derived from her tumor, commonly known as HeLa cells—the frst human cells to be successfully grown in the laboratory, and the source of the world's most commonly used human cell lines. The understanding was designed to balance the Lacks family's wish to continue enabling scientifc progress with Interpretation of Clinical Cancer Sequencing September 1, 2013 | GENengnews.com | Genetic Engineering & Biotechnology News Cell Genome Allowed with Lacks Family's Blessing the desire to publicly acknowledge Lacks' contribution to research. Researchers will be able to apply to the NIH for access to the full genome sequence data from HeLa cells, if they agree in return to abide by the terms of the HeLa Genome Data Use Agreement. Two representatives of the Lacks family will join representatives from the medical, scientifc, and bioethics communities on a new NIH-created, sixmember working group that will review proposals to access the HeLa full genome sequence data. NIH-funded researchers who generate full genome sequence data from HeLa cells will be expected to deposit their data into a single database for future sharing, accessible at http://www. ncbi.nlm.nih.gov/projects/gap/cgi-bin/ study.cgi?study_id=phs000640.v1.p1. All researchers who use or generate full genomic sequence data from HeLa cells will now be asked to include in their publications an acknowledgement and expression of gratitude to the Lacks family for their contributions. n