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18 | AUGUST 2014 | GENengnews.com | Genetic Engineering & Biotechnology News One particularly important refnement, introduced about two decades ago, is the "real time" quantifcation of DNA. The idea is to trace the rising level of DNA through- out the amplifcation step, and not just mea- sure the fnal amount of amplifed product. This idea turns standard PCR into real-time PCR, or quantitative PCR. Real-time PCR has become the most widely used nucleic acid detection technol- ogy. It is routinely used in academic research, in applied testing settings such as food-safety or veterinary testing, and in molecular diag- nostics. It continues to replace many older detection methods due to simple readouts, high sensitivity, and multiplex and quantif- cation capabilities, as well as ease of use, cost effectiveness, and throughput fexibility with only moderate equipment investments. According to Peter Urbitsch, Ph.D., head of the global assay technologies business at Qiagen, real-time PCR technology has evolved and diversifed in multiple directions. Available formats include tubes, microar- rays (96-, 384-, and 1,536-well plates), and capillary and rotor variants. Detection prin- ciples include SYBR green and probe-based detection, with the latter being increasingly diversifed into FRET, Scorpions, TaqMan, and others. In addition, multiplex detection formats are being developed using different dyes and quencher molecules. Innovations are driven by dissemination into new application areas and user pro- fles. Essentially, the technology is becoming easier to use and accessible to novices while providing more complex information faster and at lower costs. This development can be compared to computer technologies, which evolved from bulky "specialist equipment" to powerful and convenient end-user devices. As real-time PCR continues to replace tra- ditional technologies, less experienced users become routine users. While some instruments are small, simple, and accessible to almost anyone and deployable at nearly any bench, other platforms are targeting high-throughput data generation and require robust chemistry that allows automated handling and reaction set-up at room temperature. Procedures include a higher degree of process controls (such as target controls via multiplexing) or operational controls (such as the visual pipetting control in Qiagen's QuantiNova kits). This is particularly im- portant in complex applications such as mul- tiplex detection of various targets and inte- gration or cross-linking of multiple scientifc questions such as genotyping, mRNA and miRNA profling, or copy number variation (CNV) analysis. A common bottleneck for both real-time PCR and other technologies such as next- generation sequencing (NGS) is the consoli- dation and interpretation of data and results, increasingly requiring bioinformatics tools that support the interpretation of the biolog- ical meaning of gene expression data, such as Qiagen's Ingenuity Pathway Analysis and Ingenuity iReport. Beyond Instrumentation Early real-time PCR was focused on per- fecting instrumentation. Instrumentation is no longer a rate-limiting step in the produc- tion of quality data; instead, usability, soft- ware, and analysis are at the forefront. "The big problem with real-time PCR is not the amount or complexity of data, but whether or not data are any good. Every- one can get traces, especially with poorly designed primers and probes," explains Sam Ropp, Ph.D., senior business unit market- ing manager, GXD Consumables, Bio-Rad Laboratories. "The focus has shifted from hardware improvements to tools that impact data quality. When users get better data, they can have confdence in the frst run." A set of guidelines, the Minimum Informa- See Real-Time PCR on page 22 > Erasmus MC Chooses Oracle to Support Genomic Research Erasmus Medical Center Rotterdam (Erasmus MC) selected Oracle Health Sciences Translational Research Center running on Oracle Exadata Database Machine as the foundation for its next-generation genomics initia- tives to advance personalized medicine. Erasmus MC plans to use the solution, which enables researchers to simultaneously analyze clinical and omics data, to reveal new insights, such as the discovery and vali- dation of new biomarkers, which are expected to lead to more eective, personalized treatment recommendations. The inaugural project will focus on improving care and outcomes for patients with craniofacial malforma- tions. The initiative will involve whole-genome sequenc- ing for more than 1,000 patients. > BGI, Edinburgh Team Up for Synthetic Biology Project BGI and the University of Edinburgh signed a collabo- ration agreement to pursue a synthetic biology project worth up to £1 million ($1.71 million). The two institutes will team up to produce synthetic yeast chromosome VII in the Edinburgh Genome Foundry, recently funded by the U.K.'s Biotechnology and Biological Sciences Re- search Council. Faculty members from the Centre for Synthetic and Systems Biology at the University of Edinburgh and re- searchers at BGI will work together on synthesizing chro- mosome VII as part of the International Synthetic Yeast Project (Sc2.0), initiated by the Johns Hopkins University School of Medicine as the rst synthetic eukaryotic ge- nome project. The goal is to recreate the chromosome of yeast so that it can be manipulated for useful purposes. The two parties will join forces to create an internationally com- petitive and innovative research team in the eld of syn- thetic biology and work toward a technological break- through in constructing an articial yeast genome. > BioDiscovery Wins SBIR Grant to Improve TCGA Copy Number Profles BioDiscovery, maker of Nexus Copy Number soft- ware, was awarded a Small Business Innovation Re- search (SBIR) phase I grant from the National Institutes of Health to improve the copy number variation data from The Cancer Genome Atlas (TCGA). The company has selected Huntsman Cancer Institute at the Univer- sity of Utah to assist in developing and validating the new product. The commercial release of the improved TCGA copy number and sequence variant data will not only allow researchers to make further discoveries into tumorigenesis and disease progression, it will also pro- vide a meaningful validation set for internal studies. > NCGR, Simbiot Announce Big Data Partnership The National Center for Genome Resources (NCGR) and Simbiot are partnering to create new solutions for han- dling "big data" in the genomics space. The two groups are joining forces to launch Lumenogix NGS, a software platform that oers researchers knowledge mining and control over their own next-generation sequencing data. Lumenogix NGS includes data analysis capability with ve integrated pipelines and dozens of peer-re- viewed algorithms. The platform's researcher-friendly interface can allow nonspecialists to analyze complex datasets, and its data and information management fea- tures can permit samples to be tracked throughout the data analysis process. > StoneCalibre Acquires Edge BioSystems StoneCalibre completed its acquisition of Edge Bio- systems (EdgeBio), headquartered in Gaithersburg, MD. EdgeBio is a specialized manufacturer and distributor of sample-preparation and clean-up products for use in DNA sequencing. EdgeBio's consumable products can allow researchers to determine the exact genetic make- up of DNA for use in clinical and diagnostic labs, food testing, molecular medicine, ancestry studies, and other applications. n OMICS News GENOMICS & PROTEOMICS Real-Time PCR: Yet More Worlds to Conquer MaryAnn Labant The polymerase chain reaction (PCR), invented about three decades ago, soon entered mainstream use thanks to an ongoing series of refnements. Qiagen's QuantiNova kits have a built-in tracking s ys te m fo r v i s u a l i d e nt i f i c at i o n o f co rre c t pipetting.