Genomics


Figure 17 (above)


PacBio SMRT cells and 8Pac format


Figure 18 (right) The PacBio® RS High


Resolution Genetic Analyzer


patent applications in more than 80 patent fami- lies. The company is currently pursuing techniques for nanopore-based analysis using biological and solid-state nanopores, as well as hybrid versions of these, and also including a wide variety of adapta- tions and modifications (Figures 15 and 16).


Pacific Biosciences (www.pacificbiosciences.com) has developed a third generation DNA sequencing system, the PacBio® RS High Resolution Genetic Analyzer, that incorporates novel, single molecule sequencing techniques and advanced real time ana- lytics. PacBio calls this SMRT® (Single Molecule, Real-Time) technology. SMRT DNA sequencing is performed on SMRT Cells, each patterned with 150,000 zero mode waveguides or ZMWs. Each ZMW contains a single DNA polymerase, provid- ing the window to observe DNA sequencing in


36


real-time. The PacBio RS system continuously monitors ZMWs in sets of 75,000 at a time. SMRT Cells are nanofabricated consumable substrates used in conjunction with the DNA Sequencing Kit for automated processing on the PacBio RS system. One SMRT Cell is consumed per sequencing reac- tion. SMRT Cells are packaged together in a streamlined 8Pac format. Experiments can be run on a single SMRT Cell or in batch mode to meet project needs. The instrument features high per- formance optics, automated liquid handling and an environmental control centre, all directed through an intuitive touchscreen interface. Also included is a state-of-the-art Blade Center, the computational brain responsible for primary data analysis. A comprehensive informatics suite completes the package. During the DNA sequencing process, the PacBio RS uses advanced collection optics to record light pulses emitted as a byproduct of nucleotide incorporation. These signals are deliv- ered in real time to the primary analysis pipeline, housed entirely on the Blade Center. Proprietary algorithms translate each pulse into an A, C, G or T base call with its own set of quality metrics. As soon as the base call data is generated, it is avail- able for secondary analysis through PacBio soft- ware or virtually any other secondary analysis pipeline. Long readlengths, intuitive operation and throughput flexibility combine to deliver the data faster than previously possible with high accuracy and the ability to detect real-time kinetic informa- tion. PacBio RS enables targeted sequencing to more comprehensively characterise genetic varia- tions; de novo genome assembly to finish genomes in order to more fully identify, annotate and deci- pher genomic structures; and DNA base modifica- tion identification to help characterise epigenetic regulation and DNA damage (Figures 17 and 18).


At the AGBT Meeting held in Florida this February, QIAGEN (www.qiagen.com) unveiled an innovative sample-to-result NGS workflow designed to enable the routine use of this break- through technology beyond life sciences research in areas such as clinical research and diagnostics. A key element of the workflow is GeneReader, a transformational NGS benchtop sequencer that offers many features essential for customers in clin- ical research and diagnostics to create routine lab- oratory processes. Unlike other platforms, which process only one flow cell at a time and often require sample pooling for cost-efficient runs, the sequencer has a turntable design that enables the continuous loading of up to 20 flow cells for inde- pendent and parallel sequencing. Individual patient


Drug Discovery World Spring 2013


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