Microchip Biotechnologies awarded $6.1 M by NHGRI to develop next generation DNA sequencing system
The National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), today announced it has awarded a $6.1M grant over a 3 year period to Dr. Stevan Jovanovich at Microchip Biotechnologies Inc to develop a next generation DNA sequencing system to achieve a $100,000 mammalian genome ¾100 fold lower cost than is possible today. This award is one of 11 aimed at dramatically reducing the cost of DNA sequencing, in the next five years, a move aimed at broadening the applications of genomic information in medical research and health care.
As announced by NHGRI, the award to MBI and collaborators at the University of California at Berkeley, Northwestern University, and the Columbia University Genome Center is to develop a Microbead INtegrated DNA Sequencer (MINDS) System which MBI will commercialize as the NanoBioSequencer product. The NHGRI announcement states “retaining the advantages of current DNA sequencing methods, including well-developed community infrastructure, commercial availability of reagents and existing analysis software, this group will push Sanger-based sequencing toward its performance limit in a completely automated, bench-top system. The heart of the system will be a microchip-based device that can label and process DNA fragments from individual microbeads in low-volume reactions, followed by ultra-fast separation and analysis on microfabricated capillary electrophoresis channels.”
For more details about the NHGRI sequencing technology development grants, go to: http://www.genome.gov/12513162. NHGRI is one of 27 institutes and centers at NIH, an agency of the Department of Health and Human Services. Information about NHGRI can be found at: www.genome.gov.” For more information about MBI and its DNA sequencing program, contact bizdev@microchipbiotech.com.
ABSTRACT.
This collaborative project is aimed at the development of a MINDS that efficiently integrates all of the major steps in DNA sequencing, from library construction to final sequence output exploiting low-cost microfluidic devices. The automated MINDS system will combine three fundamental steps: 1) library construction, amplification, and selection using microbead colony technologies; 2) nanoliter cycle sequencing sample preparation and purification; and 3) microfabricated capillary array electrophoresis (µCAE)-based separation of DNA sequencing fragments. The library construction and amplification process will input sheared, sized DNA fragments and construct an emulsion PCR amplified library of template on beads, with each bead representing a single DNA fragment. Single beads will then be processed in a 25 nL cycle sequencing reactor to produce fluorescently labeled sequencing fragments that are efficiently captured, concentrated and purified using on-chip affinity capture. The fragments are then separated and sized on a proven microfabricated µCAE sequencer.
This project will combine the efforts of Microchip Biotechnologies Inc. (MBI) with subcontracts to three collaborating academic institutions. MBI will develop a prototype microchip-based DNA sample preparation nanoscale thermal cycling module and a prototype µCAE sequencing system using conventional sequencing chemistries. These will then be integrated to produce a MINDS microchip with arrays of 25 nL cycle sequencing sample preparation, affinity purification, and µCAE sequencing. When this has been accomplished, by 30 months, MBI will further integrate microbead-based library technology being developed by the Mathies laboratory at UC Berkeley to create MINDS System prototypes ready for beta-testing. These developments will build upon novel methods and strategies developed in tandem by the academic collaborators, in particular the µCAE separation system and bead-based microfluidic “cloning” methods. A subcontract to the Mathies lab at UC Berkeley will support the development of new microtechnologies for the amplification and selection of clones, and the integration of these methods and processes with prototype microfabricated sequencing systems. In collaboration with the Mathies group, the Barron lab at Northwestern will develop and test novel DNA separation matrices that are easily loaded into and replaced from chip microchannels, and that provide rapid, high-resolution separations. The overall project goal is to develop and then beta test a fully integrated, prototype Sanger sequencing system at the Ju lab of the Columbia Genome Center to demonstrate the feasibility of performing genomic sequencing and resequencing at 100-fold lower cost with an anticipated throughput of about 7 million bases/day/machine.
The MINDS system will greatly reduce the cost of shotgun sequencing and resequencing, by exploiting the ability of well established µCAE devices to analyze sub-nanoliter volumes through preparation of samples in volumes more closely matched to the analytical requirements, reducing cycle sequencing reagent consumption by 100-fold. Library construction will be automated in the bead-based format, with amplification and selection performed at full scale in a single bulk reaction, again reducing reagent consumption and cost. A novel polymeric separation matrix designed for microchips already shows good performance and, along with microfluidic volume reductions, will minimize matrix expense. With these combined innovations, the MINDS system will drive CAE instrumentation close to the ultimate performance possible for four-color Sanger fluorescent DNA sequencing in an ultra-high-throughput implementation for genome centers. Future work will explore the development of lower-throughput versions appropriate for core and individual laboratories.
For More Information Contact:
Microchip Biotechnologies Inc.
4059 Clipper Court, Fremont, CA 94538
Tel: 510-438-9342
FAX: 510-438-9311
Internet: bizdev@microchipbiotech.com
