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Roche and IBM collaborate to develop “bar code reader”-style DNA sequencing technology
07-07-2010
by Jeffrey Bouley  |  Email the author
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YORKTOWN HEIGHTS, N.Y. and BRANFORD, Conn.—Early this month, IBM and Roche announced a multiyear research and development agreement under which they will work to commercialize a "bar code reader" for DNA—a technology that might actually make personal genetic sequencing available to individuals for between $100 and $1,000 in the foreseeable future. The collaboration will take advantage of IBM's leadership in microelectronics, information technology and computational biology and Roche's expertise in medical diagnostics and genome sequencing

Looking at the deal in more technical terms, the partnership is aimed at developing a nanopore-based sequencer that will directly read and decode human DNA quickly and efficiently—an goal that will also serve to advance IBM's recently published "DNA Transistor" technology. The novel technology, developed by IBM Research, offers the promise of true single-molecule sequencing by decoding molecules of DNA as they are threaded through a nanometer-sized pore in a silicon chip. The approach would offer significant advantages in cost, throughput, scalability, and speed compared to sequencing technologies currently available or in development.

"By merging computational biology, biotechnology, and nanotechnology skills, we are moving closer to producing a system that can quickly and accurately translate DNA into medically- relevant genetic information," says Ajay Royyuru, senior manager of the Computational Biology Department at IBM Research. "The challenge of all nanopore- based sequencing technologies is to slow and control the motion of the DNA through the nanopore. We are developing the technology to achieve this so that the reader can accurately decode the DNA sequence."

Ultimately, the technology could serve to achieve the vision of whole human genome sequencing that will actually achieve—or perhaps even dip below—the elusive "$1,000 genome" dream that has been bandied about for years now. In comparison, the first sequencing ever done by the Human Genome Project (HGP) cost $3 billion—for just one genome.

"Sequencing is an increasingly critical tool for personalized healthcare. It can provide the individual genetic information necessary for the effective diagnosis and targeted treatment of diseases," explains Manfred Baier, head of Roche Applied Science. "We are confident that this powerful technology—plus the combined strengths of IBM and Roche—will make low-cost whole genome sequencing and its benefits available to the marketplace faster than previously thought possible."

As part of the agreement, Roche will fund continued development of the technology at IBM and provide additional resources and expertise through collaboration with Roche's sequencing subsidiary, 454 Life Sciences. Roche will develop and market all products based on the technology.

Roche's investment in future genomic technologies builds upon the strength of its currently available 454 Sequencing Systems, which generate hundreds of thousands of long, high quality sequencing reads in hours. The technology is available for large-scale genomic analysis with the GS FLX System and for benchtop sequencing with the GS Junior System.


 
IBM partners with University of Missouri on Genomics Research Initiative

COLUMBIA, Mo.—IBM  and the University of Missouri announced July 2 a life sciences research initiative using IBM high-performance computing technologies to advance the school's bioinformatics research projects. The goal of the initiative is to develop a first-of-a-kind cloud computing environment for genomics research collaboration at a regional level.

Mizzou researchers are pursuing projects aimed at fighting the spread of infectious diseases such as malaria and H1N1, as well as a number of projects involve the study of genome sequences in plants and animals to help improve the quality and quantity of food production. For example, Mizzou researchers have are studying bovine genes in hopes of increasing reproductive efficiency in livestock and looking at ways to grow corn in drought conditions.

The development of a genomics cloud also would have a significant impact on the way patients are diagnosed, because it would, as the university and IBM say, "bring human genome sequencing and analysis into a clinical setting for the first time, putting a valuable new tool into the hands of medical professionals and enabling a more personalized approach to medicine."

"This collaboration with IBM provides our researchers, and those being trained to become tomorrow's researchers and educators, access to critical high performance computing resources needed to process massive data sets and apply increasingly more sophisticated bioinformatics tools and technologies," says Gordon Springer, associate professor in the University of Missouri Computer Science Department and scientific director of the University of Missouri Bioinformatics Consortium.

In the first phase of the project, IBM will provide Mizzou with an IBM iDataPlex high-performance computing system, along with related software, that will integrate with the university's existing computing infrastructure to significantly speed the process of DNA sequencing and analysis of humans, plants and animals. The iDataPlex will also be used to collect and store the massive amounts of data that result from that work, providing Mizzou researchers with more reference points.

The second phase will involve University of Missouri and IBM working together to create a prototype cloud computing environment for genomics research, followed by a final phase in which the genomics cloud would become fully operational and be expanded to a regional domain. This first-of-a-kind cloud would allow sharing of bioinformatics resources among universities and institutions across a larger geographic area, which could potentially lead to a "Life Sciences Corridor" across Missouri and Kansas, and throughout the Midwest.

 
Code: E07071001

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