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Network Biosystems Developing Sanger Sequencing-Based Dx Instrument

NEW YORK (GenomeWeb News) - Harnessing microfluidic electrophoresis technology it developed earlier in partnership with Shimadzu, Network Biosystems is working on an integrated low-throughput Sanger sequencer for point-of-care diagnostic sequencing, GenomeWeb Daily News sister publication In Sequence has learned.
 
The Woburn, Mass.-based company, founded in 2000 by a professor at the Massachusetts Institute of Technology, initially developed microfluidic separation and detection technology in partnership with Shimadzu, which incorporated the technology into a commercial high-throughput Sanger sequencer. NetBio is now developing a clinical diagnostic sequencer on its own, integrating separation with sample prep and sequencing modules into a single unit.
 
When NetBio’s team surveyed the sequencing market a few years ago, they came “to the conclusion that the world probably had more than enough high-throughput genomic sequencing companies,” said Richard Selden, NetBio’s executive chairman. Most of these, he said, focus on the research market.
 
However, he and his colleagues decided that both clinical diagnostics and forensics could benefit from rapidly generated selective genomic information, which they believed their microfluidics-based technology could provide.
 
The company has since been focusing on developing an integrated instrument, different versions of which could be used for clinical diagnostic sequencing as well as for short tandem repeat identification in forensics.
 
The clinical Sanger sequencing system will “accept clinical samples and generate sequence within an hour,” Selden said. “Instead of trying to sequence entire genomes, we are working on generating relatively small amounts of sequence in real time at the point of care to allow a physician to make an immediate clinical intervention.”
 
The system, to be called Genebench, could be used, for example, to identify strains of bacterial pathogens and to determine their antibiotic resistance profiles, he said. Other potential clinical applications include the analysis of viral drug resistance, as well as biothreat detection.
 
NetBio has already completed the development of individual subsystems for the platform and is currently in the process of integrating them, Selden said. They include modules for DNA purification, RT-PCR for RNA analysis, multiplexed PCR, Sanger sequencing reactions, and separation and detection of the Sanger products.
 
The system will have relatively low throughput — ranging from a single sample to maybe as many as 96 samples per run — allowing users to run the instrument on an as-needed basis, rather than having to wait for enough samples to accumulate.
 
In addition to integrating all steps required for sample preparation and sequencing, it will be more rugged than conventional capillary electrophoresis sequencers, according to Selden, so it can be moved around easily without breaking. “This is not intended, in any way, to replace capillary sequencers; we are just talking about a different series of applications,” he said.
 
Integrating the subsystems will take about a year, after which the company plans to start clinical testing, he said, adding that it is too early to talk about a commercialization date for the instrument. “We still have lots to do in clinical validation work,” according to Selden.

Selden acknowledged that the clinical diagnostics market is already crowded with companies developing assays to detect pathogens. Among them are Cepheid, CombiMatrix, and Becton Dickinson. However, “we are trying to develop a single assay that would be appropriate to detect a large number of species of bacteria and also to do strain-specific identification by sequence,” he said. “I think that’s quite different from what other groups are doing.”
 
Development of the instrument and its modules has been funded in part by a grant from the National Human Genome Research Institute’s “$100,000 Genome” Advanced Sequencing Technology program. In 2005, NHGRI awarded the company $4.5 million under this program.




A more comprehensive version of this article appears in last week's issue of In Sequence.

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