SeqWright last week said it won a large-scale contract from the US Department of Agriculture to sequence 1,000 influenza virus genomes.
But the company, which prides itself as an early adopter of emerging DNA analysis tools, believes the time is not quite right for bringing next-generation sequencing in-house for this or other projects — particularly for producing sequencing data that meet US Food and Drug Administration standards, a special focus of the firm.
“From a financial standpoint, SeqWright is ready to buy any instrument,” SeqWright’s CEO Fei Lu told In Sequence last week. “We would like to introduce one as soon as possible.”
However, she said, “I think the new technologies are very geared to [analyzing] larger genomes or deep sequencing” at the moment.
Lu said she had looked into the new platforms, but in order for them to become suitable for her company’s business, read lengths have to increase, and the cost of sequencing individual samples must come down. “We are still evaluating all possibilities at the moment,” she said.
For the flu contract, SeqWright researchers are using Applied Biosystems’ 3730 capillary sequencers. The company has already begun analyzing the first samples, which were extracted from birds all over the world and provided by the USDA’s Exotic and Emerging Avian Viral Diseases Research Unit, Lu said.
Because the RNA genomes are highly variable, the project presents “a considerable technical challenge” for the company. According to Lu, this project was best suited for the current sequencing technology. None of the next-generation sequencers would have been a good fit because they do not allow researchers to sequence individual samples separately, or to pool large numbers of samples and distinguish them after the run.
(454 Life Sciences, Illumina, and ABI, as well as some customers, are working on multiplexing methods at the moment [see In Sequence 02/20/2007].)
SeqWright is not the only shop to sequence flu viruses: last week, the National Institute of Allergy and Infectious Diseases said that the Institute for Genomic Research has completed more than 2,000 human and avian flu viruses as part of its Influenza Genome Sequencing Project (see related article in this issue).
While SeqWright mostly sequences relatively small and specialized sample sets, “once in a while” it receives a request from a customer who wants to sequence an entire bacterial genome, an application for which Lu said 454’s platform would be very suitable.
However, 454 offers its own sequencing service through its Measurement Services Center, representing competition that SeqWright wants to avoid.
“If 454 did not offer the service itself, we would buy their instrument immediately,” Lu said. “We do not want to compete with the company who has a proprietary position on all the reagents and hardware.”
SeqWright also specializes in regulatory sequencing to the FDA’s quality standards, an application for which the new technologies have not been tested, Lu said. For instance, SeqWright complies with Good Laboratory Practices and has obtained a Clinical Laboratory Improvement Amendment certification.
“I think the new technologies are very geared to [analyzing] larger genomes or deep sequencing.”
And last month, SeqWright won a contract from Third Wave Technologies to perform all sequencing associated with a clinical trial to evaluate two human papillomavirus screening tests.
Next-generation sequencing platforms still need to be validated for regulatory sequencing applications like Third Wave’s, Lu said. “I think validating them will probably take a little longer than [using them] just for research sequencing.”
At 12 years, SeqWright is one of the oldest contract research firms that specializes in automated DNA sequencing. But the shop’s somewhat cautious approach with next-gen instruments is not shared by all sequencing service providers.
Eurofins-Medigenomix-MWG Biotech of Germany and Macrogen of Korea each acquired 454sequencers last year, and GATC Biotech, also based in Germany, said it will install both a 454 and an Illumina sequencer this year (see In Sequence 01/09/2007).
But judging from its history, SeqWright is not known for a wait-and-see approach when it comes to new technologies. In 2002, the company, founded by Richard Gibbs, director of the Human Genome Sequencing Center at Baylor College of Medicine, and John Belmont, a professor at Baylor, was the first commercial entity to receive ABI’s 3730 sequencer.
And it has already invested in the third generation of sequencers: In late 2004, the company made an undisclosed investment in VisiGen Biotechnologies — a year before ABI invested in the company. SeqWright and VisiGen, which is developing a single molecule sequencing technology, are both housed in the same building, and both Gibbs and Lu are VisiGen directors.
“It’s definitely very important to introduce new technology at SeqWright,” said Lu.