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454 Collaborating With Pharmas for HIV Diagnostic Applications; Rival Solexa Unmoved

HILTON HEAD, SC, Oct. 19 (GenomeWeb News) - 454 Life Sciences "is starting a number of collaborations" with undisclosed pharmaceutical companies to determine whether its newly launched sequencing technology could be used to identify drug-resistant strains of HIV, according to founder Jonathan Rothberg.


Speaking at the Genomes, Medicine and the Environment Conference yesterday, Rothberg also said his company's GS 20 instrument is "well on track" to being able to sequence a mammalian genome at 8X coverage for less than $100,000 by the end of 2006. It costs around $1 million to attain this kind of coverage using existing Sanger-style techniques, he said.


Rothberg has in the past said 454 plans to meet the $100,000 genome goal by the end of the year, but hasn't publicly defined the coverage he could generate until now.


That 454 is talking with drug makers on what are essentially molecular diagnostics applications is noteworthy because Roche, its marketing and commercialization partner, has allied itself with the company because it was able to obtain the option to use its platform if and when it can develop a diagnostic application.


Roche must "move out of PCR -- it has finite applications, and molecular testing is evolving into miniaturization, into more sequencing, more patterns, more of that type of thing that PCR can't do," Shara Rosen, an analyst with Kalorama Information, an industry consultancy based in New York, told GenomeWeb News sister publication Pharmacogenomics Reporter in May.


Highlighting the sensitivity of the GS 20, Rothberg said it can now produce 20 million-40 million base pairs of "Phred 20 or above sequence," and said that 454 collaborators have used the instrument to sequence "well over 100" de novo genomes. He also said that the next-generation instrument can sequence more than 100 million "Phred 20 or better bases ... routinely."


But John West, CEO of rival Solexa, discounted 454's diagnostic stance and said focusing attention on downstream applications that are several years away should take a back seat to the research community, which is his immediate core market.


"Our focus has been, 'How do we get to the whole human genome?'" West told GenomeWeb News today. It could take years for a company to win regulatory approval for an HIV strain-typing test --- even one that has the backing of the world's largest molecular diagnostics company, and even for such a small virus as HIV.


"The real market in the real term is the research market," West said. He added that Solexa has in he past collaborated with drug makers for similar applications for Lynx's MPSS platform, and said he hopes to collaborate eventually with pharmas with the company's sequence-by-synthesis instrument. Solexa merged with Lynx in March.


West reiterated the company's goal of launching the platform by the end of the year and to begin generated revenue from it, first as a service, by the middle of 2006.

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