Complete Genomics and BioNanomatrix rev up the fast, cheap and out-of-control genome race

Things are starting to get crowded in the race to sequence entire human genomes quickly and relatively cheaply — usually meaning somewhere in the territory of $1,000 per genome, compared to the $100,000+ it costs with current technology. At least four startups have taken on the $1,000 genome challenge, two of which have already been acquired by larger companies. (See details at the end of the first item here.)

Last week, two relatively new venture-backed startups — Complete Genomics, of Menlo Park, Calif., and Philadelphia’s BioNanomatrix — considerably upped the ante in what I’ve started to think of as the “fast, cheap and out-of-control” genome race when they announced a joint venture that aims to sequence an entire human genome in eight hours for less than $100. (Technically, it appears that this figure applies only to a single set of the 23 paired chromosomes every individual carries, so a spiffy new high-resolution “diploid” genome like Craig Venter’s would presumably take more like 16 hours and cost somewhere around $200. That’s still dirt cheap, of course.)

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This is, of course, some mighty big talk from companies that virtually no one had heard of until recently. (See our coverage of Complete Genomics here.) The companies still aren’t saying exactly how they hope to pull off this feat, although they’ve disclosed a bit more detail in their latest announcement. Apparently they plan to adapt a “novel DNA sequencing chemistry” (presumably from Complete Genomics) and combine it with a “linearized nanoscale DNA imaging” scheme (BioNanomatrix’s technology, it appears) in a way that allows them to read up to long DNA stretches of up to 100,000 nucleotide bases — those DNA “letters” we’re always carrying on about — at a time.

What, exactly, that means and whether it’s possible is something the experts will have to hash out. The best I can figure at the moment is that since BioNanomatrix specializes in “nanofluidics” systems — little gizmos that are essentially labs-on-a-chip at near-atomic dimensions — it might somehow be possible to snake long stretches of DNA into a tiny channel on a chip, where having the molecule laid out end-to-end might make it easier to tag and read out the bases in one fell swoop. But that’s just a guess at this point.

Another interesting element here is that these companies bluntly acknowledge the direct threat they pose to today’s genetic-testing industry. Existing genetic tests usually rely on antibodies or other probes that identify a single gene variant; newer varieties examine a handful of single-base variations that have been correlated with something like your risk of heart disease. The ability to read out an individual’s entire genome, however, would effectively demolish the need for such tests, as any the information the tests could turn up would be right there in your genome. (The same issue arises, albeit in somewhat less-dramatic form, with the SNP genome “outlines” that startups like 23andMe and Navigenics would like to provide — our coverage is here, here and here.) This is a potentially huge problem for companies like DNA Direct, one of the first consumer-oriented genetic-testing startups. Expect to see some fireworks on this front before it’s all settled.

The joint venture recently received an $8.8 million grant from the National Institute of Standards and Technology, which for some reason got virtually no attention at the time but for the noble exception of the Philadelphia Business Journal.

Here’s some additional detail from the press release:

“We tried to approach this project from the perspective of the clinician, looking at the requirements and opportunities associated with incorporating genetics into routine clinical diagnostics,” said Dr. Radoje (Rade) Drmanac, chief science officer and co-founder of Complete Genomics. “Accuracy, speed and low cost were paramount considerations. While there are a number of powerful and elegant sequencing strategies available or under development, we determined that we needed a completely novel approach to overcome their inherent limitations and achieve our $100 cost objective. We are optimistic that the combination of our two highly innovative approaches has a good chance of success. ”

The joint venture has proposed adapting a novel DNA sequencing chemistry combined with linearized nanoscale DNA imaging to create a system that can “read” very long DNA sequences of greater than 100,000 bases at high speed and with accuracy exceeding the current industry standard. By condensing a wide range of genetic tests into a single, cost-effective platform, the proposed technology has the potential to enable improvements in the diagnosis and personalized treatment of a wide variety of health conditions, as well as the ability to deliver individually tailored preventive medicine. The $100 genome would also have important applications in medical research and drug development.