There Is a Microbial Genomics Market and It Is Not a ‘Niche’

Or it shoudn’t be. Last week, a good article summarizing the status of Pacific Biosciences (‘PacBio’) made the rounds in science/genomics bloggysphere–this is a pretty good summary of what PacBio can currently do (boldface mine):

Turns out, PacBio didn’t die. It may never threaten the dominance of Illumina (NASDAQ: ILMN) in genomics, and may never become profitable. But in Hunkapiller’s do-what-you-say-you’re-going-to-do-and-grind-it-out way, PacBio has improved. Its instrument now has a niche. Illumina is miles ahead on the factors that count most for customers—speed, cost, and sequencing throughput (bandwidth). But PacBio is making a name for its high-accuracy genomes, its ability to detect structural genetic variations (like RNA transcripts) that other tools can’t, and for creating high-quality genomes of small organisms like bacteria, viruses, and worms. Last fall, PacBio’s stock surged when it struck a deal with Roche to develop technology for the lucrative market to come in genomic diagnostics, where some of PacBio’s technical advantages might be more highly valued.

I realize human genomics (and genetics) is all the rage, but I still think, in the short term, there’s a lot of money to be made in microbial genomics:

…microbial genomes are cheap, fast, and you can provide epidemiological relevant information to clinical laboratories, hospital networks, and public health departments. I’m not arguing that we will or should sequence everything–and today that’s not feasible–but in two or three years, I don’t see any technical hurdles to routine microbiological surveillance in hospitals. This is something already being done, just with mid-20th century technology.

I don’t know if PacBio is the right technology–currently, one machine can sequence about 8 bacterial genomes per day (I’m assuming one needs two runs to assemble a bacterial genome adequately). I haven’t worked much with PacBio, so it might be possible to get away with less data to do diagnostics. I’m pretty sure that Illumina (as well as Ion Torrent) can do this cost-effectively, especially for public health organizations. I suppose this is a ‘niche’, especially compared to the original claims circulating a few years ago. Still seems lucrative though.

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1 Response to There Is a Microbial Genomics Market and It Is Not a ‘Niche’

  1. Pingback: Forget Genomics, Just Do the Genetics That We Know How to Do: The Rape Kit Edition | Mike the Mad Biologist

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