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Mapping: OpGen Kicks Off With Schwartz Technology at Core


For a company that has no customers and just moved into its office space a few months ago, OpGen has a lot of confidence in its market position. But if you ask CEO Tim Konicek, there’s good reason for it: the optical mapping technology it’s based on has been used by the DOE and other government agencies. It has been in development for the past eight years by University of Wisconsin’s David Schwartz, inventor of pulsed-field gel electrophoresis, and colleagues Thomas Anantharaman, also of Wisconsin, and Bhubaneswar Mishra of New York University and Cold Spring Harbor. “The three are tried-and-true academics and will remain in their university positions,” says Konicek, who was recruited to OpGen and joined last December. “[David] is not all that interested in going out and knocking on doors and peddling maps — that’s what we’re going to do.”

OpGen, founded in January 2001 by the academics and Stanley Rose, licensed the technology and rights to improvements on it through the Wisconsin Alumni Research Foundation. The premise is to create restriction maps while skipping cell lysis, amplification, and electrophoresis by working directly with whole DNA. Through its own microfluidics system, DNA molecules are “laid out in long strands along the [glass] surface,” Konicek says. The molecules loosely attach to the glass, where they’re fluorescently tagged and treated with a restriction enzyme.

Then it’s as easy as peering through a fluorescence microscope to see restriction patterns and measure the lengths, Konicek says. OpGen will take snapshots of the fragments and use an algorithm to create a consensus map. “The key is being able to partially immobilize the DNA,” he adds. “It’s a fairly simple concept.” In Schwartz’s lab, the technology has achieved standard resolution of eight to 20 kilobases, which Konicek expects to improve “by at least a factor of four or five.”

Schwartz has run several different organisms through the mapping, finishing 20 maps and completing organisms with genomes as large as 20 megabases. “We are able to quickly do a relatively small genome at this time,” Konicek says. “Something like a bacterial genome, we could complete in a week or so.” Early applications of the technology are in sequence finishing, assembly, and comparative genomics across organisms or strains of bacteria, for instance. OpGen plans to sell information only; the instrument is not up for grabs.

The advanced state of the technology is giving Konicek no excuse to sit around and wait for the money to pour in (in fact, he’s been fund-raising for an $8 million financing round expected to close early this month after a half-million seed round). “Our plan right now is to be able to create a map of a human genome in a week one year from now,” Konicek says. He laughs at the thought that GT will pencil in the date and call him in a year to check on that goal: “I think my board of directors is doing the same thing,” he says.

— Meredith Salisbury


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