The age of the $1,000 genome is said to be fast approaching, and the growing availability of fast, cheap DNA sequencing is already paving the way not just for new avenues of academic research, but also for intriguing new diagnostic startups like San Francisco-based Sequenta.
This company, formerly known as MLC Dx, is announcing today it has secured $13 million in a Series B venture round that included Mohr Davidow Ventures, Index Ventures, and individual investor Jacob Goldfield, the former chief investment officer of Soros Fund Management. Sequenta, which has now raised a total of $15 million, was co-founded by Tom Willis and Malek Fahem. Those two entrepreneurs previously co-founded ParAllele Bioscience, a company that was backed by Mohr Davidow and ultimately sold to Santa Clara, CA-based Affymetrix (NASDAQ: AFFX) for more than $130 million.
The idea at Sequenta is to gather a new kind of information for physicians about whether a patient’s immune system has gone out of whack. While the 3 billion letters of DNA that make up a genome are consistent in almost every cell of the body, the immune system’s B cells and T cells are an exception. In these cells, DNA gets shuffled around in a vast array of combinations, allowing T cells to recognize specific invaders, such as flu viruses, and bacteria, and allowing B cells to generate antibodies against them. Scientists wishing to assess immune response can look at generalized markers of inflammation like C-reactive protein. But until recently, they could never really look at the vast diversity of an individual’s immune system in a specific way that could say how it reacted to infection with a specific bug, or adapted in response to a certain vaccine or therapy.
Doing this kind of immune-system sequencing was impossible just a few years ago, as it would have cost a few million dollars with traditional sequencing to examine immune cell diversity in just a milliliter of blood, Willis says. Now this kind of specific sequencing of immune cells can be done for about $100, making it possible to start a company devoted to using it as tool for diagnosing disease, and for monitoring people over time, he says.
“I can see a world, and I can’t tell you the exact time frame, when immune system profiling is a part of routine wellness management,” Willis says. “Once we know more about your immune signature in various health states, we’ll all get it sequenced, and look for early signs of cancer, autoimmunity, infections, and other losses of function.”
Rowan Chapman of Mohr Davidow, who helped seed the company and sits on its board, said: “There are so many different applications in underactive and overactive immune disease. The only tests avail today are really non-specific. I see huge potential.”
Sequenta, which is an amalgam of the terms “sequence” and “consequence,” is still being pretty stealthy about its business strategy. Like many other molecular diagnostic companies, it has plans to set up a centralized lab that processes the samples physicians send in for analysis, and makes money by charging for the service. The central lab will run on next-generation sequencing machines from San Diego-based Illumina, although Willis says he’s open to using other technology platforms over time.
The company, which has 11 employees as of today, plans to use the new cash to run some clinical studies to gather more proof of the usefulness of the approach, Willis says. He wouldn’t say who his clinical collaborators on the project, what the lead application will be, when to expect findings to be published in a peer-reviewed journal, or when the technology will be ready for the marketplace. None of the company’s methods or early proof of concept experiments have yet been published in a peer-reviewed scientific journal.
Several big name scientists are on board as advisors, which might offer clues on where this is headed. The advisory board includes Ron Levy, Ron Davis, and Larry Steinman of Stanford University, as well as Betty Diamond of The Feinstein Institute for Medical Research, Rob Holt of the University of British Columbia, and David Grainger of Cambridge University.
Willis offered up some hints about where the applications might be, speaking broadly. The immune system, as he notes, plays a role in a huge number of diseases. There are autoimmune diseases like rheumatoid arthritis in which the immune system starts attacking the joints, and multiple sclerosis where an overactive immune system attacks nerve cells. There are allergies, and cancers in which the immune system is deeply involved. Sometimes physicians want to suppress the immune system a certain amount, such as after organ transplantation, and sometimes they want to amplify a response to some specific bug, like through a vaccine.
By sequencing the repertoire of an individual’s immune system at certain points in time, there’s potential to specifically diagnose disease, offer more clarity on a patient’s prognosis, and monitor how a patient responds to therapy. “There are lots of shots on goal for this technology,” Willis says.
Sequenta says it doesn’t see any other competitor on the horizon trying to do the same thing for diagnostic purposes, although Seattle-based Adaptive TCR, a spinoff from the Fred Hutchinson Cancer Research Center, is doing something similar by providing T-cell profiling service to researchers.
Without diving into specifics about which applications come first, it’s hard to say how big the market opportunity might be segment by segment. But Chapman noted that she’s excited because each assay the company develops could have multiple applications, rather than just one like some other molecular diagnostic companies. She also has a long history of working with the founders before at ParAllele, adding, “we had a fantastic experience with them. They are incredibly smart guys.”
Willis, for his part, said he and Fahem are dreaming big at Sequenta. “We hope it’s an even bigger thing than ParAllele,” he says.
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