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Ignition Sequence Starts

Dietrich Stephan talk sequencing, health care, and D.C.

March 16, 2010 | In 2009, Dietrich Stephan, the co-founder of personal genomics company Navigenics, announced his plans to build an ambitious new academic institute in Northern Virginia—the Ignite Institute for Individualized Health. Ignite is partnering with Life Technologies and acquiring 100 SOLiD 4 instruments, which can deliver $6000 human genome sequences. Kevin Davies spoke with Stephan about Ignite and his choice of sequencing partner.

Bio•IT World: Why so many sequencers and why did you select SOLiD 4 instrumentation?
Stephan: We’re really excited about this partnership. I feel very good about the SOLiD technology, namely its accuracy, price points, and throughput. Having reviewed recent data, it looks like the SOLiD platform is extremely accurate. I really like that, because we don’t have to sequence with as much redundancy. We’re really creating a strategic partnership with Life Technologies to do co-development around the technology and understanding the interpretation in a clinical setting of the information. So it’s more a strategic partnership that swayed the decision…

I think we’re finally approaching a price point for full-genome sequencing where we can realistically start to redo all the whole genome sequencing studies (GWAS) that have been backed up for the last five years waiting for this technology. You need some horsepower to do that, and we needed some infrastructure…

We are also … putting the technology into a CLIA environment and using it in a clinical setting. For example, is there a role for sequencing the entire cancer genome out of a diagnostic biopsy from someone newly diagnosed with cancer? Pull out single cells, sequence them, and try to understand if we can prioritize the standards of care, and develop salvage therapies for the 50% of people who will eventually progress… We want to start learning how to apply the technology in a clinical setting and how to interpret it immediately.

Do you really feel it is worth revisiting all the GWAS data at the full sequence level?
I’m of the bent that all these heritable risk factors will be relevant in the aggregate. Common variants were extremely valuable in many cases, not only in risk assessment but as guideposts to uncover rare variants in those portions of the genome. But there’s epigenetic modification and copy number variation that we can now capture with the current technologies. We’re finally at a point where we can, in a systematic way, go back and rip through all those case-control studies and get close to capturing the totality of heritable risk for complex genetic disease—step 1—and then maybe even start to sub-classify those common, complex diseases, and re-name those molecularly homogenous sub-types which will likely be differentially triggered by environmental exposures and be responsive to different therapies. I believe this systematic discovery strategy will form the foundation for individualized medicine, which should improve clinical outcomes.

What will be the focus of your sequencing efforts in the clinical realm?
It’s an extension of Dan Von Hoff’s work at Scottsdale Health Care, where he ran a beautiful clinical trial using expression profiles of patients. When someone presented with end-stage cancer and was asked to be assigned to a Phase I trial, Dan would randomly assign a Phase 1 trial, the other study arm he would profile and then intelligently assign to a trial. He’s presented beautiful data that he can improve response rates. So [we’re] trying to use that same strategy but with the next evolution of technologies to see if we can’t improve outcomes with experimental or off-label therapies for those individuals who progress through current standards of care. Our work will begin in a clinical research setting then as a clinical service and hopefully soon make a similar strategy the standard of care to optimize outcomes.

You used the term ‘genome institute,’ but you’re also stressing that Ignite is about individualized health?
There’s a couple of aspects in the Ignite model that we think are unique… One is the horsepower to drive out pure molecular subclasses of disease as a starting point for personalized medicine. So renaming complex genetic diseases according to new nomenclature around molecular homogeneity. A second is aligning the disease foci to the market needs out there in the world. Basically that means the most prevalent, intractable diseases will be the ones we research.

The third aspect will be that we’ll have commercialization infrastructure surrounding the institute so we can make early go/no-go decisions. We can model the economics of new tools and strategies. For example, who is going to pay for this when we turn it on? Additionally, we have strategically located the institute in the D.C. region so that we can build trusted relationships with policy and regulatory bodies as well as access the best thinking around health policy to allow us to streamline the process of moving from “research grade” tools to “clinical grade” tools and strategies.

Another aspect is that we’ve aligned it with a tier-one partner in terms of the Inova Health System which is an excellent high-volume community health care system… If we can drive new validated tools and strategy into the community health system where most individuals receive their care through a trusted relationship, then we obviate the need for years of physician education and adoption.

So if you take a big genome institute, surround it with a commercialization infrastructure, and then place that in close partnership with a health care system, hopefully you can build those trusted relationships to quickly move from a robust discovery around a pathogenic pathway to a little biotech or drug company and then into a clinical setting quickly… Once you have a little company it often takes years and tens of millions of dollars to educate doctors, get regulatory approval, and change the standards of care and get any of them to use it… We felt a need to compress the cost and timelines.

Finally, we view our project as a national and international resource and look forward to partnering and collaborating extensively. The permanent facility will be located on a campus so that we can expand operations as these collaborations and spin-out companies take root.

What’s the status of settling on a permanent location for Ignite?
We’re currently in the Center for Innovative Technology building near Dulles Airport, it’s a state-owned building (the black upside-down pyramid building visible from Dulles). The state will put in some money to refurbish it, and we’ll leave it behind as a biotech incubator for the Commonwealth of Virginia. On the permanent site, we’re still evaluating a couple of options through a process led by, in my opinion, the best full-service health care facilities owner representative in the country—Nancy Kelley of Murphy-McManus. It looks like we’ll purchase a pre-existing shell so we can go in and very rapidly refurbish floors to grow in real time.

What about the support you’ve received from local government? 
It’s been a true public-private partnership. The Commonwealth of Virginia has been spectacular, committing $25 million to the project. Fairfax County is committed to building us a building and letting us occupy that for a certain period of time for free. And we’ve got private sector partners like Life Technologies and the Inova Healthcare System. We have excellent academic partners like George Washington University, which wants to continue to make a name for itself in health care policy. We’ve aligned with George Mason University around neurological diseases and Virginia Tech around bioinformatics and supercomputing. Virginia Tech just recruited a spectacular head of the Virginia Bioinformatics Institute, Skip Garner... As always, we are committed to open access data dissemination to facilitate research by all and look forward to delivering large “data packets” to groups like Sage Biosciences for sophisticated analysis.

Let’s talk a bit about Navigenics. You have a new CEO, Vance Vanier?
Vance is spectacular. He embodies the spirit and values and personality of Navigenics in a perfect way. He’s great!

What is the significance of the recent New York State granting Navigenics regulatory approval?
It’s a gold seal of approval, if ever there was one… I think that was the most important regulatory thing that’s ever happened [to Navigenics], simply because it is so carefully done in New York State. It allows the Navigenics Health Compass to be sold in New York through a physician channel [not direct to consumer]. I’m happy with that—it’s a medical diagnostic product. I’m thrilled that they have that kind of channel.

With the Navigenics Health Compass celebrating its second anniversary, what are your thoughts about the evolution of consumer genomics?
It’s a great question. I joke that I had my bullet proof vest on for a few years there in the scientific community. That topic has been the singular most interesting development is the scientific acceptance of risk strategy, as far as I can tell. People are now comfortable with the science… The concept is still as fresh today as it was back then—the notion that personalized preventive risk stratification is critical to reducing health care spend and the burden of disease… The Health Compass infrastructure was built to be able to turn on these personalized preventive risk estimates, and over time we would populate the rules engine and the technology engine with more robust things. And that’s what we’re doing.

You tried to seek areas of common ground with the other DTC companies regarding risk calculations and assumptions?
Yes, the Navigenics team did propose the standards setting exercise, and there has been movement toward convergence around the prevalence estimates around the diseases. Navigenics still doesn’t test for quantitative traits and non-medically relevant things—that’s an area lacking agreement. We probably don’t have perfect convergence now but we’re heading in the right direction.

One of your original arguments for Navigenics was the soaring health care cost. How do you regard the ongoing health care debate?
I think it’s been a healthy discussion around increasing efficiency and reducing redundancy in delivering health care and I hope we see some progress. I think we can cut tens of percents off our health care spending with reform. But that’s not going to change the slope of the burden of chronic disease—it will only push it out by a couple of years. I hope that Round Two follows shortly, where the discussion focuses on truly altering that slope, otherwise the same thing is going to happen. Extending a healthy lifespan and reducing the time you’re sick is still I think the key to all this.

This article also appeared in the March-April 2010 issue of Bio-IT World Magazine.
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