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Illumina CEO Jay Flatley on the Future of Genomics, Part 2

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in the three to five-year timeframe. There are lots of people who say, “We’ll get there faster than that.” And they are talking about the sequencing only. The sequencing will get there faster than that.

X: What’s one of the more exciting experiments you’ve seen come out lately with people who are using the better/faster/cheaper form of sequencing? The kind of questions that were never possible or practical to ask even a couple of years ago?

JF: That’s one of the most exciting things about where we are today. We founded Illumina 11 years ago now. We knew someday it would be directly applied medically, but we were still a long way from that. But now we are at the cusp where sequencing is being directly used for patients. The work of professor Marco Marra in Canada, about a year ago, looked at an individual who had exhausted all the existing treatments. The individual started out with cancer of the tongue, and it had metastasized to the lungs. They had used all traditional treatments and nothing was working. They sequenced, and they discovered a novel pathway in the cancer that wasn’t known before, and they went and surveyed the drugs that were already on the market. And they found a drug that had never been applied to this cancer previously that hit this pathway. They got permission to administer the drug, and the tumors dramatically receded. It’s a great example of how understanding cancer at the molecular level will modify treatment.

That’s just the first example; there are now a whole series of these now over the past year. There’s a couple of cases at Yale, one was in an infant with a severe bowel condition that they couldn’t diagnose through any other means. Sequencing gave them exactly the right diagnosis and they cured the patient. There have been a handful of examples like that. I think sequencing is really at the cusp of being applied medically.

X: Were these experiments done by people who are physician/scientists, or were they done with scientists and physicians working in tight collaboration? Because that seems to be where things often break down, in the silo-ization of specialties which creates issues that make it hard for people to talk each other.

JF: It’s the latter model. Typically what happens is you have a treating physician, or treating oncologist, who somehow gets connected with a scientist who has access to the technology and an understanding of what it can do. They work together to make this happen. The scientist doesn’t understand the background of the cancer itself. They might understand the genetics but not the cancer details, so they have to work together with the physician.

I think you’re going to see in the very near future, very significant efforts to begin to apply sequencing directly to cancer. Our view here is that in five years or so, every biopsy will be sequenced. We’ll know it, and we’ll have characterized these cancers well enough that that’s the way you’ll figure out on the molecular level what it really is, and how to treat it.

X: Five years out, will we be doing this sequencing in a completely different way with none of the fluorescent tags that are used now, more like what Oxford Nanopore does [direct detection of ion charges associated with chemical units of DNA]?

JF: We hope so. If Oxford works, it will be, for sure. There’s probably a home for fluorescence based instruments at least out to a five-year time frame. But the newest ways will not use laser-based fluorescence instruments five years out, it will be more about direct detection. That’s how you get the size down, and the capital costs down, and you begin to scale the market in a serious way.

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  • http://www.xconomy.com/author/ltimmerman/ Luke Timmerman

    Here’s a good follow-up question I got from a reader, Dan Meyer. I relayed this to Jay Flatley, and you can read his response below:

    Dan Meyer: “The industry has been focused on cost and throughput, but hasn’t really focused on accuracy, certainly not in a way that will make sequencing a clinical reality. For example, in the clinical oncology market, we can’t apply the existing offerings if we are concerned about large scale variation (which we have known for a couple years now is more of an issue that we thought—see http://bit.ly/cioRRr).

    So I’d be interesting in knowing how he thinks the industry needs to improve in accuracy performance and measurement. And also if accuracy will be the next key differentiating factor as cost and throughput/speed reach levels that are closer to commodity levels (e.g., sub-$1000 per genome in an afternoon).”

    Jay Flatley: The goal of improved accuracy is being aggressively addressed in multiple ways:

    —Better chemistry that reduces read errors

    —Improved informatics to more accurately extract bases

    —Increased output and more affordable sequencing

    Illumina’s recently released HiSeq 2000 is a significant milestone in this regard, reducing the cost of human genome wide sequencing to less than $10,000 and providing intuitive single operator workflow systems that dramatically increase output (200G). This machine has the potential to improve accuracy by sequencing more genomes to a greater depths as a result of the huge increase in read output, in a short time period (about one week per human genome, though two human genomes can be sequenced simultaneously on this machine).

    Note that the HiSeq 2000 achieves an output of 200 Gb of data per run with 80% of the reads error-free at a sequencing depth of 1X. This is a significant improvement over what could be achieved just a couple of years ago.

    More evidence of increased accuracy by the Illumina system is seen with the dramatic increase in routine read lengths of 100-150 bases reported by Illumina customers.

    Better chemistry and informatics are also contributing to accuracy. On this front, Illumina is offering customers reagents with improved chemistry and enzymes with higher proofreading properties.