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

Xconomy San Diego — 

Yesterday, we ran the first installment of a wide-ranging interview with Illumina CEO Jay Flatley. He talked a bit about some of the major competitors he sees emerging in the fast-paced world of gene sequencing, and how he hopes San Diego-based Illumina (NASDAQ: ILMN) can maintain an innovative edge, even as it grows into a big company with about 1,800 employees.

Today, we offer up the second half of the conversation.

Xconomy: In terms of being in San Diego, you’ve got Illumina, and you’ve got some critical mass with your competitor here in Life Technologies in sequencing. You’ve also got wireless talent here with Qualcomm. How do you see the genomic instrument capabilities converging over time with wireless technology in a way that’s useful for a healthcare system moving more toward wellness?

Jay Flatley: It’s absolutely going to happen. It’s already starting to happen. Our instruments increasingly will be spitting out their data over wireless networks. We already have the ability to monitor and control our HiSeq product from an iPhone application. Our customers can sit in their living room and monitor the quality scores coming off their HiSeqs. From a management of the instrumentation perspective, that’s already happening.

We’ve built a prototype iPhone application that is sort of a delivery vehicle of how someone could carry genomic information and communicate and interact wirelessly. That could be with your physician. It could be over social networks. It could be in a bar. I think wireless is the way it’s going to go. The data will be in the cloud, and it will be moved around wirelessly.

Jay Flatley

Jay Flatley

X: But your bread and butter business is still going to be selling those instruments, which are an expensive piece of equipment. How much bigger do you see this market getting in unit volume, or maybe becoming more democratized as the price of sequencing comes down and more researchers can do it?

JF: Our goal is to make this as ubiquitous as PCR [polymerase chain reaction], and I think that’s where it’s headed. Sequencing will become such a fundamental tool of molecular biology research that every lab that’s serious in the field will have to have access to next-gen sequencing one way or another. Either in their lab or the lab next door. The footprint of the instruments is going to shrink. Usability will get better. Sample prep is going to get simpler. We’re probably less than 10 years from the day when a drop of blood gets put in and the sequence comes out 10 minutes later. That’s the way it’s going to be. We think all babies are going to get sequenced in 10 years, that will be a routine way you do post-birth characterization. The data set will go into an electronic medical record. There will be some filtered masks over that data set that allow different constituents to access it under certain privacy controls for different reasons. You may need to authorize your physician to look at parts of it, you may want them to look at all of it. But I think that’s where the technology will head.

X: It’s interesting that you brought up privacy. I was meaning to ask whether there are any policy changes that you think need to happen before people can become comfortable enough with this idea to really participate in a big, broad way?

JF: The GINA [Genetic Information Nondiscrimination Act of 2008] bill went a long way. It set a framework for preventing discrimination based on genetic information. What’s going to have to happen is there will have to be some test cases. How does that look when it’s applied and executed? No doubt we’ll see some test cases there in the next five years. But the thinking is moving … Next Page »

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One response to “Illumina CEO Jay Flatley on the Future of Genomics, Part 2”

  1. 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

    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.