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

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pretty fast there. One of the goals we had in the early launch of our consumer program was to make that thinking go faster. So that when the technology could sequence everybody for $500, that we’re not then beginning to think about privacy and data management problems and regulatory issues. All of that gets pushed out of the way in advance of this becoming an enormous market. It’s moving really quickly. You see full conferences on consumer genomics. You couldn’t imagine something three years ago like a consumer genomics conference, yet here we are.

X: How is this really going mainstream? I noticed you had a release that said [the actress] Glenn Close said she’s gotten her genome sequenced. Are you encouraging people who are recognizable to go out on television, and talk to the public? This is genomics, which is not everyday dinner table talk, right?

JF: One of the challenges that companies like Illumina have is to figure out ways of abstracting the complexity of genomics. That’s what an iPhone app is going to do ultimately. It still doesn’t quite get where we want it to be. Even today, people say “Your doctor doesn’t know what this all means.” Sure, he doesn’t. But the truth today is that when a doctor orders a test today, if you ask them, “Describe how that test works,” he has no clue. Even if it’s an immunoassay. You could say “Tell me what the binding reaction is that gives you that result.” He has no idea. All he knows is that it comes back in some range. Whether it comes back in this range, or that range, he knows what to do differently with those two outcomes. That’s where we need to get with this. We’re a ways away from that. We have to abstract it beyond anybody having to understand what the genomic piece is about. What that’s going to require is another five years of compiling lots of genomes, figuring out what those reading means, and creating actionable data sets from that collection of genomes. That’s where we are headed in the next couple of years.

X: What’s your prediction on when we’ll get to the $1,000 genome?

JF: We’ve been a little cautious to not go too far out on a limb there, and it will matter a lot what you count. If you count bioinformatics, if you count sample prep, if you count data storage in the number. If you count it all, then it’s somewhere … 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.