A First Step – Cheap, Rapid Whole Genome Sequencing

by Bradley Miller on July 30, 2009

Clearly, the title of this post is something that has been talked about for quite some time.  There’s even an X-Prize for the first team to do 100 whole genomes in 10 days for under $10K per genome.  I don’t think that I’m revealing any big shocks here – this type of sequencing will radically open up doors.  That is, until it shows us that which we as of yet don’t know we don’t know.

There are a number of companies, as mentioned in my last post – Complete Genomics, Pacific Biosciences, 454, etc – who are pushing new concepts to old technologies.  Who knows, maybe their approaches will become the standard, but the reason I think not is that despite their high technology (which, don’t get me wrong – they’re brilliant), I think it’s going to have to take a complete shift in how sequencing is done – away from Sanger sequencing.  Now, my bet is that these are going to be marvelously successful companies while the next generation technologies come about.  That is, these companies will bring down the cost of sequencing, which will dramatically promote more research, which will beget more research, and on and on.

That research will lead us to begin to truly understand genomics and its relevance to medicine and mainstream science.  For example, we might actually begin to understand which genes and epigenetic/metagenetic factors combine to produce cancer.  We’re just now discovering the genetic profiles of cancers, and that work will only pick up as whole genome sequencing becomes more readily available.  But it’s going to take a dynamic shift in thinking and sequencing techniques to quickly and effectively sequence the genome.  New technologies from companies like Halcyon will have base sequence reads in the hundreds of thousands to millions – instead of in the hundreds as we see today.  When you do the math, there are significant gains of several magnitudes in speeds, reliability and accuracy of these next generation technologies.  For now, though, they all remain very rusty – I’ve seen them myself – but I really think they’ll come along and continue to change the market.

For now, we’re stuck with current technologies – which should come on line by the end of 2009 or at least by the middle of 2010.  As research performs its work using these more expensive technologies, the findings will pour in and advances in medicine and other areas will be discovered.  By the time all this happens, the next generation of even cheaper sequencing will be available and be ready to go mainstream.  The current, more expensive technologies are setting the stage for tomorrow’s cheaper, more reliable technology.  Kinda reminds me of the computer industry and Moore’s Law.  And, much like microchips and then hardware, DNA sequencing will be subject to commodification – decreasing margins and altering business.  Hopefully this will lead to improvements in sequencing and cost – we all benefit from this type of competition.

But, the commodification of DNA sequencing will lead to mountains of data, which will have to be dealt with.  And it will be . . . in my next post.

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