Some clarifications about Ion Torrent PII and NextSeq 500

Yesterday’s Ion Torrent Proton PII™ and Illumina NextSeq 500™ post certainly got a reaction from several quarters, including detailed pricing information about the 1x75bp format for the high-throughput configuration on the consumables. Instead of making edits to the original here are some clarifying points, as it is clear that Illumina is making a break from … Read more

Error, alignment, and the myth of the complete genome

Centaur by {a href=”http://www.flickr.com/photos/consciousvision/”}JustMN{/a} via Flickr.

The myth of the complete genome is something that is not commonly known to active observers of genomic technologies. (The term ‘active observer’ is from the point of view of one with varying degrees of background in the biological sciences, and is in noway an aspersion.) The ‘first draft’ of the human genome was announced at a Clinton-era press conference on June 26, 2000, and it was an agreement between the two famously competitive individuals (Francis Collins and Craig Venter) representing the public (NIH and DOE) effort and the private one (Celera). This first draft was exactly that – about 90% complete, and the completed version was declared in 2003. This is not to discount the first seminal publications of this draft, as in 2001 when these papers were published (in Science and Nature respectively) the largest previously sequenced genome was 1/25th the size. In other words, the human genome represented a 25-fold leap in size and complexity of anything done to-date.

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What’s so special about single molecule sequencing?

Photo courtesy of {a href=”http://www.flickr.com/photos/kyz/”}kyz{/a} via Flickr Creative Commons.

A few days ago I reviewed in brief the history of Helicos Biosciences (HCLS), a company that held out the promise of single molecule sequencing, but failed to deliver on several fronts to the next-generation sequencing market. (This would include accuracy, throughput per dollar, and ease of use / reliability was yet another factor.)

But why is single molecule sequencing so attractive in the first place? What can it do that other technologies cannot?

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Helicos Single Molecule Sequencing – A Pioneer

The next-generation sequencing market continues its downward trajectory – routinely violating Moore’s Law by an estimated 3x, the cost per megabase curve started to significantly bend downward around 2007 when the Solexa 1G started selling in volume, and gave the 454 GS20 (as it was known then) the first competition for massively parallel sequencing the market had seen.

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Next-Generation Sequencing – its historical context

Photo of J. Craig Venter Inst. circa 2005 by {a href="http://www.flickr.com/photos/jurvetson/"}jurvetson{/a} via Flickr.

Even though the history of next-generation sequencing is short (the 454 GS20 came out in 2005, the Solexa 1G in 2007, and the SOLiD 2 in 2008), there is a robust genomic revolution going on, and a fierce battle in the marketplace with plummeting costs and soaring throughput. Whether Moore’s Law is beat by some 2.5-fold or even faster, there is no question that we are in the middle of burgeoning growth, remarkable discovery, and new insights and discoveries just about every day.

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