James and the Giant Corn Genetics: Studying the Source Code of Nature

January 29, 2010

New SOLiD Sequencers, and the ever dropping cost of sequencing

Filed under: Uncategorized — Tags: , , — James @ 8:20 pm

David Dooling, writing at PolITgenomics, brings word of the announcement of a new generation of SOLiD sequencing machines. The statistics aren’t quite as impressive as the Illumina HiSeq 2000 announced a couple of weeks ago, but it will be cheaper per gigabase of sequence.

As long as SOLiD sequencing can keep giving Illumina a run for its money, the price of sequencing is going to keep dropping, and the R&D departments of both companies will be working round the clock to keep the improvements coming (SOLiD is already promising upgrades that will triple the amount of sequence generated per run, while cutting the cost of each run by half (6x reduction in cost/GB of sequence)… by the end of this year.)

People talk about Moore’s law as saying computers double in speed every 18 months.* I’ve heard estimates that the cost of sequencing is dropping as much at 90% per year. To get a sense of how impressive that is, if those rates of growth keep up, after nine years, computers would be 64 times as fast, and sequencing costs per base pair would be less than one-billionth  (that is 1/1,000,000,000) what they are today.

*This isn’t what was actually stated as Moore’s law, and even if it was, the speed of computer processors stopped growing some time ago, with the extra transistors (the thing actually predicted to increase by Moore’s law), getting devoted to additional cores instead. So todays computers can’t do a single task faster than last years computers, but they can do more things quickly at once (depending on the task programmers can down get around this by breaking individual tasks down into smaller pieces that can each be worked on by a different processor core at the same time). Read more on wikipedia.


  1. A professor here once described inexpensive sequencing as a tsunami that will hit the field of biology any year now, that it’ll be a complete revolution and people in the future won’t understand how they didn’t see it coming. It’s obvious to genetics/computational people like us but it’s not even on the radar of most ecologist/physiologist/molecular biologists I know. It’s pretty incredible to be in science right now and watch this happen.

    I sat through a seminar on grape genomics out of the Buckler lab this week where sequencing was used to get SNPs to make an array to type the USDA germplasm collection – by the time they actually got the array data it would already probably have been cheaper to forget about arrays and just use sequencing directly on the whole collection…

    Comment by Matt — January 30, 2010 @ 8:50 am

  2. Last time I had a chance to talk to Buckler, he was saying he sounded really enthusiastic about multiplexing sequencing within a single channel of a solexa machine as a way of using sequencing to efficiently genotype individuals and was hoping he’d be able to get his hands on a PacBio sequencer sometime this spring.

    You’re absolutely right that there are all sorts of biologists who are barely even aware of the possibilities this amount of cheap sequencing power is already opening up for their own research. I haven’t heard anyone even speculate about how massive sequencing could best be used in, for example, plant ecology (well beyond the meta-genomics anyway).

    Comment by James — January 30, 2010 @ 7:47 pm

  3. When I started grad school our lab had just started toying with the idea of using the new-at-the-time 454 technology to profile small RNA. Looking back, it is pretty crazy how far the field has moved since then.

    Comment by Noah Fahlgren — January 30, 2010 @ 12:22 pm

  4. The idea that got me was in a recent discussion with a couple of other grad students out here we figured out it might actually be cheaper to use Solexa to sequence a pool of F2 mutant plants rather than do conventional mapping. Right now, with on campus rates, generating a gigabase of sequence (enough for ~6x coverage* of an arabidopsis genome) with solexa costs <$1000 dollars, kit and all. The numbers didn't add up unless we included the savings of not having to pay her to work for the extra time conventional mapping would take, plus I don't know if people already do this, so I couldn't promise there'd be ready made tools for interpreting the sequence data she generated. But it was weird to think we're getting quite close to the point where normal way of mapping new mutants will go the way of screening phage libraries (at least in species with sequenced genomes). *6x coverage isn't enough to spot a single SNP, but it should effectively give you mapping data on markers throughout the genome so you can narrow down your search to a region with a few candidate genes, plus provide candidates for the actual mutagenesis induced SNP within the candidate genes, that would still have to be validated with sanger sequencing.

    Comment by James — January 30, 2010 @ 8:06 pm

  5. http://www.nature.com/nmeth/journal/v6/n8/full/nmeth0809-550.html


    Comment by JS Hoyer — January 31, 2010 @ 7:09 pm

  6. Sorry your comment got caught in my spam filter for so long, it can be overzealous, but the alternative is to have the site constantly bombarded by every ad and scam imaginable.

    Those are great papers. I’ll be using the second one as my proposed model for mapping a mutation next time I get into this debate (it’s come up several times just in the past years). Thanks!

    Comment by James — February 2, 2010 @ 11:50 am

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