Comments on: New SOLiD Sequencers, and the ever dropping cost of sequencing http://www.jamesandthegiantcorn.com/2010/01/29/new-solid-sequencers-and-the-ever-dropping-cost-of-sequencing/ Genetics: Studying the Source Code of Nature Thu, 12 Jan 2012 03:50:37 +0000 hourly 1 http://wordpress.org/?v=3.3.1 By: James http://www.jamesandthegiantcorn.com/2010/01/29/new-solid-sequencers-and-the-ever-dropping-cost-of-sequencing/comment-page-1/#comment-4615 James Tue, 02 Feb 2010 19:50:55 +0000 http://www.jamesandthegiantcorn.com/?p=1290#comment-4615 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! 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!

]]> By: JS Hoyer http://www.jamesandthegiantcorn.com/2010/01/29/new-solid-sequencers-and-the-ever-dropping-cost-of-sequencing/comment-page-1/#comment-4606 JS Hoyer Mon, 01 Feb 2010 03:09:25 +0000 http://www.jamesandthegiantcorn.com/?p=1290#comment-4606 http://www.nature.com/nmeth/journal/v6/n8/full/nmeth0809-550.html http://jcclab.science.oregonstate.edu/node/view/67650 http://www.nature.com/nmeth/journal/v6/n8/full/nmeth0809-550.html

http://jcclab.science.oregonstate.edu/node/view/67650

]]> By: James http://www.jamesandthegiantcorn.com/2010/01/29/new-solid-sequencers-and-the-ever-dropping-cost-of-sequencing/comment-page-1/#comment-4603 James Sun, 31 Jan 2010 04:06:54 +0000 http://www.jamesandthegiantcorn.com/?p=1290#comment-4603 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. 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.

]]> By: James http://www.jamesandthegiantcorn.com/2010/01/29/new-solid-sequencers-and-the-ever-dropping-cost-of-sequencing/comment-page-1/#comment-4602 James Sun, 31 Jan 2010 03:47:11 +0000 http://www.jamesandthegiantcorn.com/?p=1290#comment-4602 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). 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).

]]> By: Noah Fahlgren http://www.jamesandthegiantcorn.com/2010/01/29/new-solid-sequencers-and-the-ever-dropping-cost-of-sequencing/comment-page-1/#comment-4599 Noah Fahlgren Sat, 30 Jan 2010 20:22:40 +0000 http://www.jamesandthegiantcorn.com/?p=1290#comment-4599 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. 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.

]]> By: Matt http://www.jamesandthegiantcorn.com/2010/01/29/new-solid-sequencers-and-the-ever-dropping-cost-of-sequencing/comment-page-1/#comment-4597 Matt Sat, 30 Jan 2010 16:50:55 +0000 http://www.jamesandthegiantcorn.com/?p=1290#comment-4597 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... 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…

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