Why not sequence a genome?
digitalbio
reasonable price.
You can find the info here: http://cofactorgenomics.com/index.php
Sandra Porter
Discovering Biology in a Digital World
http://scienceblogs.com/digitalbio
Jason Bobe
http://omicsomics.blogspot.com/2009/03/next-level-in-genomics-term-papers.html
Quote:
Right on their front webpage they advertise they will generate & assemble 680Mb of sequence (from an Illumina machine) for the paltry sum of $4.7K. Wow! That would fit on my credit card when I was a graduate student (though it would have been a few months stipend). 680Mb is 100+X coverage of an E.coli-class genome, or about 50X coverage of Saccharomyces. It's even well over 0.5X coverage of an awful lot of interesting eukaryotes.
$4,700 across 700 DIYbio folks is less than $7 per person. I'll kickstart the fundraising with a pledge of $100. Post your pledge and/or proposed organism here:
http://diybio.pbwiki.com/Sequence2009
This might be a good opportunity to explore -- in depth -- possible model organisms that could by amateur engineers (e.g. BL1 safety profile, or better). Or, some neglected species which is just darn interesting...
Thanks,
Jason
Jason Bobe
Director of Community
Personal Genome Project
Harvard Medical School
www.personalgenomes.org
Tito Jankowski
Tito
Sounds like a great idea. Lets do it!
Cofactor will ask course organizers for a 1 page description of how their ~700Mb sequencing project will be used as an effective teaching aid in their class. We will review and choose the best entries the first week of May. Those entries will be awarded a free sequencing project including project consultation, sample QC, library construction, sequencing, and computational analysis.
More details can be found at:
http://www.cofactorgenomics.com/classroom.php
Thanks for your thoughts on this Keith. I was a big fan.
Jarret Glasscock, CTO
Cofactor Genomics
jar...@cofactorgenomics.com
http://www.cofactorgenomics.com/contact.php
Bryan Bishop
> $4,700 across 700 DIYbio folks is less than $7 per person. I'll kickstart
> the fundraising with a pledge of $100. Post your pledge and/or proposed
> organism here:
>
> http://diybio.pbwiki.com/Sequence2009
>
> This might be a good opportunity to explore -- in depth -- possible model
> organisms that could by amateur engineers (e.g. BL1 safety profile, or
> better). Or, some neglected species which is just darn interesting...
At first I scoffed at the high prices, but now I see this and Tito's
message and there seems to be some opportunities here. Does anyone
have some organisms that should be model organisms that need to be
sequenced, and why they haven't been sequenced before, or what would
sequencing allow us to accomplish specifically?
I also note this line on the Cofactor Genomics page:
human genome: $22,900
(22,900/50 = 458)
So, what if we did a sequencing lottery? A lottery ticket will have a
minimum price of $50, and anything higher is acceptable; remaining
money raised will go back into diybio somehow (this needs to be more
thoroughly written up); whoever is the lucky winner- either by random
draw or nomination by the community- will have their genome sequenced,
and more importantly be given the digital data as well. Maybe there
will be a few provisions- such as releasing the information into the
public domain or under some license in particular so that this
information can be used by the community- or something else like that.
What do you think?
Nathan McCorkle
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics
Jeroen Van Goey
The only case that I could see it worthwhile to sequence a human genome at this point is in the case of the father in this article http://www.wired.com/medtech/genetics/magazine/17-02/ff_diygenetics whose daugther has a rare genetic disorder.The nation's finest medical experts are all baffled by the girl's strange array of symptoms so has decided to dig into her genetic code and find the answer himself.
But even then (1) is it more worthwhile to sequence only some regions of interest on the genome of the girl (and some other family members for comparison) then to do a full blown complete genome analysis, and (2) even if the exact genetic cause is found, is it still a long way from finding a treatment.
That said, if the community can agree on a good organism to sequence I would be more then willing to hip in $100 as well, and help out with the bioinformatics analysis.
Kind regards,
Jeroen Van Goey
Bryan Bishop
<jeroen....@gmail.com> wrote:
>> are there no open source/public domain genomes out there already?
>
> Yes, the James Watson genome (http://jimwatsonsequence.cshl.edu) and the
> Craig Venter Genome (http://huref.jcvi.org/).
Right. I don't know if anyone else is interested in being able to
modify this list to say "James Watson, Craig Venter," and "and
Mackenzie Cowell" or "and Tito Jankowski, some random DIYbio fellow
spokesperson for amateurs every where". You know you want to.
> The only case that I could see it worthwhile to sequence a human genome at
> this point is in the case of the father in this article
> http://www.wired.com/medtech/genetics/magazine/17-02/ff_diygenetics whose
> daugther has a rare genetic disorder.The nation's finest medical experts
> are all baffled by the girl's strange array of symptoms so has decided to
> dig into her genetic code and find the answer himself.
Yes, that's certainly a case where it is very worthwhile, and actually
has immediate practical results.
> But even then (1) is it more worthwhile to sequence only some regions of
> interest on the genome of the girl (and some other family members for
> comparison) then to do a full blown complete genome analysis, and (2) even
Well, SNP analysis via 23andme or deCODEme is certainly an option.
Maybe my suggestion can be transformed into a separate snp sequencing
lottery, although I would really still like to be able to add an
amateur- any amateur- to the list of genomes decoded and in the public
domain.
> That said, if the community can agree on a good organism to sequence I would
> be more then willing to hip in $100 as well, and help out with the
> bioinformatics analysis.
Me too.