Re: [DIYbio] Cambrian Genomics

I am interested in why the process is cheaper? Is it because you use less solutions?
I watched the video with Austen and comparing Sequencing to Synthesis seems like a moot point. Sequencing will always be able to be done cheaper because you can remove things from the reactions. Eventually, if people use carbon nanotubes the price of sequencing with be the price of just using the machine.
Whereas with Synthesis you are actively creating a quantity of something so your price can only be as cheap as the price of ligating together dNTPs. Even PCR probably costs $0.001 a base(enzyme($50/100 reactions, dNTP $100/200 reactions, buffers?? say you amplify 1000 bases). Throw in primer synthesis and template purification and it is closer to $0.01. Futhermore, doing it for $0.0001 or less is much different from selling it for that. Taking into account the costs of equipment, wo-manpower. I don't see DNA synthesis drastically dropping in price because it is reagent limiting.

"The price of gene synthesis has fallen drastically over the last decade. However, the current commercial price of gene synthesis, ~$0.40–1.00/bp, has begun to approach the relatively stable cost of the CPG oligonucleotide precursors (~$0.10–0.20/bp)¹, suggesting that oligonucleotide cost is limiting." Kosuri, Church and company Nature Biotech 2010

Using lasers seems cool but how much time does it save over taking a few minutes to run something over an HPLC column?

How are you assembling the kilobase pieces? Ligation? PCR? This seems like the slow step not the amplification part.

The method you are talking of is similar to one published by George Church and he says the error rate is only decreased 500 fold with the major errors being in wrong calls for sequencing and polymerase errors Cambrian Genomics method doesn't seem to decrease this? He mentions the error rate is still at 29% compared to what you said 36%. Matzas, Church and company Nature Biotech 2010

Thanks,
     Josiah Zayner

http://DoItOurselfScience.blogspot.com


On Thursday, April 25, 2013 2:34:59 AM UTC-5, Anselm Levskaya wrote:

Hello all, 

Cambrian is very real.  We're making lots of progress, fast, but doing hardware/bio work is definitely a slower game than software development!

@bryan : this is not an 'interesting' approach.  It's a practical one informed by decades of experience building synthetic DNA constructs and optical systems. i.e. one that might actually work. ;)

Brief synopsis:

The basic problem of synthesis is that serial programmatic polymer synthesis is intrinsically error-prone.  Per-cycle monomer coupling efficiencies are never above 99.5% and generally more like 99% for microarrays.  This means that for a 100mer the percentage of correct, full length oligo molecules is only (0.99)^100 = 0.36 -> 36%  Two thirds of the stuff made at this length has deletions.  If you assemble this pool your synthetic gene will be riddled with frameshift errors.  No good.

Other companies have tried to correct this by using error-correction enzymes that chew apart mismatched DNA to eliminate the random deletions.  While this is fruitful when using traditional plate oligos, the errors are so bad in microarray-sourced DNA that you end up with horrible final yields, and even if you do end up getting something correct in the end it takes so much additional screening work that the cost of post-processing erases any marginal gains made by beginning at the larger microarray scale.  I know several companies and academic groups that have investigated these batch pcr-strategies for making synthetic fragments from arrays, but believe that none have demonstrated sufficient speed and throughput of error-free synthetic fragments to make a convincing leap over traditional bulk-oligo assembly pipelines. (i.e. 15cents/bp for 1kb fragments from geneart w. 6 day turnaround).

We're basically building a lot of custom optical / sequencing / laser gear to sample single molecules of a microarray pool and to cherry-pick out the correct ones.  Instead of enzymatic tricks, we're doing physical separation upfront of the good from the bad, while simultaneously de-scrambling the ~10^5-10^6 pools into defined small assembly sets for very rapid, very high-throughput assembly of larger kilobase pieces.

The key spirit of what we're doing is to minimize biological complexity and trickery throughout the process and to backload complexity onto hardware and software - the domains where we're good at engineering.  I've been doing bio for over a decade, and if you don't keep it simple you're hosed!

-a

On Wed, Apr 24, 2013 at 9:01 PM, Nathan McCorkle <nmz...@gmail.com> wrote:

Yep, see here for laser specifics:

http://www.youtube.com/watch?feature=player_detailpage&v=7yscphwaWNs#t=707s

On Wed, Apr 24, 2013 at 8:54 PM, Bryan Bishop <kan...@gmail.com> wrote:

On Wed, Apr 24, 2013 at 10:37 PM, Sumon Sadhu <sumon...@gmail.com> wrote:
> They just closed several million dollars in funding from patient and forward
> thinking silicon valley investors.

I had an informant living with Cambrian Genomics and I never got this
tiny detail:

"Cambrian Genomics brings in lasers only once the plate is covered
with many thousands of DNA-carrying beads, and once each of the beads
has been sequenced. With so many copies made, some predictable portion
will have been made error-free, and an automated laser flits about
over the plate and blasts any beads with a desired sequence off of the
plate and into a collector."

Using a laser to avoid contamination was the missing detail...
otherwise Cambrian's idea doesn't seem interesting.

- Bryan
http://heybryan.org/
1 512 203 0507

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+un...@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+un...@googlegroups.com.
To post to this group, send email to diy...@googlegroups.com.
Visit this group at http://groups.google.com/group/diybio?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.

--
-Nathan

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+un...@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+un...@googlegroups.com.
To post to this group, send email to diy...@googlegroups.com.
Visit this group at http://groups.google.com/group/diybio?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.