Some Sanger and some NGS for work we do in-house. Most of our DNA Synthesis providers have moved to NGS, but I can't say with certainty who has and who hasn't.
If you are still doing sanger sequencing then you should check out our software (see my profile for details). The customer I mentioned in my other post is using it to significantly reduce the amount of sanger sequencing they have to do to check all their constructs.
Hi Barry, how do you guys know that this accounts for 10% of global DNA synthesis production? Some companies synthesize their own DNA with custom instruments and my guess would be that this production is unaccounted for.
Perhaps they mean synthetic genes from the major market players. It's definitely not 10% of all DNA synthesis. For example, oligos produced on microarrays alone can produce this much DNA on a single chip. I'm assuming they mean assembled, sequence verified DNA. For that, I'm not sure where they are getting their numbers.
I assumed that they meant unique sequence. The oligo pools for microarrays really only need to be synthesized a single time and a single oligo can be present multiple times. Synthesizing 100M bp is really trivial if you amplify any bit of DNA :)
I wasn't talking about copies of the same sequence. Agilent for instance makes 1M oligo arrays, and you can get these at 200nt each with arbitrary sequence. That's 200M bp of synthetic DNA spec'd to design on a single chip.
Yep, thanks for clarifying. We're using the figures quoted by gene synthesis firms to get the 10%. That makes sense because we're buying 100Mbp of gene synthesis:) We buy lots more DNA in other forms (chip-synthesized oligos etc.).
I supply our software to one company that I know is synthesising on the order of 100Mbp per year that is all internally so I know there is a fair bit of unaccounted gene synthesis going on.
Yes that is right. I can’t really talk about what our customers are doing (other than saying it is legitimate), but they are handling everything internally for internal projects.
This is completely unrelated, but do you guys have plans for summer internships / co-ops? There are a bunch of really interesting biotech companies with 1year internships but most don't have short-term
As someone who runs a biotech company the reason why is in biotech it takes a long time to get a intern up to speed - biology is just so messy that you have to learn an awful lot of background information just to get to step one.
I get that (I've experienced the pain of bringing new people up to speed in a lab), but it seems like this some of this could be solved by moving the selection process to earlier (e.g. January) and then having the background knowledge learned with checkins throughout before starting.
It is just a shame that, in my current position as a wetlab researcher getting a computational Master's degree, finding internships that appeal to both sides is quite difficult. And I'm somewhat turned off by a lot of the computational summer internships because they basically don't expect anything out of you because your work isn't worth using once you've left -- they're offering internships because the government told them they had to if they wanted to keep their funding.
Tangentially related, I used to work with a bunch of IDT's scientists. Their large oligo synthesis process, at least of as a few years ago, was kind of disappointing.
In theory it would be possible to do this, the major problem is not letting the pre-interns flailing around as they don’t really know where to start. The pre-intern also has to be really motivated.
On this topic when I used to be an academic I used to try and get my honours students (4th year research students) and PhD students to start early learning all the background material a few months out of their official start date so they would hit the ground running. Not a single student ever managed to make any progress (most did absolutely nothing) despite having the entire summer to get up to speed.
