I'm in the market to buy a DNA extraction robot, and would really appreciate any suggestions/experience/advice.
With the projects we recently landed we're expecting to process on average about 3000-5000 noninvasive samples per year (scats, urine, saliva - all taken from the environment not from the animal directly). DNA extraction is a total bottleneck in our lab, it's difficult to do quality control when hand-extracting (sample mixup, pippetting errors...) and is too labor intensive (hence expensive) and slow.
I'm not too keen on the magnetic beads technology (tested some machines, didn't like them) and I'd like something that could automate regular spin column (silica membrane) extraction. QiaCube from Qiagen seems an option, but it only does 12 samples at a time. I'm looking at about 100 samples per day throughput, and can spend about 30,000€ on this (well, 40,000€ tops). Contamination prevention is critical with noninvasive sampling applications.
I'd really appreciate any help with this.
I am using MaxWell 16 DNA extractor, is from Promega, you can run 16 samples in 45 minutes, risk of contamination is zero.
The extraction cartridges (for scat) are 200 euros per 48 samples but are very efficient (20-30 nanogram per microliter DNA concentration from scats). The price varies with number of cartridges ordered.
All the best,
Ancuta Cotovelea
Ancuta, thanks! Can I ask how much you paid for the machine? How much manual work is sample prep before you load it?
Another thing... you're working with bears, right? What sort of genotyping success rate from scat samples are you getting with this machine? With manual extraction using spin columns we're getting about 88% success rate from scats subjectively estimated to be max. 5 days old and collected in ethanol.
We are also using the MaxWell 16 DNA from Promega for scat and tissue extractions. We have recently started putting the scat samples into Roche STAR buffer before extracting and we are getting very good results (previoulsy using Integrated science OneStep PCR inhibitor removal kit after extracting - but this was becoming costly). STAR buffer is working well using lower than recommended volumes. Only processing 16 at a time is still time consuming but the Maxwell platform has a very small footprint compared to automated equipment than can handle larger volumes.
Cassandra, thank you! Did you ever try comparing the DNA quality obtained by Maxwell with the DNA "hand-made" with spin-column extraction? Otherwise this machine sounds quite good, looks perfect for our lab, there is local support and we're already negotiating one for testing. Thanks for the Roche buffer tip - we'll try this. Do you mind if I pick your brain about running this machine efficiently if we end up buying?
No problem Tomaz. I haven't compared manual methods against the Maxwell. The Maxwell is a very user friendly piece of equipment. [email protected] if you need more information. I have also used a few other automated extraction machines including Qiagen but not with the work I am doing now.. previous human pathology work
Cassandra, thanks. I'm arranging to have the machine (and one from AnalytikJena and one magnetic-beads-based from Qiagen) in our lab for testing, and we'll explicitly compare their performance with Qiagen's Stool Mini kit using a representative number of samples. I'll post the results.
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