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Old 11-16-2012, 01:58 PM   #1
docbio
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Default Automation for NexteraXT Library Prep

Curious if anyone has any experience automation platforms and the NexteraXT library preparation kits.

We're looking at several possibilities, including an epMotion 5075 TMX. I've also recently learned a little about the SciClone from Caliper and I've seen mention of some other platforms. Eppendorf has a 5075 with a built in cycler but I don't think I'd trust it for library prep, and have no problem with manual intervention for the thermal cycler steps. I've seen some old threads regarding careful programming to avoid magnetic bead carryover with the epMotion, other than that, seems like information is scarce.

Illumina tech support was surprised I'd want to automate because the XT kit is already so fast, and it is, but I'd rather the robot be pipetting while I write grants, etc. We tend to work in full 96-well plates, too.

Curious to know other's experience, if any, with these automated platforms.

TGIF
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Old 05-08-2013, 11:45 PM   #2
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Have you gotten any further on your search for automation for Library Prep (Nextera specifically)? We have been approached by Qiagen regarding their Syphony, Perkin Elmer regarding their NGSx. It's difficult to tell simply by the specs how easy to use they are so personal experience advice would be greatly appreciated.

Thanks,
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Old 05-09-2013, 02:33 AM   #3
james hadfield
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Why are you automating Nextera XT?

It is not clear how many samples you want to process, our experience is that Nextera and Nextera XT can do without automation. Both protocols can be completed in one day by a single user so even 100s of samples can be processed without automation.

We've done 3000 Nextera custom-captures, two people eight weeks work. No robots, just replicants!
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Old 05-09-2013, 03:29 PM   #4
pmoplast
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Hi James:

more specifically, we want to automate Nextera Rapid Capture (extended exome capture). The issue is not so much how long it takes but rather that we plan on using this kit for clinical purposes and automation is a better way to avoid cross-contamination, human contamination, and foreign species contamination than manual pipetting, not to mention avoiding common human errors. It's a QA/QC thing :-)
Do you have any recommendations specific to the kit we are using?
Thanks,
Paula
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Old 05-09-2013, 09:12 PM   #5
docbio
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Quote:
Originally Posted by pmoplast View Post
Have you gotten any further on your search for automation for Library Prep (Nextera specifically)? We have been approached by Qiagen regarding their Syphony, Perkin Elmer regarding their NGSx. It's difficult to tell simply by the specs how easy to use they are so personal experience advice would be greatly appreciated.

Thanks,
pmoplast
We have an Eppendorf Epmotion 5075 TMX in house now. We've been working with their technical reps to develop the NexteraXT protocol for the platform and optimize it. It has required a little bit of work and some water runs to fine tune the pipetting steps to avoid mag bead carryover, but we have done our first few validation runs and the results have been very good. Other robotics solutions were either far more expensive or couldn't handle 96/384 samples. We have some other Qiagen robotics in house and haven't been particularly pleased with service/support.

The mag bead carryover issue was the one thing we heard about from other users. It seems the key is to optimize your pipetting speed and position, very similar to the way we had to slow down our electronic multichannel when we were doing it manually. Once you have settings that work, the protocol is good to go.

To answer James' question, we wanted to automate to help decrease the chance of human error and to free up our humans to do other tasks in lab. The NexteraXT protocol is very straight forward and easy to do, but it still takes time away from other tasks.
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Old 05-09-2013, 11:31 PM   #6
james hadfield
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We have a Tecan Evo but are mainly using it for qPCR setup and normalisations.
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Old 05-10-2013, 01:04 PM   #7
docbio
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Also want to point out we designed our protocol with two interventions to do the tagmentation step and the amplification step off robot in a thermocycler. We didn't trust the TMX module to hold the temp for the tagmentation step but it's possible it might work. You can get a robot with a cycler built in from Eppendorf but it constricts the configuration in some other ways that we didn't like.
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Old 06-03-2013, 04:00 AM   #8
yuen.chan
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We are using the Sciclone G3 for the automation of the NexteraXT protocol, which appears to be working well. But we are still in the early phase of testing it out.
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