Is anyone else using (or struggling with!) ABI's new SNP genotyping assay?

It would be helpful to be in touch with other users to thrash out issues and problems, particularly users who aren't using it for linkage mapping.

My lab just purchased a 3130 from ABI (it is still in the box!). We are going to use it mainly for sequencing, but are interesting in learning more about the SNPlex capability. I am interested in hearing more about your experience so far...

Hi jetobin,

I've kind of put SNPlex on hold just now. It's been designed for mapping projects really, and that's not what we were hoping to use it for. It's good enough for mapping, but you can't rely on it for diagnostic SNP calling as yet.

I think to be honest, ABI have just released it too soon (and they've had a few staff change problems on the SNPlex side of things). They don't have a control DNA plate on sale yet - it'll be a couple of months - and they seem unable to answer a lot of questions that I put their way. And in a business, I can't wait months for them to bat questions back and forth between countries and departments before I get answers.

There's meant to be a SNPlex user meeting in april so I'm going to go to that and speak to other users, though the one lab I have spoken to who've used it have had similar problems. Maybe we'll pick it up again after that.

Don't get me wrong though, for mapping it's probably a useful tool, and I don't have any problems with the wet lab side of it. It's a clever technique, and with a bit more tweaking, it could probably be a very powerful method.

labrat

How did the User Meeting go?

The user meeting was incredibly useful - and very open (ABI didn't stifle anyone's criticisms in their presentations). I'm quite impressed with the wet side of the technique. It's a clever use of well understood techniques put together in a novel way.

If anyone is considering using the technology I would recommend waiting a little while though. ABI are about to bring out a better version that combine a couple of steps, meaning you don't need to set up the first stages of the reactions on ice, and also the control are not yet commercially available.

I'd have no hesitation is suggesting it as a mapping tool, but it's not that appropriate as a diagnostic genotyping tool.

And it'sa much more tailored towards human studies because in the design process they use human genome screens to screen out some potential assay problems.

Do you have a specific interest in the technology Fas?

I'm interested in all genotyping technologies- and also their evolution. Any new technology is helped by user feedback and modification. It is encouraging to hear that improvements are being incorporated.
The only lab I saw using this particular system was struggling a bit, but they were one of the first users

We've been testing out ABI SNPlex over the last few months and have been bumping into problems here and there. We've found that the main problem is at the stage of DNA fragmentation and making sure that is consistant over large numbers of samples. We want to be able to run SNPlex as a service to our community but the majority of our customers already have their samples plated into master plates. Many of these masterplates contain DNA of different ages and quality so individual fragmentation of the samples becomes a very time consuming and possibly a dangerous proposition due to the possibility of sample mix up. Has anyone else running SNPlex come up against this and come up with a solution which does not mean fragmenting individual sample one at a time? Is anyone using WGA (Genomiphi) as a substrate? Is anyone having any success with this technique?

I'd also be interested to hear how the changes to the assay design process have increased the success of the probe pools. We have only experience before the updated website was released.

With SNPlex, we have produced some nice results - when the assays and the DNA work, they work really nicely and give high success, analysis on Genemapper is nice and easy too. We've integrated the programs onto our Biomek FX and they work really nicely so set up, although time consuming, is not too big a deal.

Thanks,
Alison

Hi Alison,

I've still not picked up SNPlex again (other priorities pushing it back and waiting for known controls to be commercially available).

Most, if not all of the groups present at the user meeting were using Genomiphi. I would suggest you contact your SNPlex rep and ask to be put in touch with other groups who have used it. If not, I could try and get hold of some names for you.

It's not something I've used, but I have found the DNA concentration required and the fragmentation steps to be the most troublesome of the process.

It seems to have been designed for lots of panels to be tested on a few, heavily optimised DNA samples, rather than one panel to be routinely tested on hundreds and hundreds of DNAs which is the way we'd like to work it.

If you have any success in coming up with a 'non-DNA normalising' method that cuts out all the extra wok at the start then I'd be very interetsed to hear about it.

So we solved our WGA problems. We tried different fragmentation times on the WGA DNA and found that fragmenting for 2 minutes gave good results.

But in the long run we have abandoned plans to provide SNPlex as a service. All for the reasons already discussed.

Alison

Hi

Could someone please recommend a downstream program/s that they found most useful in analysing data generated from SNPLex/genemapper v.3.7.

Cheers

Dave

What are you wanting to do with the data?