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captainentropy 01-28-2011 02:58 PM

Cost to run/maintain/use a GAII?
So my lab just inherited a GAII. It's ours free and clear from a lab that is moving and I believe is also upgrading to a HiSeq.

What I would like to get is a rough estimate on how much we should expect it to cost to run and maintain one both in terms of $$ for consumables and maintenance and in time and effort? Do we need a dedicated technician? It would not be used as a core facility - it would be just for our use. Is it a waste of our resources just as it would probably be to do our own Sanger sequencing to verify cloning etc.?

We would use it routinely for sure and I'd be in charge of it.


GERALD 01-28-2011 06:08 PM

So they're just leaving them out on the sidewalks now? Sad...
It's probably better to have it than not, if your lab does a lot of sequencing, but there are some things to keep in mind.
  • First, you should plan out who in the lab will run it, especially for projects from collaborators outside your lab.
  • Also, you probably want to make some provisions to charge people, JIC. While I can understand not wanting to be a core, you'll probably find that people keep asking to run samples.
  • You also might want to hire a technician, who could help out with other things around the lab. Perhaps you could get your department to pay some or all of their salary.
  • Also, if it breaks (which happens more frequently when they get older) then they can be very expensive to fix. Service contracts also tend to be very expensive.
Good luck, and welcome to the club.

captainentropy 01-28-2011 06:16 PM

Thanks Gerald.

I'd be the one in charge for sure. Based on our projects I'm sure we would use all the lanes on every flowcell. Running samples for others was suggested and that might happen. But the nearby labs either have their own GAII/x/HiSeq machines or contract out due to their huge volume from their projects.

We need another tech anyway. That would be good but knowing my PI we would probably hire another postdoc instead.

The service contract is the biggie. I guess I can talk to Illumina about that.

Do you run one? What kind of time commitment does it require for say running one flowcell per week?

csc 01-28-2011 08:21 PM

If you plan on using it a lot, it isn't an instrument I would try to run without a service contract. A single failed run can cost thousands of dollars in replacement reagents, let alone the cost of getting it fixed if there is an actual hardware problem (i.e. if your mode scrambler or a laser dies). The service contract is a big pain at ~$50K. The GAII isn't the most user friendly instrument out there but once you run it a number of times it can be just as simple as operating any other piece of instrumentation. I've logged about 200 runs on our GAI/II but we did the trade-in for the HiSeq so the GAII is probably getting packed up about a month from now. I agree that it is probably best to have a dedicated operator for it.

Running one flow cell per week isn't a huge deal in terms of time commitment assuming the libraries are ready. Clustering is fairly simple (especially if you have a cBot) and doesn't require too much hands-on time. Setting up the sequencer isn't too bad once you have had some practice. It can be a bit of a pain when you are new to it.

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