Re: DNA- genescan

Mary Kay Dolejsi (marykay@fred.fhcrc.org)
Fri, 15 Oct 1999 08:17:21 -0700

Well, it's been quite a while, but I thought I would post the solution that
seems to have done it for us. (Dare I write this down?) Thanks to all who
sent suggestions. Most all of them were things we had tried, and I hadn't
specified, like re-running matrices, re-loadind firmware, re-loading
software. We and PE (thanks to specialist Candia Brown) were pretty
convinced this was some hardware problem, not chemistry or software. So,
the engineer (kudos to Pat McSwain!) persisted in systematically replacing
parts. The answer is: a gel optics block. (whatever that is.) The 2
instruments in question were purchased, installed, and presumably
manufactured at the same time, they have sequential serial numbers.
Possibly something in that batch or manufacturing had a susceptible part.
PE is looking into this.

Again, thanks for your suggestions.

At 11:21 AM -0600 10/1/1999, Linda Wood Ballard wrote:
>Mary Kay,
>
>Did you ever get any resolution on this? I had no good ideas myself to give
>you, but I keep thinking about it and thought I would ask.
>
>Linda
>
>
>Mary Kay Dolejsi wrote:
>
>> I'm hoping that those of you running frament analysis on PE 377's might
>> have some help for us. We have a problem that is baffling us and
>> PE-Applied Biosystems.
>>
>> For the past couple of months, a group running lots of GeneScan has been
>> seeing greatly reduced signal intensities of their marker bands, but only
>> when run on 2 particular instruments. If we take the same samples, and load
>> them on either of 2 other instruments, in a different room, different
>> floor, the signal intensities are normal.
>>
>> Sequencing runs on all the instruments, using primarily Big Dye
>> terminators, look beautiful and normal.
>>
>> We have taken a gel from one machine mid-run, and moved it to one of the
>> other sets, and seen the change of intensities.
>>
>> We have loaded the same batch of samples and demo standards on parallel
>> runs on the same machines, and seen the different intensities.
>>
>> We have checked:
>>
>> plates, gel mixes, buffers, formamide,
>>
>> PE-biosystems has changed:
>>
>> lasers, power supplies, CCD cameras, other optical components.
>>
>> This problem is starting to feel like voodoo or black magic.
>> Unfortunately, I'm a muggle scientist, and not a wizard, so the solution
>> still eludes me. Can any of you suggest things we might be overlooking, or
>> should check differently?
>>
>> I appreciate your support, as always.
>>
>> Mary Kay Dolejsi, Ph.D.
>> Manager, Biotech lab
>> marykay@fred.fhcrc.org
>> phone: 206-667-4197
>> fax: 206-667-6497
>>
>> Mail address:
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave N., B1-080
>> PO Box 19024
>> Seattle, WA 98109-1024
>
>--
>
>Linda Wood Ballard
>Genomics Core Facility
>Huntsman Cancer Institute
>4A 430A School of Medicine
>University of Utah
>Salt Lake City, UT 84132
>
>(801) 581-3875
>FAX (801) 585-2978

Mary Kay Dolejsi, Ph.D.
Manager, Biotech lab
marykay@fred.fhcrc.org
phone: 206-667-4197
fax: 206-667-6497

Mail address:
Fred Hutchinson Cancer Research Center
1100 Fairview Ave N., B1-080
PO Box 19024
Seattle, WA 98109-1024