I have been running the Genomics Core Facility at the University of Utah
for 8 years. We have three 373's and will soon have two 377's with
96-well capability. Unlike some facilities which only run client
samples in lanes, we handle fragment analysis from PCR through scoring
alleles.
To partially answer your second question, I'm going to attach an excel
spreadsheet which we used to determine our pricing structure. The
actual pricing structure can be found at our website
http://www.hci.utah.edu/groups/genomics/ If the spreadsheet gets to
you with all the formulas intact, you should be able to play with it and
see how different variables affect your cost.
Cost of genotyping is highly dependent on your ability to multiplex and
the sheer volume of genotyping you are able to generate. Fixed costs
are relatively high, so the higher your genotyping volume, the cheaper
it is. Higher multiplexes are better because although the gel itself is
cheap, there is a high cost in labor for cleaning, pouring, loading,
etc.. and for the size standard in each lane. We have also found that
time (labor) for analysis and scoring is not trivial.
As for the second question, microarrays are really tempting and we will
all probably be there sometime, but since you already have the automated
sequencers, you might as well use them unless they are already running
at full capacity. We use our 373's for running microsatellite markers
for linkage analysis, microsatellite instability and LOH. We do SNP
detection by SSCP and allele specific PCR. And we are starting to do
some AFLP for plant identity.
I'm sure others will have different ideas, but there's my 2 cents.
Contact me off line if you want more details.
Linda
Robert Lyons wrote:
> I would like to tap into your genotyping expertise, if I could.
> The University of Michigan has not yet offered a genotyping service
> (much to the consternation of our many geneticists). For various
> reasons, we may begin such a service in the not-too-distant future.
> Because I operate automated sequencers, it would be easy for me
> to expand operations to include GeneScan work. However, I am badly
> uninformed and inexperienced with genotyping, and need some info
> to help me decide how to proceed:
>
> - Can someone who routinely does GeneScan runs on ABI sequencers
> please give me a rough estimate of typical cost per marker?
> (the real operational costs, assuming we'd buy commercially-
> available primer sets).
>
> - SNP-based genotyping seems to hold great promise for the
> future. Would I be foolish to start up gel-based genotyping
> instead of, say, array hybridization against SNP oligos? or
> one of the other new SNP-based technologies?
>
> Thanks a million for any clarification or discussion.
>
> Bob Lyons
> University of Michigan
>
> -----------------------------
> Robert Lyons, Ph.D.
> Director, DNA Sequencing Core
> University of Michigan
> -----------------------------
--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