Dear Colleagues:
The Association of Biomedical Resource Facilities (ABRF) Fragment
Analysis Research Group (FARG) would like to announce the opening of the
FARG 2001 Study.
Here is a scenario you could be faced with:
Investigator Dr. Smith is studying a particular disorder. A screen
and analysis of the data has revealed a region of interest on chromosome 4.
Dr. Smith would like to do fine mapping of the region and has come to you
with synthesized primers for several additional markers in the region. You
run his sample set with the markers and present him with the data. Data for
two of the markers is uninterpretable because they are dinucleotide repeats
that display a +A stutter. Dr. Smith says these markers are key for
fine mapping of the area so you suggest that the reverse primers be
resynthesized with a tail which has been shown to eliminate the +A
stutter with most dinucleotide markers. Analysis with the tailed primer set
gives interpretable results for one of the two sets. Dr. Smith is thrilled
but really needs the other marker for fine mapping. He asks if there is
anything else that can be done. You search the databases and find that
there is a trinucleotide repeat marker that is mapped to the same location
and has just as high a heterozygosity value. You have the primers
synthesized, run his samples, and present him with the data. Fine mapping
analysis has shown there to be linkage of the disorder to this area, Dr.
Smith publishes his findings and can't thank you enough for your genotyping
expertise.
The FARG has prepared two samples containing three different PCR
sets: A dinucleotide which is untailed, the same dinucleotide generated
with a tailed reverse primer and a trinucleotide. We were hoping to
demonstrate the differences between tailing and not tailing a dinucleotide
repeat and the difficulties that can arise with automated allele calling of
untailed dinucleotides due to +A characteristic of taq polymerase.
Hopefully the untailed sample is difficult for everyone to call and is
representative of how binning this data would be impossible especially for
linkage studies, while the tailed sample is more easily analyzed. The
trinucleotide also has a +A but the products for this particular tri
never show mixed species (even if it did binning isn't an issue).
This year's study is designed to be educational in nature but we
also hope that we can collect further data on the factors which are
important for accurate and reproducible fragment analysis to complement the
FARG 2000 study.
Please go to http://162.129.76.21/Farg01cover.html to participate
in this study. There you will find full instructions on how to request
samples and then submit your analysis files and fill in a webform that
inquires about the exact conditions under which the samples were run.
All data received by December 1, 2000 will be included in the
report of the data presented at the ABRF 2001 meeting February 24-27, 2001
in San Diego, CA in the Fragment Analysis Research Group presentation and
as a poster at the meeting. The results will also be available shortly
thereafter on the ABRF homepage under ResearchCommittees/Fragment Analysis.
We hope that you have fun with these samples and find participation
in this study to be a worthwhile and educational experience.
Thank you.
The ABRF Fragment Analysis Research Group
Doug Bintzler, University of Cincinnati, (chair)
Pamela Scott Adams, Trudeau Institute
Linda Wood Ballard, University of Utah
Yongde Bao, University of Virginia School of Medicine
Duane Bartley, John Hopkins University
Laura M. Kasch, Johns Hopkins University
Lynn Petukhova, The Rockefeller University
Caprice Rosato, Oregon State University
Catherine Terrell, University of Cincinnati
Laurey Steinke, University of Nebraska (ad hoc)
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