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DNA Sequencing Study

Theodore Thannhauser tt34 at cornell.edu
Tue May 18 16:29:21 EST 1999


Announcement of the Continuation
of the ABRF DNA Sequencing Committee 
1999 Standard and Difficult Template Studies

Dear Fellow DNA Sequencers: 

Please note that the ABRF DNA Sequencing Research Committee 1999 Standard and
Difficult Template Study is again open for sample submissions.  The study has
two parts.  The first part involves study of DNA sequence results with a
standard pGEM template.  Information on how to submit data for this Standard
Template Study is posted at http://mbcf.dfci.harvard.edu/dsrc.html.  The second
part of the study involves the sequencing of two challenging templates.
Instructions on how to request samples and submit data can be found at the
Difficult Template Study web site at http://brcweb.bio.cornell.edu/dsrc99.  

A preliminary report of the results of data submitted so far was presented at
the ABRF’99 meeting in March of 1999 and will be posted on the web soon.  New
data submitted through June 1, 1999 will be presented at the 11th
International Genome Sequencing and Analysis Conference this September.  

The overall goal of this study is to analyze the effect of different sequencing
methods, chemistries, and instrumentation on the quality of sequencing
results.  Sequence data are submitted anonymously by ftp or http and details of
the sequencing conditions are collected on web based survey forms.  Data is
posted on a web site in a format that can be used as a benchmark for
sequencing.  The results of this study may be used  (1) to anonymously evaluate
the quality of sequencing results relative to that achieved in other
laboratories (quality control); (2) to systematically evaluate different
instruments, chemistries and protocols when considering either equipment
purchases or modifications to standard operating procedures (decision making);
and (3) to determine the causes and solutions to technical problems (trouble
shooting).

Our aim is to analyze sequencing results obtained both with the standard
techniques used in DNA sequencing laboratories and with new technologies (such
as porous combs, 96-well upgrades, new dyes, and high throughput
capillary-based instruments).  We encourage submissions of data from
instrumentation that have not been well represented in our past studies,
including low throughput capillary-based instruments.  We encourage
investigators that have submitted results to the 1998 and the preliminary 1999
study to send additional and more recent results to the current 1999 study. 
Moreover, we encourage investigators that have not submitted data to
participate in the 1999 study.  Please keep in mind that this is a survey
study, not a contest.  A typical run or a poor run can provide as valuable
information as your best run.  We hope to receive results from the oldest
machines to the newest, from beginners to experts.  This is an opportunity for
self-evaluation and to share your successful techniques with others.

Please note that the results from last year’s study are available at
http://www.abrf.org/ABRF/ResearchCommittees/dsrcreports/abrfdna2/dsrc98.htm.

Thanks for participating in this ongoing study.  Your participation will help
us define the "art" of DNA sequencing in 1999.

- The ABRF DNA Sequencing Research Committee

Theodore Thannhauser, Cornell University, Ithaca, NY (chair)
Pamela Scott Adams, Trudeau Institute, Saranac Lake, NY
Duane Bartley, John Hopkins University, Baltimore, MD (ad hoc) 
Mary Kay Dolejsi, Fred Hutchinson Cancer Research Center, Seattle, WA
George Grills, Albert Einstein College of Medicine, Bronx, NY 
Susan Hardin, University of Houston, Houston, TX
Amy Lambert, The Jackson Laboratory, Bar Harbor, ME
Kathryn Lilley, University of Leicester, Leicester, UK (ad hoc)
Paul Morrison, Dana-Farber Cancer Institute, Boston, MA (ad hoc)
Ron Niece, Research Resources & Technologies, Irvine, CA (ad hoc)
Margaret Robertson, University of Utah, Salt Lake City, UT


------------------------------------------------------------------ 
Please direct questions about participation in this study 
to Ted Thannhauser at tt34 at cornell.edu 
Theodore W. Thannhauser, Ph.D.
Director, BioResource Center
Rm. 149 Biotechnology Building
Cornell University
Ithaca, New York 14853-2703
Phone: (607) 254-4850
FAX:   (607) 254-4847
Email: tt34 at cornell.edu

http://brcweb.bio.cornell.edu




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