2nd Announcement
of the ABRF DNA Sequencing Group
Standard Template Study
To all investigators involved in DNA sequencing:
The 2001 ABRF DNA SEQUENCE RESEARCH GROUP STANDARD TEMPLATE STUDY is open for
sequencing data submissions. Please submit your data by April 25, 2001. We
ask that you submit chromatogram (electropherogram) analysis files of the
results of sequencing standard pGEM template using an M13 forward primer with
any chemistry, run condition, and machine type. In particular, we are
requesting data from relatively new types of instrumentation (such as the ABI
3100 and ABI 3700).
To participate in this "Never Ending Story (NES)î study, please click on
"SUBMIT" at:
http://nes.biotech.cornell.edu/nes
The goal of this study is to analyze the effect of different sequencing methods
on the quality of sequencing results. Sequence data are submitted anonymously
via the web and details of the sequencing conditions are collected on a web
based survey form. The effect of factors such as different types of
instrumentation and chemistries are examined. Data is posted on the NES web
site in a format that can be used as a benchmark for sequencing. The results
of this study may be used to: (1) anonymously evaluate the quality of
sequencing results relative to that achieved in other laboratories (quality
control); (2) systematically evaluate different instruments, chemistries and
protocols when considering either equipment purchases or modifications to
standard operating procedures (decision making); and (3) determine the causes
and solutions to technical problems (trouble shooting).
Our aim is to analyze sequencing results both from standard techniques (such as
the ABI 377) and from new technologies (such as new dye chemistries and
capillary-based instruments like the ABI 3100 and ABI 3700). The study will
analyze the results of sequencing pGEM-3Zf(+) template sequenced with the
M13(-21) or M13(-40) forward primers. Submissions are restricted to these
template and primer combinations, but there are no restrictions regarding
sequencing conditions, protocols and instrumentation. We encourage submissions
of data from instrumentation that have not been well represented in our past
studies (including the ABI 310, the Megabace, the CEQ2000, the Alf, and the
BaseStation). We encourage investigators that have submitted results from
1998-2000 to send additional and more recent results to the 2001 study.
Moreover, we encourage investigators that have never submitted data to
participate in the 2001 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 the 1998 study are available at
http://www.abrf.org/ABRF/ResearchCommittees/dsrcreports/abrfdna2/dsrc98.htm.
The results from the 1999 study are available at
http://www.abrf.org/ABRF/ResearchCommittees/dsrcreports/dsrg99/dsrg99.pdf
An analysis of data received by April 25, 2001 will be presented at the Cold
Spring Harbor Genome Sequencing and Biology Meeting in May of this year.
Detailed results will then be posted on the web on the ABRF home site at
http://www.abrf.org under Research Groups/DNA Sequence. The NES database/web
site resource at http://nes.biotech.cornell.edu/nes will continue to be open
after May for new submissions and to allow investigators to take advantage of
the web siteís analysis tools.
Thank you for your past and future participation in this ongoing study. Your
data will help us define the state of the art of DNA sequencing in 2001.
The ABRF DNA Sequencing Research Group
Dina Leviten, ICOS Corporation, Bothell, WA(chair)
Lawrence Hall, Albert Einstein College of Medicine, Bronx, NY
John Hawes, Indiana University School of Medicine, Indianapolis, IN
Tim Hunter, University of Vermont, Burlington, VT
Emily Jackson-Machelski, Washington Univ. School of Medicine, St. Louis, MO
Kevin Knudtson, University of Iowa, Iowa City, IA
Theodore Thannhauser, Cornell University, Ithaca, NY (EB liaison)
Duane Bartley, Johns Hopkins University, Baltimore, MD(ad hoc)
George Grills, Albert Einstein College of Medicine, Bronx, NY(ad hoc)
Margaret Robertson, Cimarron Software, Salt Lake City, UT (ad hoc)
James VanEe, Cornell University, Ithaca, NY (ad hoc)
Pamela Scott Adams, Trudeau Institute, Saranac Lake, NY (ad hoc pro term)
Susan Hardin, University of Houston, Houston, TX (ad hoc pro term)
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Please direct questions about participation in this study
to Dina Leviten at dleviten@icos.com
or to George Grills at grills@aecom.yu.edu
This archive was generated by hypermail 2b29 : Tue May 01 2001 - 14:07:05 EDT