DNA Sequencing Standard Template Study

George S.Grills grills at aecom.yu.edu
Mon Apr 16 17:20:49 EST 2001

2nd Announcement=20
of the ABRF DNA Sequencing Group=20
Standard Template Study

To all investigators involved in DNA sequencing:

sequencing data submissions.  Please submit your data by April 25, 2001.  W=
ask that you submit chromatogram (electropherogram) analysis files of the
results of sequencing standard pGEM template using an M13 forward primer wi=
any chemistry, run condition, and machine type.  In particular, we are
requesting data from relatively new types of instrumentation (such as the A=
3100 and ABI 3700).

To participate in this "Never Ending Story (NES)=94 study, please click on
"SUBMIT" at:

The goal of this study is to analyze the effect of different sequencing met=
on the quality of sequencing results.  Sequence data are submitted anonymou=
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 we=
site in a format that can be used as a benchmark for sequencing.  The resul=
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 an=
protocols when considering either equipment purchases or modifications to
standard operating procedures (decision making); and (3) determine the caus=
and solutions to technical problems (trouble shooting).

Our aim is to analyze sequencing results both from standard techniques (suc=
h 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 wil=
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 submiss=
of data from instrumentation that have not been well represented in our pas=
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.=20
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 =
or a poor run can provide as valuable information as your best run.  We hop=
e 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. =20

Please note that the results from the 1998 study are available at

The results from the 1999 study are available at

An analysis of data received by April 25, 2001 will be presented at the Col=
Spring Harbor Genome Sequencing and Biology Meeting in May of this year.=20
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/w=
site resource at http://nes.biotech.cornell.edu/nes will continue to be ope=
after May for new submissions and to allow investigators to take advantage =
the web site=92s analysis tools.=20

Thank you for your past and future participation in this ongoing study.  Yo=
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)=20
Lawrence Hall, Albert Einstein College of Medicine, Bronx, NY=20
John Hawes, Indiana University School of Medicine, Indianapolis, IN=20
Tim Hunter, University of Vermont, Burlington, VT=20
Emily Jackson-Machelski, Washington Univ. School of Medicine, St. Louis, MO=
Kevin Knudtson, University of Iowa, Iowa City, IA=20
Theodore Thannhauser, Cornell University, Ithaca, NY (EB liaison)
Duane Bartley, Johns Hopkins University, Baltimore, MD(ad hoc) =20
George Grills, Albert Einstein College of Medicine, Bronx, NY(ad hoc) =20
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)

Please direct questions about participation in this study=20
to Dina Leviten at dleviten at icos.com
or to George Grills at grills at aecom.yu.edu


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