DNA Sequencing Study

George Grills grills at aecom.yu.edu
Thu May 7 19:39:14 EST 1998

UNTIL MAY 15, 1998

(1)  Please go to http://mbcf.dfci.harvard.edu/dsrc.html to participate in
this study. 

(2)  Submit sequence analysis files and fill in specific sample information
forms at the web site.

(3)  Fill in the general sequencing techniques survey. 

Full instructions on how to FTP your analysis files and fill in the survey
forms can be found at the above location.

The sequence analysis files should be chromatogram (electropherogram) files 
of the results of sequencing standard pGEM template with the M13 (-20)
forward primer.    

(4)  Please note that there has been a change in the FTP server name since
the last time this study was open for submissions.
In addition, you no longer need to specify a directory for FTP. 
Just type: 
name: abrf 
password: abrf

(5)  Samples submitted by manufacturers of sequencing machines or
sequencing products should indicate that the samples are from the
manufacturer and include the name of the source in the comments field of
the sample information form.  Samples from manufacturers are the only
samples that we request not to be anonymous submissions.  A number of
manufacturers have expressed interest in submitting samples to this study
(manufacturers have not participated in our previous studies).  Samples
from manufacturers will not be included in the pool of samples analyzed for
the general sequencing study, but will be used in a separate analysis. 

Data received by May 15, 1998 will be presented at the Tenth International
Genome Sequencing and Analysis Conference, September 17-20, 1998 in Miami,
FL.  In addition, analyzed results of the survey will be included in a web
site linked to the homepage of the Association of Biomolecular Resource
Facilities (ABRF).

This study is conducted by the ABRF DNA Sequencing Research Committee


To all investigators involved in DNA sequencing:

     The ABRF DNA Sequence Research Committee 1998 Study is open for new
sequencing data submissions until May 15, 1998.  We ask that you submit
chromatogram (electropherogram) analysis files of the results of sequencing
standard pGEM template using the M13 (-20) Forward primer with any
chemistry, run condition, and machine type. Please go to
http://mbcf.dfci.harvard.edu/dsrc.html to participate in this study.

     We reopened the study to allow for analysis of more results with: (1)
current "standard" sequencing techniques using established instruments such
as the PE-ABI 377, 373, and 310 sequencers, the Li-Cor sequencers, and the
Pharmacia ALF; and (2) newly developed techniques, such as porous combs,
PE-ABI 377 96-well upgrades, Amersham new dyes, dilution buffers, and new
instruments such as the Molecular Dynamics MegaBACE and the GeneSys
Technologies GTI-9600 system.  We encourage investigators that have already
submitted results to the study to send us additional or more recent
results.  The newly collected data will be pooled with previously submitted
data.  An analysis of the results from this study will be presented this
year at the Tenth International Genome Sequencing and Analysis Conference,
September 17-20, in Miami, FL.

     The first goal of this study is to examine the sequencing results that
are being obtained in most labs with both standard and experimental
techniques.  One aim of this part of the study is to create a web site for
comparing a standard template sequenced under various protocols.  This web
site will be an on-line repository of sequence results and the conditions
used to generate them.  This resource will allow researchers to compare,
anonymously, the quality of their sequence data with that of colleagues.
In addition, this data could be valuable in making crucial decisions
regarding new chemistries and equipment upgrades.

     The second goal of this study is a general survey to "take the pulse"
of the DNA sequencing world.  The aim of this part of the study is to
determine the answer to questions such as what types of machines and
chemistries are being used and what are the range of current charges for
facility services and research time.

     The preliminary results from this study were presented at the ABRF'98
meeting in San Diego (reference below) and will soon be posted on the
Association for Biomolecular Resource Facilities (ABRF) web page:  

Adams, P.S., Dolejsi, M.K., Grills, G., Hardin, S., McMinimy D., Morrison,
P. and Rush, J. (1998)  1998 ABRF DNA Sequence Research Committee Study:
Assessing the Current State of the Art in DNA Sequencing and Creating a
Quality Control Resource.  ABRF '98: From Genomes to Function: Technical
Challenges of the Post-Genome Era: An International Symposium Sponsored by
the Association of Biomolecular Resource Facilities, pg. 32 (abstract).

     We appreciate your past and future participation in this study.

The ABRF DNA Sequencing Research Committee:

George Grills, Albert Einstein College of Medicine, Bronx, NY (chair)
Pamela Scott Adams, Adirondack Biomedical Research Institute, Lake Placid, NY
Duane Bartley, John Hopkins University, Baltimore, MD (ad hoc)
Mary Kay Dolejsi, Fred Hutchinson Cancer Research Center, Seattle, WA
Karl Hager, Yale University, New Haven, CT (ad hoc)
Susan Hardin, University of Houston, Houston, TX
Doug McMinimy, The Jackson Laboratory, Bar Harbor, ME
Paul Morrison, Dana-Farber Cancer Institute, Boston, MA (ad hoc)
John Rush, Howard Hughes Medical Institute, Harvard Medical School, Boston,
MA (ad hoc)
Theodore Thannhauser, Cornell University, Ithaca, NY

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