DNA Sequencing Study - ABRF 1998

George Grills grills at aecom.yu.edu
Fri Jan 30 04:59:53 EST 1998


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

Please submit sequence analysis files and fill in sample information surveys.
The sequence analysis files should be chromatogram (electropherogram) files 
of the results of sequencing standard pGEM template with the M13 (-20)
forward primer.    

Please fill in a general sequencing techniques survey. 

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

Data received by Feb 15, 1998 will be presented at the ABRF'98 meeting in
March, 1998 in San Diego. 
Analyzed results of the survey will also be included in a web site linked to
the homepage of the Association of Biomolecular Resource Facilities (ABRF).

Study conducted by the ABRF DNA Sequencing Research Committee


Dear Fellow DNA Sequencers:

	The last few years have seen numerous improvements in DNA sequencing
chemistry and the introduction of several new DNA sequencing instruments.
Just the past year has seen the introduction of new dRhodamine dyes, new
energy transfer dyes, and new vendors for standard dye terminator kits.
Currently, new instrument upgrades, sequencing chemistries and sequencing
platforms are being tested and implemented.

	There are always questions when new technology is introduced.  What old
problem does the new technology solve? How much of an improvement in results
does the new technology offer?  Does the improvement justify expenditure of
capital which is usually not readily available?  What new problems are
associated with the new technology?  These are particularly important
questions for core labs, who sequence a variety of template types and work
with researchers of varying sophistication.  To properly answer these
questions, data is needed - and lots of it.  An analysis of what machines
and chemistries are being used and what sort of results are being obtained
would be very useful for establishing a basis for self evaluation and for
making decisions on new technologies.

	To this end, the DNA Sequence Research Committee (DSRC) of the Association
of Biomolecular Resource Facilities (ABRF) is launching a two-part study
this year.

	The goal of the first part of this study is to analyze the sequencing
results that are being obtained in most labs.  We request that you submit
chromatogram (electropherogram) analysis files of the results of sequencing
standard pGEM template using the M13 (-20) forward primer with your current
"standard" chemistry and run conditions.  Most sequencing labs run this
standard routinely, so we hope that this will be data that is easy to
submit.  A webform sample survey needs to be filled in for each sample that
is submitted.  The survey requests the exact details of the conditions under
which each submitted sample was run.

	The second part of the study is a general survey to "take the pulse" of the
DNA sequencing world.  The goal of this part of the study is to determine
the answer to questions such as what types of instruments and chemistries
are being used, how old are the instruments, and what people are charging
for their services.

We hope to answer the following questions:

1.  How do the recently released dyes (e.g., dRhods, Big Dyes, etc.) compare
with previously available dyes (e.g., rhodamine)?  In particular, effects on
read length, signal sensitivity, dilution tolerance, and ease of use will be

2.  How do dye terminators and enzymes from different sources (e.g.,
Amersham, ABI) compare with each other?

3.  How does the new filter wheel upgrade which enables the 373 to use the
Big Dyes perform?

4.  How does data quality compare between different automated sequencer
manufacturers and models?

5.  How do various DNA basecalling/analysis programs impact on data analysis

6.  Is editing still as important as indicated in our previous study or do
the new improvements minimize the need for manual editing?

	Our goal is to create a web site for comparing a standard template
sequenced under various protocols, an on-line repository of sequence results
and the conditions used to generate them that will allow researchers to
compare, anonymously, the quality of their sequence data with that of
colleagues.  In addition, we hope that being able to see what results other
labs are getting may help you make crucial decisions regarding equipment
upgrades and/or chemistry changes.

	Please go to http://mbcf.dfci.harvard.edu/dsrc.html to participate in this
study.  You can submit samples and fill in the sample survey, or just fill
in the general survey, or do it all.  Full instructions on how to FTP your
analysis files and fill in the webforms can be found in this location.

	Please send us samples of your current "standard" chemistry and run
conditions.  Please send us any results from experimental conditions as
well.  If you try a new chemistry or a different gel mixture or modify your
instrument, please send us your standard runs from before and after the
changes.  There are no restrictions as to the type of sequencing conditions.
The only stipulation is that all submissions must be pGEM template sequenced
using the M13 (-20) forward primer.  Please keep in mind that this is a
survey, not a contest.  A typical run or even a poor run can provide as much
valuable information as your best run.  It is important to receive
information from as large a cross section as possible - from the oldest
machines to the newest, from beginners to experts.  All data is valuable.
As always, the information is anonymous.  Data received by Feb 15, 1998 will
be included in the preliminary report of the data presented at the ABRF'98
meeting March 21-24, 1998 in San Diego.  Such data will also be included in
the web site of the poster collection of previous studies presented on the
ABRF homepage http://www.medstv.unimelb.edu.au/abrf.html under Research
Committees/DNA Sequence.  We hope that you will have fun with this and help
the Committee to help all of us in the "art" of DNA sequencing.

The ABRF DNA Sequencing Research Committee

Pamela Scott Adams, Adirondack Biomedical Research Institute, Lake Placid, NY
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
Doug McMinimy, The Jackson Laboratory, Bar Harbor, ME
Paul Morrison, Dana-Farber Cancer Institute, Boston, MA
John Rush, Howard Hughes Medical Institute, Harvard Medical School Boston, MA


 George Grills
 DNA Sequencing and Oligonucleotide Facilities
 Albert Einstein College of Medicine
 713 Ullmann Building           
 1300 Morris Park Avenue       
 Bronx, New York 10461-1602    
 Tel: (718) 430-2657
 Fax: (718) 430-8778
 E-mail: grills at aecom.yu.edu
 DNA Sequencing: http://leper1.ca.aecom.yu.edu/dnacore
 Oligonucleotide: http://sequence.aecom.yu.edu/oligo

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