DSRG BAC study 2nd reminder

Margaret Robertson margaret.robertson at cores.utah.edu
Thu Nov 16 11:49:57 EST 2000


The purpose of this message is announce the re-opening of the DNA
Sequencing Research Group's (DSRG) 2000 Study on BAC Sequencing. In this
two-part study we will focus on factors that affect the accuracy and
quality of sequence when Bacterial Artificial Chromosomes (BACs) are
used as the sequencing template. This study is being conducted to assess
a DSRG recommended protocol which has been extracted from data submitted
to the original study. Since the large scale production of BACs is more
problematic than that of standard plasmid templates we will not be able
to send the sample materials out in a mass mailing as we have done in
the past (e.g.Standard and Difficult Template Studies). In order to
participate in this study it will be necessary to request materials in
advance.

Part 1 of the study will concentrate on the operational steps directly
related to the sequencing of BACs and will specifically address the
efficiency and success of the recommended protocol in producing good
sequence data. The DSRG will provide all registered participants with a
sample of a standard BAC, an appropriate primer and a recommended
protocol.  Participants will then sequence the standard BAC using the
recommended protocol provided on the instrumentation currently being
used in their laboratories. We request that they send us the sample
files electronically, in either .scf or .abi format, and a completed web
form concerning the methodologies used to produce the sequence. The
sequencing data will be analyzed and compared to the previous data
collected. We strongly encourage participants who have previously
submitted data to the part 1 study, to test out the recommended protocol
and submit new data using their original four digit ID numbers. This
will enable us to directly compare the success of the recommended
protocol.

Part 2 of this study will concentrate on the operational steps relating
to the isolation of BAC templates for use in sequencing. The DSRG will
provide all registered participants with an agarose stab of bacteria
containing the standard BAC. Participants will then grow up the bacteria
and isolate the BAC by the methodologies utilized in their respective
laboratories. We request that they send the purified BAC to us for
sequencing along with a completed web form concerning the methods used
in the isolation of this material. The sequencing
results will be analyzed and compared with the information available on
the web form in order to identify practices that correlate well with
high quality sequence. These will form the basis of the recommended BAC
preparation method.

It is not be necessary to register for both parts in order to
participate in this study, although we encourage everybody to do so. To
request the materials necessary to participate in this study please use
the following url:
 
 http://brcweb.bio.cornell.edu/dsrg2000/
 
You will receive your sample of the standard BAC and/or the bacterial
stab shortly after registering. Additional information concerning how to
return the
sequence, the purified BAC, where to find the web forms etc. will be
provided at that time.
 
The closing date for participation in this study is December 31st 2000.
Results will be presented as a poster at ABRF 2001.

I hope you will take the opportunity to participate in this study.


Margaret Robertson
Director, DNA Sequencing Facility
University of Utah,
4A 432A, SOM
50 North Medical Drive,
Salt Lake City, UT 84132
Tel: 581-4736
Fax: 585-2978
margaret.robertson at hci.utah.edu
http://www.hci.utah.edu/groups/sequencing


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