DSRG BAC Study

Margaret Robertson margaret.robertson at hci.utah.edu
Mon Oct 9 14:07:17 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.

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/

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.
 
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, DSRG chairperson,
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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