ABI 377 GENOTYPER

Ali Zareh zarehar at ccmail.apldbio.com
Tue Jun 6 21:05:41 EST 1995


In article <n.morrison-250595131943 at 129.94.136.143>,
n.morrison at garvan.unsw.edu.au (Nigel Morrison) wrote:

> WHEN WILL THE ABI 377 GENESCAN SOFTWARE BE READY?
> 
> We bought two ABI377 "ABI PRISM" machines for automated genotyping and DNA
> sequencing.  We were not told that the software GENESCAN for the automated
> genotyping was not ready for the powermac.  Despite this problem ABI is
> advertising (in Biosystems Reporter issue 24, February Page 1) that the
> famous geneticist JOHNTODD of the new Wellcome Trust Center for Human
> Genetics at the University of Oxford, used the ABI PPRISM to map the
> polygenes involved in diabetes suceptibility.  John Todd's paper (Nature
> 371:130-136) was a beautiful example of genetic analysis of complex
> disorders.  The suggestion that John Todd uses the ABI PRISM (377)
> certainly influenced our level of comfort in buying these machines. 
> Quoting the Biosystems Reporter " "We could not have completed this project
> in the time we did without the ABI PRISM Automated Genotyping Sysem," Todd
> commented." For future work in mutation detection, it will be invaluable." 
> The Biosystems reporter also stated that: "Todd's group was able to rapidly
> (in six months) and accurately screen the entire human genome for
> micosatellite marker alleles that might be linked to diabetes."  
>   Now we find that the software is not ready, so how could he have used the
> ABI PRISM?; or does ABI PRISM now refer to the ABI373 model which is
> superceded by the ABI 377.  The questions are, what model machine was used
> for the Nature paper, what computer software is reliable and when will the
> ABI GENESCAN software be ready?  We are waiting for the software, and it
> appears that we will be waiting more than the six months it took Todd to
> finish his project.
> 


Response To GeneScan Questions on the Net

This is in response to recent inquiries on the Net in regard to the
availability of the GeneScan Software on the new ABI PRISM 377
instrument and other existing ABI platforms, and their compatibility with
new and older Macintosh models.

Background Notes
GeneScan Software was first introduced as a Software option  for DNA band
sizing and quantitation on the ABI 373 DNA Sequencer in  1991.  Since its
introduction, the GeneScan Analysis Software has undergone three version
changes, evolving in each version to reflect the growing needs and
diversity of customer applications.  The GeneScan  software has been
written in accordance with Apple's software development guidelines. 
Overall, Applied Biosystems Division of Perkin Elmer (ABD)has one of the
largest Apple Software Engineering groups dedicated to the design of
software programs for  the scientific researcher.  

The ABI PRISM Brand  Name
ABI PRISM was introduced as a brand name for all Applied Biosystems
Division of Perkin Elmer fluorescent products for basic research.  The ABI
PRISM Genotyping System includes the instrument, software, accessories and
reagents required for genotyping.  Prior to January of 1995, the system
was based on the ABI PRISM 373 DNA Sequencer. This is the instrument used
in Dr. Todd's research.  In January, the ABI PRISM 377 DNA Sequencer
replaced the 373 in the market.  However, both instruments will be
supported going forward, and the GeneScan Analysis Software will be
available on both platforms for genotyping and fragment sizing
applications.

GeneScan Software on ABI PRISM 373 Instrument
The latest GeneScan Analysis Software available for customers using  the
ABI PRISM 373 is v. 1.2.2-1.  This version of the software has been
available since summer of 1994.  After the release of the latest
GeneScan software  in 1994, Apple changed  their method of mapping
images on the screen in certain new  models of computers.  This change
caused a problem with image display using GeneScan Analysis 1.2.2-1 on
the Quadra 630, and Macintosh AV models.  The problem did not occur on the
Centris 650 and Quadra 650 computers which were sold with the ABI 373
instruments.  Thus, the ABD9s recommended computer for customers who
wanted to purchase a secondary computer for further GeneScan analysis
was always the Quadra 650 or for higher computing power, the  Quadra 850
or 950.  However, there were a handful of customers who for a variety of
reasons only had access to the Quadra 630 or Macintosh AV series
computers.  Therefore, Applied Biosystems designed a  modified version of
GeneScan Analysis 1.2.2-1 that fixes all imaging incompatibility issues. 
This  modified version is available to these customers through our
technical support representatives worldwide.

GeneScan Software on ABI PRISM 377 Model
For GeneScan analysis on the 377 a new Power Mac version of GeneScan
software is necessary.  This version of the GeneScan Analysis Software,
version 2.0,  is now in the final stages of release.  This software has
been one of the most thoroughly tested software packages in the history of
Applied Biosystems. The alpha versions of the GeneScan Analysis Software
2.0 has been use tested since January on the ABI 377 platform by both 
internal and external test sites including  the Applied Biosystems
Division's Genotyping, Forensic and Agriculture groups, and one external
test site. It has been in beta testing since April of this year.  The
GeneScan software is currently shipping to  confirmation test sites to
ensure our system's ability to install and train 377 customers as is
required by the Applied Biosystems Division quality procedures.  This
software is scheduled for release by June 30, 1995.

The introduction of the ABI PRISM 377 instrument with its flexibility and
sensitivity has allowed us to optimize the GeneScan capabilities even
further.  We have a dedicated group of individuals consisting of molecular
biologists, chemists, hardware and software engineers working together to
improve the system for genotyping and fragment sizing applications.  This
work has led to the introduction of many new products in addition to the
GeneScan Analysis Software and will continue to be a focus in our R&D
efforts.


If you have any further questions in regard to GeneScan or Applied
Biosystems9 Genotyping systems please send me an e-mail at
zarehar at ccmail.apldbio.com or give me a call directly at (415) 638-5547.

Thank you.
Ali R. Zareh
Product Specialist
Genotyping Systems
Genetic Analysis Group



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