21337MGR%MSU@ICNUCEVM.CNUCE.CNR.IT ("Jonathan.Walton") (06/14/91)
My department is considering buying an automated DNA sequencer. Some are
enthusiastic ("The Time Has Come") but I've personally heard mainly negative
things - too cumbersome, error rates too high, no net savings in time and
money, etc. Could I solicit from subscribers to this bulletin board that have
had experience with automated DNA sequencing a summary of their experiences
and opinions? Information about particular machines would also be very
helpful.
Thank you very much.
Jonathan Walton (21337mgr@msu.bitnet)
Plant Research Laboratory
Michigan State Universitydonnel@helix.nih.gov (Donald A. Lehn) (06/16/91)
In article <9106140059.AA13341@genbank.bio.net> 21337MGR%MSU@ICNUCEVM.CNUCE.CNR.IT ("Jonathan.Walton") writes:
->My department is considering buying an automated DNA sequencer. Some are
->enthusiastic ("The Time Has Come") but I've personally heard mainly negative
->things - too cumbersome, error rates too high, no net savings in time and
->money, etc. Could I solicit from subscribers to this bulletin board that have
->had experience with automated DNA sequencing a summary of their experiences
->and opinions? Information about particular machines would also be very
->helpful.
->
->Thank you very much.
->Jonathan Walton (21337mgr@msu.bitnet)
->Plant Research Laboratory
->Michigan State University
I think anyone who invests in the current state of DNA sequencers is making
a big mistake. We have an Applied Biosystems 370A sequence sitting in our
lab here at NIH and no one has yet to use it (although a few have tried).
Simply put, this machine is too complicated for the average bench scientist
to use. From what I have seen, in order for these instruments to be
sucessfully utilized, they "MUST" be run by a skilled technician. If you are
planing on buying one of these macines, you better also plan on having the
bucks to hire a technician whose sole mission in life is dedicated to
maintaining and operating this instrument. If you think that someone can walk
up to the machine and start sequencing with little effort, think again.
In terms of saving time -- even if the instrument worked to its full potential,
I very seriously doubt whether it would save much time over traditional
sequence methods. When our instrument was set up the A.B. tech. rep did
some sample sequences with M13. After the run, he had to manually edit the
output base by base since about 5% of the nucleotides were listed as "N". This
editing took as long as it would take me to read AND edit (at the same time)
an autoradiogram. In addition, while someone is editing a sequence on the
instrument, it can not be used for sequencing at the same time.
My advice for anyone who is doing a lot of sequencing is to invest in a half
dozen good sequence apparatus and hire a couple of good workers as technicians.
You will get the sequences just as fast.
Donald A. Lehn
NIH/NCI/DCE/LMC-ProteinNETADM@DBNMEB1.BITNET (Peter Hakenberg) (06/18/91)
In article <1593@nih-csl.nih.gov>, donnel@helix.nih.gov (Donald A. Lehn) says: .. >I very seriously doubt whether it would save much time over traditional >sequence methods. It is only usefull if you need to sequence more often. >n addition, while someone is editing a sequence on the >instrument, it can not be used for sequencing at the same time. > You should use the multifinder on the mac and perhaps 1-2mb more RAM bye pi (Peter Hakenberg)
ouellett@newsserver.sfu.ca (Francis Ouellette) (06/19/91)
In <91169.084826NETADM@DBNMEB1.BITNET> NETADM@DBNMEB1.BITNET (Peter Hakenberg) writes: >In article <1593@nih-csl.nih.gov>, donnel@helix.nih.gov (Donald A. Lehn) says: >> addition, while someone is editing a sequence on the >> instrument, it can not be used for sequencing at the same time. >> > You should use the multifinder on the mac and perhaps 1-2mb more RAM and it appears (a rumor?!) that ABI is "releasing" their software, ie all who want it can get it (source codes too), so that it should be simple to go do the editing on another MAC while the other is busy sequencing. There is a group of researcher here at Simon Fraser University which have obtained $$$ to bye a machine. Now they have to chose which machine they will buy. We have lots of Pharmacia and ABI reps comming around to attract out this purchase. The major factors which have influenced the poeple here are: *cost of running the machine (synthesis and labelling of oligos), here Pharmacia is best, simpler and cheaper. *software, here ABI is better. The way they run their system (different dyes in the same lane) has produced problems for them which they had to correct with software, and it appears they have done a good job of this. But pharmacia has a new beta version of their software that they will come to demo tomorrow, I will let you know! other factors off course include ease of use, input from other users (again ABI is favored here), and speed of run (output). As far as the output is concerned, although Pharmacia claims a faster nucleotide/min rate, both machines probably move faster than sequencing reactions will reach them ;-) ... So it may not be an issue at this point. The users here will have a dedicated person to operate the machine, but each group/lab will have their own plates that they will pour themselves. The cleanliness of the plates appears to be an important factor in the obtention of good patterns. Some (here at SFU) say that we should wait a bit longer ... that we don't need this technology. At the type of $$$ they are asking you can hire a good tech and lots of 35^S ... which is probably true ... the saga continues ... I will keep you posted! francis PS Please insert usual disclamor here ... thank you -- Francis Ouellette "Je cherche a` comprendre" Dept of Biological Sciences Jacques Monod Simon Fraser University ouellett@whistler.sfu.ca Burnaby, BC, Canada V5A 1S6 userBFFO@SFU.bitnet