Fri Apr 25 10:43:58 EST 1997
At last, the reply to the question I posted all those months ago (!)
summarised for you. First up I'd like to thank all those people who
replied to my postings it was good of you all to take the time and
effort to write to me and volunteer your opinions. Next up I suppose
I'm going to have to include all the usual disclaimers (you know the
story by now) - this document does not represent the opinion of my
employers, some of it doesn't even represent my own opinions...I'm
only passing them on and removing the names. I've tried to make
everything fair, but not everybody out there with robots replied, so
some sections may slant one way or another a wee bit! In the last few
months I've spoken to people seen machines, and even tried one of two
and the best advice I can give is that if you are looking for a system
talk to your local reps and see for yourself. In the mean time feel
free to use this as a guide to what other people out there are using.
Oh, just before the main body of this message, in the course of this I
spoke to someone who reminded me that what these machines actually do
is mechanise the process of template prep, reaction set-up, and
cycling (depending upon the platform used). None fully 'automate' the
process into one 'dynamic whole'. Perhaps a solution to this would be
to PCR up the fragment of interest, and then go into sequencing...it
could all be done in a stand alone system...perhaps this should be
kept in mind!
Here goes...(in no particular order)
There is a dye terminator (DT) protocol fully functional for the
Biomek, and now DNA preps available too apparently you can perform
plasmid isolation for $0.45 instead of $3-$4. This platform is quite
easy to use, but it should be noted that labware specs need to be
fairly exact - tips can be bent. Also, comes with a variety of
'tools' - although the 2005L acts more like a 1255L tool when used
with barrier tips. Also there were some reports from users with
respect that handling volumes below 55L does not fair well in some
The Biomek set-up time is roughly 25 minutes for 192 sequencing
reactions with single primer from a master mix. Perhaps useful with
shotguns but set up time for anything else maybe too great (too many
The Biomek is actually designed as a high throughput repetitive
96-well based screening platform, so varying numbers of samples on a
day to day basis may present a problem. The machine itself is said to
be reliable, and doesn't miss wells too often.
The operating software is OK - being the usual, point-and-click type
which makes operation easier for first-timers!
Overall, a good, versatile platform, but some users point to it being
perhaps too slow for anything other that repetitive 96 well shotgun
There are two types of robot in circulation from the producers of the
373a and 377 (oh! and the 310...) - that Catalyst and the 877. The
catalyst (which I believe no longer available) was blessed with a not
too great user interface which was very inflexible. However reports
allege that the 877 has much improved software, it now being an easy
to use user interface (again of the point and click variety), the
overhaul resulting in a more flexible platform than the Catalyst.
This platform has a high throughput capability, and seems to be
primarily designed to be used for high throughput genotyping projects
that require each sample to be run with multiple markers (either one
at a time, or multiplex) and the software reflects this. In general
the software is liked by most people - being clear and easy to follow.
The 877 seems to have been the only machine anyone reported as being
happy pipetting volumes below 35L with...as the 877 seems to have been
specifically designed to be used as a small volume pipetter and, with
ever increasing cost saving needed as well as better enzymes and dye
incorporation, smaller volumes may become more vogue than at present.
It should also be noted that there is no disposable tip option with
this platform - just a steel needle which, although ABI say no carry
over is present, some people report worries over. Also there is no
multi-tip option unlike other platforms.
Other reported problems seem to be mainly based around leaks and
suchlike - although a fairly major problem with M13 forward primer
reaction efficiency (and accompanying artefact peak at 70-80 bases)
that are unsolved at present, but are possibly due to cycler block
contamination. At the time of writing the solution to this is
Packard Muitiprobe 204DT
Not too much feedback on this particular machine, but what did get to
me indicated that it's a good platform for DT set up ( you can use
fixed tip or disposable) but can only be used down to 35L with the
small disposable tips, after this volumes are likely to be 'some'
rather than a specified amount). Liquid sensing helps when doing DNA
preps, but not so much for DT set ups. Possibly some stability
problems, but is cheap.
Again, not too much feedback for this platform either, again it is
reported as being good for reaction set up. As for the use of the
Tecan it has a cumbersome9 user interface and programming interface.
Pipetting below 55L could pose problems unless the tip touching
function is used (then goes down to 25L). Set up time is about 1hr
for 96 reactions. Very reliable and very flexible, but perhaps it
might be quicker to do some things by hand!
The 9600 is an automated template prep machine from Qiagen. It brings
with it the reputation of the company that produces one of the most
popular DNA prep kits. This robot is basically an mechanisation of
the manual prep method, which uses the Qiagen kits on top of a vacuum
manifold to speed things up.
The 9600 works in multiples of eight or in a 96 plate format. The
biggest gripe about the machine seemed to be that in the set-up of
samples the software was a bit cumbersome, as it isn't of the 'point
and click' variety (you have to write protocols) which means that
without extensive effort you can't run samples with different primers
with ease. However, all this is supposed to change with an upgrade in
the software (due soon), along with the addition of a pump which will
halve the current prep time of 96 samples. The 9600 does require some
hands-on time mid run - to change over the columns etc. etc.
The machine is also capable of setting up sequence reactions, and any
other pipetting reactions. This system is also due an upgrade, with a
disposable tip option being incorporated.
The Autogen robot gives fairly good results but are slow in comparison
with newer types of machine (and maybe more expensive too). Problems
occur in their inflexibility with regard to change in demand -
protocol development is not easy as they are hard wired into the
system. NB This is a miniprep machine and does not set up PCR
Again, this reply produced both positive and negative feedback. This
platform is this only fully integrated machine that will go from cell
pellets to finished reaction without coming off the robot at any
The Vistra uses a magnetic purification system (called FMP) to
isolate the DNA (quick point from someone in the survey - if this is
such a good isolation method is anyone using it manually??). The
purified DNA is then added to a sequence reaction, which is completed
on the machine.
There are protocols available for both M13 and ds plasmid work,
however the success of them seems to be an issue with some reports of
the ds template prep giving problems (one site seems to do manual
plasmid preps and use the labstation for it's ss isolation, then set
up all reactions on the labstation, as the ds isolation gives them
problems). Another report says that it is quicker to perform DT
reaction set-up by hand rather that use this robot. On the other hand
some people seemed happy with it, and use it for both ss and ds work.
More information about the Autoseq