Frequently Asked Questions
NuGEN Automation Solution
Q1. What is the NuGEN Automation Solution?
The Automation Solution is comprised of 3 components:
- The Reagent component:
Fill sizes sufficient for processing 96 or 2 sets of 48 samples (call for information) - Tools Component:
Includes a set of scripts for the specific automation workstation, and a set of instructional and
worksheet files to help install and utilize the automation scripts and - Service Component:
Automation consulting services
Q2. Can I automate all of NuGEN’s products?
NuGEN’s automation program is designed to respond to user’s needs. The first in the Automation
Solution series is the automation of Ovation™ Whole Blood Solution, implemented on the Biomek®
FX workstation. Other solutions are in progress, so for the latest information on automation of other
NuGEN products, contact our customer services at custserv@nugeninc.com, or call 888-654-6544.
Q3. What platforms do these Automation Solutions address?
The first is the Biomek FX but other common platforms are also being considered for future
Automation solutions.
Q4. Are these walk away solutions?
Generally these methods are semi-automated solutions that require some manual intervention so
they are not strictly walk away approaches. For example the enzyme master mixes must be
prepared manually and the assembled reactions in thermal cycler plates must be manually
transferred to and from the instrument for incubations. Walk away solutions necessarily require
fixed instrument configurations and peripherals, while this approach enables the flexibility to adapt
to different customer platforms.
Q5. Do I need to purchase any specialized equipment for my robot in order to run the
procedures?
No, the methods assume standard platform configuration, for example the methods for the Biomek
FX are built for a platform that has two liquid handling arms: a 96-tip pod with gripper and a Span8.
A tiploader, wash station, and standard microtiter plate ALPs are all that are necessary for the robot
to perform its task. Useful items to purchase would be a Peltier device to keep reagents cool and an
on-deck thermal cycler, although the methods can be performed without this equipment.
Q6. What kind of help can I expect from NuGEN to install and support the application?
Documentation is supplied with the automated methods that provide complete installation
instructions. This should be sufficient to the experienced automation users. For those requiring
more assistance, consulting services can be provided on a case-by-case basis.
Q7. What level of expertise do I need in order to operate the procedures?
A reasonable level of platform software expertise is required for proper methods installation and
instrument configuration. Once the methods have been uploaded, configured and tested, operation
by non-expert users should be possible.
Q8. How is the assay different than the manual procedure outlined in the product user
guides?
The procedural steps are in principle, the same as performing the process manually. However
automating entails a number of minor adjustments to steps outlined in the user guide but have in
fact been validated for the automation solution. These are steps such as:
- Master mix volumes must take into consideration sample batch sizes and the source well’s
dead volumes - For distribution of reagents the volumes in an individual source well must be appropriate for
the total number of samples in the corresponding row of the destination thermal cycler plate. - Generally bead purification methods are preferable for automation solutions although in the
user guide for manual processing a column option may be listed as recommended.
Q9. Do I need to use more total RNA input for automation applications compared to the
manual approach?
No, we validate our Automation Solutions and methods for the same input and RNA quality
requirements as for the manual approach.
Q10. Is the amplification product different in reproducibility, composition, length or yield
when compared to the manual approach?
Generally automating this process, results in a slight improvement in reproducibility and consistency
in amplification results as demonstrated in the data provided in Automation Solution technical
reports.
Q11. Has NuGEN performed reproducibility studies on the Automation Solutions validated to
date?
Yes, included in the validation process for all Automation Solutions is extensive reproducibility
testing, generally these results meet or exceed the reproducibility results obtained using the same
NuGEN product processed manually.
Q12. Is the quantitation of the cDNA amplification product included in the automated
methods?
The automated methods include the preparation of a plate containing an aliquot of amplified product
for quantitation but the actual measurement and subsequent importation of the data requires
manual intervention. The methods were written with the view that a minimal approach will be of
greater utility for customers with constraints on instrument configuration. Adaptation to more
complex configurations can be accomplished but it is best done on a case by case basis. The
documentation package also includes helpful worksheets and instructions for cDNA quantitation.
Q13. Are the reagent volumes in the automation fill sizes sufficient for multiple batches?
The reagent fill sizes are sufficient for a maximum of 2 batches, allowing processing of 96 or 2 sets
of 48 samples at a time. Processing fewer samples at a time will result in recovery of less reagent
volume.
Q14. What is the minimum number of samples that you recommend users process by
automation?
We recommend that no fewer than 8 samples be processed at a time. Our Automation Solution
methods enable as few as 8 but obviously the advantages of automation increase with increasing
sample size. In general automated processing of fewer than 24 samples is considered inefficient.
Q15. What are the chances of sample cross contamination and how have you addressed or
mitigated it for automation?
Validation testing of the automated methods included an evaluation of the degree of cross-
contamination by QPCR. The results indicated that automating the process created no risk of crosscontamination and likely reduced such risk by the increased consistency of performance of
automated systems (see Automation Solution Technical Report #1).
Q16. Can I use my own automation expertise to modify your method’s deck layout for the
recommended application?
Yes, we provide open methods and extensive documentation and methods descriptions so users
can modify scripts to accommodate their specific deck layout or change the level of automation that
is implemented. We do not recommend making any changes in the method that affect the procedural steps required for successful amplification and product performance.
Q17. Can I use my own automation expertise to modify your methods for other non-NuGEN
applications?
We do not recommend trying to modify these methods for other applications. All the variables and
scripts have been designed and implemented for the specified application and we will not be able to
support or troubleshoot these Automation Solutions for any non-NuGEN validated applications.
Q18. Can I purchase or obtain your Tools components (automation methods and scripts) if I
am not a NuGEN customer?
You may place an order for the Tools component only after or at the time of, reagent components
purchase.