Alleviating Hours and Errors Common in Manual Agarose Gel Size Selection
Blog Jan 31, 2014
At the recent Society for Laboratory Automation Meeting in San Diego (SLAS2014) Hamilton Robotics announced a partnership with Coastal Genomics to launch the Microlab® NIMBUS® Select workstation with Ranger Technology. This new, automated system promises a faster and more economical automated solution to agarose gel selection of DNA fragments.
We caught up with Matthew Nesbitt, President of Coastal Genomics, and Bobby Chavli, Associate Director, Marketing, Hamilton Robotics to understand more about the partnership and the benefits this workstation offers.
AB: Hamilton Robotics announced a partnership with Coastal Genomics at SLAS, how did this partnership come about and what has it enabled?
Matthew Nesbitt (MN): Coastal Genomics originally envisioned building its own robotic workstation but after some thought, we realized that the established liquid handling industry had strong options that we could leverage. The real unknowns for pursuing this option boiled down to the following:
- Could we find a partner that could appreciate our vision in the potential for automated agarose gel size selection to the point that they themselves would be willing to support us?
- Could we find an OEM partner that could provide a high-functioning workstation that was cost-effective all while having an established reputation?
We looked at numerous big players that were established players in the liquid handling automation field. Hamilton Robotics was a clear winner because their NIMBUS workstation worked well and was cost-effective. Most importantly, they bought into our vision. They supported us with weekly teleconferences at which high-level engineers would always attend. No conditions were put on us for immediate and large capital outputs; this allowed us to prototype without incurring additional costs. Finally, when it came to integrating our assemblies, Hamilton took the lead in developing new components that would be required. In short, Hamilton was the company that made it most possible for a small company to launch a great technology with a known name in liquid handling behind it.
AB: The workstation was launched at the recent SLAS meeting, how was it received?
MN: We had a great reception. Our attendance at the event was covered by SLAS itself, which awarded us a spot on Innovation AveNEW. We generated interest in Ranger Technology through talks given at the LRIG session as well as Hamilton Robotics' NGS workshop. The leads we generated doubled the number of groups we know of that are seriously interested in Ranger Tech. These leads are complemented by those collected by Hamilton Robotics for Ranger Technology on the NIMBUS Select workstation. Finally, we won a New Product Award, which recognizes the best of new technologies based on market opportunity, impact on the field of lab automation, extraordinary technical originality and quality of supporting data.
AB: The Microlab® NIMBUS® Select workstation with Ranger Technology offers gel-based size selection, what advantages does this offer over bead technologies.
MN: Beads are perfect for a number of applications, but they do have some limitations.
1. For applications that need efficient rejection of fragment lengths that are close in size to that of the target DNA fraction (i.e. miRNA-Seq, ChIP-Seq, cloning of gene synthesis products, etc.), Ranger Technology ensures high yield recovery that excludes undesirable fragment lengths. The resolution of bead-based size exclusion cannot accommodate this because efficient rejection of undesired fragments leads also to large losses of material that is close in size to said undesirable fragments.
2. Tight size selection (i.e. recovery of a narrowly defined range of fragment sizes) is a characteristic result produced with Ranger Technology that is not attainable using beads. Tight size selection can improve normalization of samples and result in improved sequencing yield. In addition, tight size selection can improve bioinformatic assembly of sequence generated with paired-end technologies (i.e. Illumina). This can lead to improved master sequence generation from mRNA-Seq projects and de novo genome sequencing projects.
3. Sequencing projects that utilize long reads (i.e. Illumina's Moleculo long-read sequencing technology or Pacific Biosciences RS platform) deal with fragments that are greater than 1,000 bp in length. Beads cannot be used to conduct size selection on DNA fragments above 1,000 bp. Ranger Technology can be used to accurately size select DNA for these projects.
4. Finally, when groups use beads, they normally also have to take some of the sample and analyze it with a gel or capillary electrophoresis. This is because beads don't provide any visual confirmation on the presence of DNA, or what the fragment length distribution profile of the input DNA is. Ranger Technology visualizes the DNA and can generate analytics based on that info. Because of this, Ranger Technology has the potential to consolidate the steps of QC via capillary electrophoresis and bead-based size selection into a single run.
AB: In terms of error, how does the workstation compare to manual gel preparation?
Bobby Chavli (BC): In terms of yield and purity, agarose gel electrophoresis has been ideal for DNA size selection; however it has also been labor intensive and subject to human error, variation and problems associated with UV cross-linking. DNA from gels provide separation ranges from 100 bp – 40 kbp, which is a much broader than bead technology extraction. The precision and speed of the NIMBUS workstation, which has gone through validation studies, eliminates the problems associated with manual processing.
AB: What other benefits does it offer over manual processing?
BC: The workstation can process up to 96 samples per run in less than two hours. Sample loading and elution of the Ranger gel cassettes is fully automated and the system is equipped with a camera channel and imager to monitor the run and provide QC checks. This helps to limit the number of clones screened and saves time by reducing cloning step failures.