With the advent of PCR-based genomic screening assays, scientists can ask more questions—and get faster answers—than ever before. Concomitant advances in liquid handling and automation make it possible to boost sample throughput, as well as save time and increase reproducibility. Here’s a look at some new liquid-handling features available to researchers today for automating PCR-based genomic screening assays.
Systems with greater automation
Partially or completely automated liquid-handling systems are increasingly available for genomic assays. Eppendorf’s electronic Xplorer pipettes are often used to automate pipetting steps in quantitative PCR (qPCR), or PCR-based screening assays. Xplorers contain a motorized piston that reduces thumb fatigue and increases reproducibility. For increasing throughput over handheld devices, the epMotion 96 is a 96-channel pipettor that dispenses liquid into all 96 wells of a plate simultaneously (as when dispensing master mix), according to Brandt Winder, product manager for pipettes. Fully automated systems such as Eppendorf’s mid-range throughput epMotion 5073 provide a complete walk-away solution for eliminating user errors, he says.
Tecan also offers a range of automated instruments for PCR-based screening, from the D300e Digital Dispenser for miniaturized qPCR set-up, to fully automated solutions with high flexibility on the Freedom EVO®, or maximized throughput on the Fluent®. “For PCR-based genomic screening assays, accuracy in pipetting low volumes and contamination-free operation is a must,” says James O’Brien, VP and head of life science and applied markets.
O’Brien adds that their customers are using Tecan’s liquid-handling systems for PCR-based screening, including assay set-up for paternity testing, genetic monitoring, genotyping, population genetics and disease monitoring. Tecan’s systems are also used for qPCR set-up, quantification and normalization workflows, and next-generation sequencing (NGS) sample preparation.
Because every lab is different, many companies offer a range of automated systems that differ in throughput capacities. Beckman Coulter’s Biomek Liquid Handlers, including the newest Biomek i-Series Automated Workstations, are designed to be flexible for a range of applications and throughput levels. Hamilton Robotics also offers platforms that vary according to throughput needs. Their newest system, the highest-throughput Microlab® VANTAGE Liquid Handling System®, includes low-volume, contact-free dispensing using NanoPulse® technology. The Microlab NIMBUS is geared toward lower throughput such as might be used by smaller diagnostic labs. The mid-range throughput Microlab STAR™ platform is currently used by Siemens to run their VERSANT® Zika RNA 1.0 Assay, an in vitro molecular diagnostics assay for detecting Zika virus. Hamilton’s automated liquid-handling systems are also used in applications such as forensics, food safety, infectious disease, gene editing and screening donors for blood banks.
Because every lab is different, many companies offer a range of automated systems that differ in throughput capacities.
Sha Liao, genomic scientific leader at Hamilton Robotics, says that a common customer request is the opportunity for increased automation. Hamilton Robotics offers an integrated on-deck thermocycler (ODTC), to further automate genomics workflows, as do several other vendors. A unique feature of Hamilton’s technology is their independent pipetting channels. “Dynamic x, y and z positioning of Hamilton’s independent pipetting channels makes cherry-picking, random access and normalization simple and straight forward,” says Liao.
Labs with space constraints may prefer smaller instrumentation. Marc Hamel, director of U.S. sales at Integra Biosciences, notes that their customers appreciate their instruments’ small footprint—“all products can be used inside a standard safety cabinet or fume hood,” he says. “Our pipetting systems are flexible enough to accommodate most applications involving 96- and 384-well plates.” According to Hamel, Integra users are especially interested in “automatic mode pipetting for hands-free operation, and the improved quality of pipetting that results.” Integra Biosciences offers a range of automated liquid-handling tools, including their handheld Viaflo II Electronic Pipettes, the Viaflo 96- or 384-channel pipettes, and the Viaflo ASSIST Hands-Free Pipetting Station.
Software and integrated interfaces
Any automated system must be easy to use if it’s going to save researchers time. Tecan’s O’Brien says that researchers are particularly interested in user-friendly software and interfaces of liquid-handling systems. For example, the TouchToolsTM PCR Wizard operator interface for the Freedom EVO, allows you to define parameters in advance, and then modify sample numbers or master mix allocation in run time mode. Tecan’s FluentControlTM software uses integrated Smart Commands for simplified programming of PCR-based genomics screening assays.
Alisa Jackson, market development manager at Beckman Coulter Life Sciences, says that their customers appreciate the ease-of-use built in to Beckman Coulter’s Biomek software. “It enables quick method editing for simple processes and setting up PCR-based assays from a file providing the flexibility for each well to be processed differently if necessary,” says Jackson. “This enables qPCR assays, and entering that data to the Biomek software for calculation and processing to complete normalization and pooling activities typically associated with genomic applications like sequencing and microarrays.”
Labs that do a lot of qPCR may benefit from Gilson’s PIPETMAX, which performs fully automated sample preparation and normalization for qPCR. The touch-screen software, qPCR Assistant and Normalization Assistant, make it easy to automate sample preparation for qPCR—even for lab members with no previous experience with liquid handlers. “Automated liquid handling is expanding beyond core facilities and high-throughput applications,” says Tristan Berto, automated liquid-handling product manager at Gilson. “Our customers need automation that’s easy to customize and run, regardless of experience.”
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Today’s liquid-handling tools include advanced features that boost accuracy and reproducibility. Hamilton Robotics uses two methods to detect liquid levels: capacitance for conductive liquids, and pressure for nonconductive liquids such as organic solvents. “Pressure detection is essential for working with small volumes of liquids to assure quality pipetting,” says Liao. “This becomes increasingly important as scientists use lower reaction volumes to conserve reagents.” Hamilton’s air displacement technology also makes small-volume pipetting more accurate.
In May, Eppendorf will introduce a new 10-Microliter Pipetting Tool for the automated epMotion systems, for pipetting lower reaction volumes while maintaining accuracy and precision. “Our customers are concerned about saving reagents and precious samples,” says Daniel Korostyshevsky, product manager for automation at Eppendorf. “The precision of our system could also help to reduce the amount of serial dilutions needed in qPCR work.” He adds that applications of epMotion systems tend to be wide-ranging—such as NGS set-up, forensic analysis, PCR and qPCR set-up, and nucleic acid purification—because of their possible features. “You can have up to three Peltier elements for heating or cooling, a built-in vacuum or thermal mixer,” says Korostyshevsky.
Acoustic technology
Acoustic technology is also making strides in liquid handling. Labcyte’s Echo® Liquid Handler uses acoustic liquid-handling technology to transfer samples and master mix—minus physical contact with any plastic tips or tubing. “This truly noncontact technology can eliminate the transfer error and cross-contamination seen with conventional liquid handling, greatly improving the accuracy and reliability of assay data,” says Randy Dyer, Labcyte’s director of product marketing.
The Echo Liquid Handler is capable of transferring varying concentrations of fluids, which can save researchers time, for example when optimizing conditions for PCR assays. “Users can build complex assay layouts and multifactorial or combinatorial layouts for assay development and optimization in a single protocol,” says Dyer. The Echo Liquid Handler can also transfer increments as small as 2.5 nanoliters. This facilitates assay miniaturization to conserve samples and reagents, and also increases throughput via the use of high-density formats such as 1536-well plates.
As such, the Echo Liquid Handler is often implemented where increased throughput is required. “SNP genotyping of blood or forensic samples, high-resolution melt analysis for genotyping of crop samples and yeast and bacteria samples, are some of the more common high-throughput workflows we see our customers performing,” says Dyer. With new and improved liquid handling features evolving, it’s likely that automating liquid handling will become increasingly common in genomic screening assays.
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