October 15, 2011 (Vol. 31, No. 18)

Technology Miniaturizes Reactions in Highly Automated Inline Platform

Microplate-based technology often limits the ability of laboratories to meet current industry demand for highly automated, flexible systems capable of quickly and inexpensively processing large numbers of samples.

Laboratories responding to the demand for high-throughput (HT) capacity must add many identical, isolated workstations to process more microplates. Integrating these processes includes moving microplates between workstations, resulting in either the loss of skilled labor to simple, repetitive tasks or the addition of large, complex, and expensive robotics. When costs are evaluated, many laboratories consider neither to be a viable solution to achieve HT capacity.

New and innovative technologies are required to meet industry demand for highly productive, economical HT processing solutions.

Douglas Scientific’s Array Tape™ is capable of replacing microplates for HT screening. Made from a continuous strip of plastic, Array Tape is embossed with reaction wells in SBS or customized arrays (Figure 1). Reaction volumes (1–30 µL), unique well geometries, and non-SBS formats are inexpensively customized in Array Tape compared to microplates. Thin and bendable, Array Tape is spooled onto compact reels (90 mm wide by 560 mm in diameter) holding in excess of 200 microplate equivalents for processing or storage.

Figure 1. Excel-based line separation method used to plot, group, and call raw data from Array Tape (A) and microplate (B) platforms. Standard scatter plot: Two call lines (gray) splitting FAM/Heterozygous and Heterozygous/VIC groups and one rectangular box (gray) delineating drop-outs.

High Throughput

Douglas Scientific developed the Array Tape platform to meet the needs of HT laboratories. Platform instrumentation includes modular inline liquid handling and sealing (Nexar®), large-batch thermocycling (Soellex™), and high-speed scanning (Araya®) optimized for Array Tape. Indexing holes running along the edge of Array Tape guide the fully automated movement of the plastic strip through discrete, inline modules where individual arrays of reaction wells are independently processed.

Case Study in AgBio

AgBio laboratories increasingly rely on HT automation to screen and identify genetic markers necessary to efficiently develop new and improved plant varieties as well as assure the genetic integrity of established lines.

Douglas Scientific collaborated with Rijk Zwaan to customize modules for their SNP genotyping protocol. On-site validation completed in their Netherlands-based laboratory demonstrated that the highly automated, miniaturized reactions in Array Tape produce high-quality SNP genotyping data comparable to their existing microplate-based platform (Figure 2).

For this validation process, DNA source material was extracted from vegetable leaf tissue using a protocol developed by Rijk Zwaan. DNA (approximately 2 ng/µL) was dispensed into 384-well arrays in Array Tape and 96-well arrays in microplates. Reaction volumes were approximately 50% smaller in Array Tape (800 nL) compared to microplates (2 µL), representing the only significant difference in the reaction assembly between platforms.

Figure 2.Continuous Array Tape in customized and standard SBS formats

Raw data from both platforms was independently plotted and called by Rijk Zwaan and Douglas Scientific with 98.2% agreement. Douglas Scientific used the same call method to show 98.35% agreement in calls for the 4,959 samples run in both Array Tape and microplates (Table). The remaining 1.65% was due to drop-outs called in either Array Tape (1.51%) or microplates (0.14%) but not in both. The drop-out rate of both platforms falls well below the threshold for adequate data quality defined by Rijk Zwaan.

Throughput Potential

The Array Tape platform proved capable of processing over 200,000 SNP reactions in an eight-hour work day. Throughput advantages are realized through the speed and efficiency of parallel processing in continuous, inline liquid handling, sealing and fluorescence scanning modules, and large-capacity thermal cycling. Specific baseline evaluations at Rijk Zwaan show that, compared to their microplate-based platform, reagent dispense and fluorescent reading are twice as fast in the customized Nexar and Araya modules, respectively.

Thermocycling large batches of samples in Array Tape also dramatically increases throughput potential for users. Three reels of spooled Array Tape (230,000 assay wells) may be processed simultaneously in the Soellex three chambered water bath. Thermocycling a similar number of samples this quickly in microplates would require 18 water baths (32 microplate capacity) or 150 (4 microplate capacity) block heaters. The effect is increased throughput, reduced manual labor, and a smaller laboratory footprint.

The highly automated Array Tape platform with miniaturized reaction wells allows Rijk Zwaan to cut project timelines as well as the cost of labor and reagents. Furthermore, the simplified workflow reduces manual handling of analytical material and frees skilled labor for more productive work.

Kjersten Larson-Cook, Ph.D. ([email protected]), is bioscientist, strategic projects, Satish Rai, Ph.D., is director of scientific operations, and Terry Rusch is director of engineering at Douglas Scientific. Edwin Van Zon is technical analyst,molecular biology at Rijk Zwaan Breeding.

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