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To automate or not to automate?

Are you asking the right question?

Considerations for when to automate, from common drivers to what you really should be thinking about.

Over the past several years I’ve worked with researchers in a variety of lab environments. These include both individual labs and genomics core labs, both in academia and commercial settings.

When considering automation systems for workflows such as genotyping or gene expression by real-time PCR, the most common driver for adoption is sample number. Researchers often feel that unless they are routinely processing hundreds to thousands of genomic samples, investments in an automation system do not make sense.

Consideration of sample volumes is important, and no doubt automation can save money at high volumes of samples, but these are not the most important reasons to consider automating your genomics workflows.

First and foremost, automation leads to more robust assay performance with improved reproducibility. The length of many genomics workflows requires several small-volume pipetting steps, mixing, incubations, and transfer steps. Each of these steps can introduce considerable variance, leading to questionable results and the need for assay replicates to minimize variable findings. When automation systems are employed, such processing steps are standardized and lead to less variability.

For example, one of the more commonly used assays with Fluidigm® microfluidics technology is genotyping performed on the Biomark™ X system with a 96.96 Dynamic Array™. This system can generate 9,216 datapoints from 96 samples and 96 individual PCR reactions run in parallel. The equivalent experiment using conventional systems requires preparing 96 x 96-well plates.

Imagine the variability that could be introduced between reactions due to manual processing at this scale, not to mention the additional time and costs incurred. In contrast, the Dynamic Array is a closed system that automatically runs single-plex reactions at the same time.

Many of the processing steps are fully automated on Biomark X, including thermocycling and data acquisition. Because of the exacting standards for the design and manufacture of the Biomark X system components, you can be assured of great reproducibility between samples, runs, and laboratory operators. Definitely consider sample volume when you think about automating genomic workflows, but understand that the most important reason is to improve the reproducibility of your assays and hence the reliability of your experimental results.

About the author:

Steve Kain, PhD, MBA, combines his scientific knowledge with commercial experience in genomics, cell biology, drug discovery, next-generation DNA sequencing, and botanical science & testing services.

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