Striving for the best seeds – SNP genotyping with Fluidigm microfluidics and the ASSIST PLUS
Sakata Corporation’s products have enjoyed success in over 130 countries since the company’s founding in 1913, and its business continues to expand in both new and existing markets. Quality is a hallmark of Sakata’s business model, and the company continuously analyzes plant physiology, germination rates, seed health and genetic data to ensure only the best quality seed is supplied to customers.
The European QC team, led by Jean-Phillippe Pichaut, was therefore tasked with developing the new laboratory facilities and workflows to address the company’s ongoing business needs and help meet annual sales growth targets. Jean-Phillippe explained: “A large part of the day-to-day activities in the laboratory involves the extraction and analysis of DNA, but this is a challenging sample preparation workflow that can take a long time when manually loading samples onto the Fluidigm microfluidic chips we need to use. Although our current throughput is relatively low, and therefore manageable when performed manually, we know this will soon change. Our annual activity is forecast to grow three-fold within three years, resulting in an exponential increase in the number of samples for QC testing. We therefore needed to ensure that we could manage this growing workload easily and efficiently. We had a clear view in our mind that we wanted to use automated liquid handling for our high throughput genotyping assays, and so began the search for the perfect solution.”
Jean-Phillippe discovered INTEGRA products after a recommendation from a former colleague. He quickly realized that the VIAFLO 96 handheld electronic pipette and ASSIST PLUS pipetting robot could provide the relatively small team with the ability to increase their workload in line with Sakata’s growth plans, effortlessly integrating with the laboratory’s Fluidigm microfluidics workflows. Manon Vendredi, a genotyping lab technician, added: “We purchased a VIAFLO 96 system for our DNA extraction workflows, as well as an ASSIST PLUS robot equipped with an 8 channel VOYAGER adjustable tip spacing pipette. The combination of the ASSISTS PLUS and VOYAGER allows us to transfer DNA samples from 96-well plates to almost any microfluidic chip format, streamlining analysis on our Biomark PCR Analyzer. The INTEGRA team and Fluidigm application specialists worked in partnership with us to ensure a seamless workflow, and the end result is ideal. It’s so easy to use, and adds a huge degree of scalability to our workflows. It saves us a lot of time, is much more cost-effective, and reduces the number of errors when compared to manual processing.”
The benefits of an automated solution
The laboratory team is now in a much better position to meet the increased demands of business expansion: “We have been able to automate the entire process, which offers significant benefits for the laboratory staff, and will ease the strain associated with the 300,000 DNA extractions we aim to complete annually,” noted Jean-Phillippe. Manon added: “The VIAFLO 96 allows us to perform DNA extraction on every well of a microplate in parallel, and the automated function of the ASSIST PLUS means that all we need to do is set it up to transfer samples from the microplate wells to the chips, then simply leave it to run. We can be confident that, when we come back in half an hour, we have three accurately filled chips ready to be loaded into the Fluidigm system. This set-up not only uses less sample volume and has lower reagent costs, but it also means we can analyze more genes simultaneously.”
Thanks to the ease of use of the INTEGRA solutions, the benefits of automated pipetting have reached beyond the QC workflows. Jean-Phillippe continued: “Once we discovered how easy the INTEGRA systems were to use, the team was also keen to use them in our pathology lab for preparing qPCR plates. It was a very smooth transition; the simplicity meant that it only took them 30 minutes to set up this additional protocol, so there was no need to call out any specialists. We had not initially planned to use the equipment in both laboratories but, due to the possibilities offered by this system, it was an easy decision to make. All day-to-day operations in our laboratories are now running much more efficiently, and are a lot less labor intensive, making it far easier to manage our workload in the long term.”
A reliable partner
“Setting up a completely new laboratory and all its workflows can be fraught with difficulties. However, we know that INTEGRA and Fluidigm are both always on hand for help and support when we need it. Both companies offered a huge degree of support from the initial equipment purchase through to set up, and even with ongoing queries. This ensured that everything was – and continues to be –effortless. We really enjoy working with the team, because getting in contact with the right people is never a problem,” Jean-Phillippe concluded.