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Automating NGS Workflows At The VIB Nucleomics Sequencing Core Facility

Stephane Plaisance, a molecular biologist at VIB, championed introducing automation to improve his lab’s NGS library prep workflows for long- and short-read sequencing.

A rising demand for sequencing services is pushing laboratories to find ways to increase capacity and improve workflow efficiency. Laboratory automation is an effective means to both streamline and expand sequencing operations. VIB Nucleomics, a sequencing core facility at one of Belgium’s leading Life Science Institutes, stand to benefit as they juggle heavy workloads and the need to develop and customize their services.

The problem – Complex and tedious lab work limits laboratory efficiency

VIB Nucleomics is a sequencing core that serves VIB researchers and external academic and industrial researchers studying various life science disciplines. Stephane Plaisance, an NGS Analysis Specialist at VIB, works alongside nine other laboratory scientists carrying out techniques including NGS library preparation, long- and short-read sequencing on different platforms, and genome-wide expression analysis. Several years ago, his team encountered challenges with efficiency. The long and tedious pipetting required for sequencing was limiting their productivity and placing a strain on their lab technicians. The team recognized that automation would improve the workflow, but many large NGS robots lacked the flexibility to accommodate the diversity of projects managed by their laboratory.

We started looking at the large, more expensive robots, but these are more suited for high-throughput, routine work, whereas we need to adapt our processes to each project we undertake. We chose Opentrons for the flexibility and the price.

Stephane Plaisance
The solution – Integration of lab automation into sequencing core workflows

After conducting a comprehensive market analysis, the Opentrons OT-2 liquid handling robot was selected for its affordability and ability to adapt to custom workflows. The Nucleomics core initially used the Opentrons custom protocol development services to help with onboarding. You can check out the initial VIB protocol here. The OT-2 was well received by laboratory staff and the protocols were slowly adapted to meet specific lab requirements. The protocol code was modified to be slightly slower than the original high-efficiency program, which matched the needs of the lab perfectly. Less than two years after acquiring their first robot, VIB Nucleomics acquired four more, and now has five OT-2 robots assisting them with different laboratory tasks. Three robots are used for Illumina NGS library preparation and are specialized for either pre-or post-PCR sample processing.

Our robots are specialized. For Illumina DNA library prep, we do the initial sample manipulation on one robot in a dedicated pre-PCR room, and then we take the plate out of that room to do PCR, and then we use a second robot for post-PCR steps.

– Stephane Plaisance

One robot is used for research and development and the last robot is used for re-pooling of samples after library prep is complete. The flexibility of the OT-2 system and the product support offered by the Opentrons team, combined with the ingenuity of Plaisance and the VIB team, made this facility’s investment in lab automation a huge success. Meanwhile, a 10,000 sample metagenomics project has been successfully executed with the OT-2 pipeline and more large projects are coming!

Watch the video below to learn more about VIB core facilities:

Find out more about automating NGS on the OT-2 here