Automating Illumina DNA library prep. with flowbot® ONE

Many labs performing next generation sequencing choose to automate the liquid handling processes to get a more reliable and efficient library preparation. One of those labs can be found at the Leiden University Medical Center.

With Stefan Boers, Medical Molecular Microbiologist, in the driver’s seat and flowbot ONE as their pipetting partner, their clinical lab has automated the Illumina DNA library preparation kit for whole genome sequencing. This has reduced hands-on time from 125 minutes to 25 minutes, generated good quality genome assemblies as well as consistent and reproducible results.

“Automating our lab was an obvious choice. Especially an NGS workflow has such as extensive library preparation that there is no upside to doing it manually. Choosing flowbot ONE was also an easy decision. It checked all of our boxes,” says Stefan Boers.

The lab is currently using whole genome sequencing for initial identification of rare pathogenic microorganisms, the detection of microbial resistance mechanisms and for epidemiologic tracking of microorganisms within and outside hospital systems.

The lab is sequencing around 8 bacterial strains per week. This is not impossible to do manually, but library prep. is tedious, error prone, and takes a lot of time – time that Stefan Boers wanted to spend on more valuable tasks.

When implementing the flowbot ONE, hands-on time was reduced to 25 minutes compared to the 125 min needed when performing 8 library preps. using the manual workflow.

“Freeing up 100 minutes to use on more valuable work in the lab is a fantastic outcome. It’s a great way to utilize our lab technicians’ full talents and get more time for tasks such as innovation. And, of course, it frees them from spending their energy on tedious work,” says Stefan Boers and adds that the flowbot ONE also enables the lab to easily scale up if needed.

The same experiment revealed that a library prep. workflow on the flowbot ONE generates robust and high-quality DNA libraries.

“Results obtained from 16 library preps. that were performed both manually and automatically showed comparable library DNA yields (median of 1.5-fold difference), similar assembly quality values, and 100% concordance on the final core genome multilocus sequence typing results,” confirms Stefan Boers and adds that the results have been consistent since flowbot ONE was implemented and that no dropouts have been encountered.

Reproducibility of results was confirmed by re-processing eight of the 16 library preps using the automated workflow.

For more data, please see the publication in Scientific Reports 14