The Best Reasons to Use SLIMS for NGS

By Céline Kessler, LIMS specialist| August 28th, 2018|Categories: Blog|

In the last few years, Next Generation Sequencing instruments and bioinformatics software have undergone tremendous progress. However, to get the most out of those revolutionary advances, NGS labs need one more tool. A LIMS automates lab work to maximize efficiency and minimize errors, ensures the quality of each sample’s metadata for secondary and tertiary analysis, is flexible enough to cope with the constant evolutions of lab workflows, and finally, allows the user to monitor and improve the quality and efficiency of the lab process.

No matter how smart the instrument is, there is some point where you must make the connection between the produced result and the processed sample. Identifying the samples and transferring the identifiers from step to step is not only a boring task, it is also extremely error prone. SLIMS does all this boiler plate work automatically. Once the samples are selected, it generates the sample sheets for any instrument, monitors the run status in case of long sequencer processes, and captures result files directly from the instrument. Combined with the use of bar-coded tubes, a plate barcode reader, and a liquid handler, the risk for sample swapping is lowered to null, as is the time spent on this type of repetitive task.

In complement to the instrument integration, SLIMS guides lab users through their tasks. SLIMS provides a graphical overview of all the ongoing procedures in the laboratory. It is possible to focus on one procedure or one instrument and see what samples are ready for it or in progress, just as the focus can be turned to the samples assigned to a specific technician. Imagine what happens when a customized view best suits your lab organization: each member of the lab knows what they need to do next, even with little experience. This is enhanced when specific layouts for each role are defined in the lab so that each person only sees what he needs.

To get the best results from secondary and tertiary analysis at the end of an NGS workflow, it is necessary to monitor and save all the details of the process. This information should not only be as exhaustive as possible, it should mostly be usable, re-usable, searchable, and maintainable, whether samples were processed years ago or yesterday. No need to build a complex system of folders; SLIMS centralizes and organizes all the metadata related to a sample for the user. From the original patient to the sequencing result, any data collected at any step of the process are saved and can be retrieved at any time, whether it is a storage location or a QC result. Any input or output parameter of the instruments and any used reagent is saved and linked to the instrument run which is further linked to the processed samples. This recollection makes it possible to pinpoint inconsistencies and batch effects.

The amount of data that can be collected is huge, but a management system like SLIMS keeps it organized and structured. Aside from being profitable to NGS analysis results, SLIMS can generate automatic reports gathering all relevant data about a patient or about the lab process itself to give some insight on the reliability of the instruments or the mean execution time of a workflow.

Finally, SLIMS handles precise access rights at user, group, and role level ensuring that data are only accessed by authorized personnel and eliminating the risk of inadvertent data manipulation.

Recommended workflows are expected to upgrade regularly. SLIMS is designed to cope with these evolutions. Configuration is managed through the web interface and can be customized without requiring a user with IT skills. In addition, out of the box configurations are available via the SLIMS Store to import pre-established configurations based on NGS best practices. Of course, each workflow is versioned so that there is no ambiguity on the process a given sequence is issued from.

The flexibility of SLIMS is extended by its REST API which provides further possibilities to interface with any other software, requesting data from SLIMS, or pushing data to SLIMS from another system.

Automating the lab process with SLIMS is highly profitable to any NGS laboratory. Human interaction is limited to the tasks requiring it, automation through direct integration with the instrument saves time and prevents errors, and a huge amount of data can be stored in a way that makes it usable and reusable for higher quality and reproducible results. Efficiency and quality are improved without restricting the flexibility needed by any lab.