Savitra Sharma explains why a LIMS is vital for managing your NGS lab
Managing a next-generation sequencing (NGS) laboratory is a daunting task. NGS sample preparation and sequencing is incredibly complicated, and even small mistakes can have disastrous consequences.
A laboratory information management system (LIMS) can be an essential tool to keep a lab running smoothly. Several key considerations and features of a LIMS are overviewed here.
Google Docs is not a LIMS!
Tracking everything in your lab can feel overwhelming. Sometimes the path of least resistance is for your “interim” solution (such as Excel or Google Docs) to be used indefinitely, because creating a long-term solution feels too difficult.
Unfortunately, these short-term Excel or Google Doc solutions are incredibly insufficient in many key ways. With regard to data security and user access, within Excel or Google Docs, it is impossible to both appropriately secure and provide access for all required users to sensitive information such as protected health information (PHI) and/or intellectual property (IP). Even a single instance of information being inappropriately accessed can result in staggering fines and/or permanent theft of highly sensitive company information.
When it comes to outdated, missing or moved Files, it is very difficult to constantly keep a long list of individual files both updated and in the right folder. As everyone has experienced, your system of files/folders will quickly become an outdated hairball, where nothing is accurate or can be easily found. Data auditing is another weakness of using existing solutions. Many labs are required to know when information was entered, who entered it and when it was changed. This type of precise auditing is essentially impossible to do in a user-friendly and accurate manner if you are using a temporary solution such as Excel or Google Docs.
Tracking your samples is critical
Every NGS lab has thousands of tubes with samples, libraries, pools, or reagents. For a lab to run smoothly, it is essential to both know where your samples are physically located and what testing has been performed on them. Additionally, other information may be important to capture during testing, such as which reagent lots or pieces of equipment were used, or which personnel processed the samples. Only a sophisticated LIMS will be able to both easily capture this information and allow for it to be easily reviewed/queried at a later date.
Track each sequencing library index to prevent index clashing
Tracking the index sequence on each library is a fundamental job for NGS labs, and it is also one of the most challenging tasks that labs must do. Even a single error can ruin a costly sequencing run.
To reduce or eliminate errors, it is important to decrease manual data entry for index tracking. For example, a LIMS can have all the index sequences pre-loaded, allowing users to simply select from the available indexes. This ensures that no errors arise due to manually entering, or copy and pasting index sequences into a temporary file.
Additionally, it is now always critical to assess for index clashing between libraries in a pool, or between all libraries when multiple pools are pooled together. These “super-pools” are particularly error prone because individual pools are usually prepared by different people, and there is frequent miscommunication about which indices were used. These tasks are very difficult for a human to manually perform, but these types of bulk sequence comparisons and error checking are very easy for a computer-based LIMS!
Automated NGS-Specific calculations can be vital
All NGS workflows have a few steps where there are some very difficult calculations that need to be performed. This includes calculating mastermix volumes, input normalisation amounts during library preparation, and library pooling volumes. Even small errors in any calculation could result in failed sample preparation. Having a LIMS perform these calculations automatically will drastically decrease events of human error.
Automated sample sheet generation
A sample sheet is a very difficult file to manually create without any errors. Inaccurate sample information can have catastrophic and costly consequences, requiring scientists to re-prepare and sequence samples. Fortunately, a LIMS can automatically generate a sample sheet directly for input into your sequencing or sequencing analysis pipeline. This file can be customised and formatted in whichever manner your lab specifically needs, and contain whichever data elements you require. This will both save time for your lab and prevent costly errors.
Track reagents and consumables
Accurately tracking all the reagents and consumables in a lab is both tedious and pivotal for the success of the lab. Running out of vital reagents will leave a lab dead in the water, incapable of performing scheduled tests.
There are many vital functions a LIMS can perform to help users track reagents, including: track reagent lots; track reagent location or tube identifiers; warn when reagents are running low or are close to expiring; record the number of freeze/thaws; track individual components within a kit; automatically reorder reagents.
Any NGS lab will greatly benefit from implementing a LIMS. This system will be instrumental to the success of the lab, as it will help keep things both running smoothly and prevent many common and costly errors.
The key areas a LIMS can help an NGS lab are: tracking sample identities, locations, and data; tracking library indices and assessing for index clashes in pools; automatically performing NGS-specific calculations; automatically generating a sample sheet; and tracking reagents.
Savitra Sharma is the founder of Third Wave Analytics