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Implementing LIMS in NGS: Investing in a Vision

By |2018-09-13T14:01:40+00:00July 2nd, 2018|Categories: Blog|Comments Off on Implementing LIMS in NGS: Investing in a Vision

Understanding the role DNA plays in living creatures was the trigger for incredible scientific development that furthered analysis and interaction with life’s blueprint to help improve the human condition. Decoding the genomic sequence of single individuals allows detection of personal disease risk factors and the development of personalized treatment [1]. High throughput sequencing techniques are increasingly in demand and Next Generation Sequencing (NGS) is the latest achievement in this field [2].

The most advanced sequencing techniques involve modern instruments capable of processing a large number of samples in a single run and require informatics tools able to analyze and organize massive amounts of generated data. A Laboratory Information Management System (LIMS) is a powerful tool for organizing a laboratory, even more so in a context where mistakes must be reduced to zero because of their implication in terms of money and time, and the need for quality of results.

What does Integration look like?

In this article we want to share our experience of implementing a LIMS in the context of a laboratory devoted to sequencing. We will consider two different situations bringing distinct experiences: the case of a lab that was implemented with an integrated LIMS, and a situation in which a LIMS was introduced after the fact to a productive lab.

If you are in the situation of creating a new NGS lab, the “Implement LIMS” task should appear in your check list with the other activation steps: “Hire sequencing experts,” “Order instruments,” and “Contact potential customers,”etc. You may be thinking that the LIMS check box does not deserve as much importance as the rest. You may even imagine that a LIMS is just like another piece of software for which you pay the license and start playing the day after. If that’s the case, you are bound to be surprised by the first visit of LIMS engineers. You will be led to review your workflow from beginning to end, because the LIMS needs to be programmed step by step in detail. You will be asked to make decisions about the protocols to use, the quality standards to offer to your customers, the inventory organization, and so on. This process may cause a slower advance than you predicted, but in the end, your lab will start on solid ground with layers of quality protection and the ability to evolve with the scope of your project.

In the opposite situation, we find labs which have been established and in production, possibly for years, that make the wise decision to introduce a modern LIMS system to manage their business. These labs already have experts, procedures, and customers in place. They were probably pushed towards adopting a LIMS by a constantly increasing number of requests or the need for higher quality standards. If you find yourself in this situation, you probably know your lab workflow in-depth, where it is going well, and where there are problems and bottle necks. This knowledge should speed up the implementation process, but be aware that the goal is not to translate the old system onto the new one exactly as it is now, but to make every improvement possible with the transition. A modern LIMS should offer more powerful features than a system based on spread technologies (paper documents, Excel files on multiple PCs, etcetera) and make some of the conventions you were used to obsolete.

To make a finer point…

Let’s go over a simple example. It is useful to define a unique identifier for each sample going into the lab and use it to label all information related to the same sample, tubes, files, or paper documents. In a no-LIMS lab that will probably be the only way to keep the information together, which increases the risk of information loss. A single human error or incorrectly written identifier may break the chain of custody of a sample. By contrast, in a LIMS-based lab, that attribute (a sample id to label all information) is a clarifying option, but it is not the fundamental ingredient of the information chain. A good LIMS system offers multiple ways to link different pieces of related information together. The design of your LIMS solution should make sure that all links will be correctly created and maintained throughout the life of the project.

The Highlights

To summarize, if you decided to implement a LIMS system in your laboratory, remember the following key points. It is important to take the time needed to find the correct design, which also allows you to review and optimize the lab workflows. Share your implementation ideas and current system state with the LIMS engineers, as it helps them realize the vision of what your lab could be. Do not be afraid to take a step back and lean on the engineer’s experience enriched by serving the needs of multiple customers. Finally, remember that each lab experience is unique and a good LIMS system will adapt to the specific needs of each lab.

More information about SLIMS for NGS is available on the following link here.

References

[1] https://newsinhealth.nih.gov/2013/12/personalized-medicine
[2] https://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)

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