Next-Generation Sequencing workflow by LabCollector at the Biology institute of Lille
Our UMR 8199 Genomics and Metabolic Diseases unit from CNRS and Lille Biology Institute (IBL) is led by Professor Froguel. This unit has approximately 60 people. UMR 8199 is equipped with several new generations of sequencers and a platform of DNA microarrays. Research is focused in two major areas: obesity and diabetes.
Our project that made us decide to acquire a LIMS was to identify rare coding variants associated with risk of type 2 diabetes and obesity. We also wanted to characterize the functional effect of these variants on the pathophysiology of these diseases. Using next generation sequencing (NGS), we plan to analyze the coding regions in 850 candidate genes for diabetes and obesity of over 10,000 people. This project will run for 5 years with funding by both public and industrial sources. The initial sequencing phase will be 2 years.
Our goal in purchasing a LIMS was the acquisition of a software package that meets quality requirements, and allows sample tracking, management of: users, instruments, inventory, equipment used, documents and computer files.
We already had a LIMS to manage bank DNA samples but it didn’t offer the functionalities found in LabCollector.
LabCollector was able to answer our requests and more. We really appreciated the easy communication with the support, plus being a French company that made the whole process smoother. One of the strongest features of LabCollector is to offer extreme flexibility and a scalable system being able to adapt with the Illumina-NGS workflow, as well as offering instrument linking to recover our results from the many equipments we have including the Illumina Sequencer HiSeq. We can then retrieve our results automatically inside LabCollector that made our work simpler and productive, a very important point when we are handling a big NGS project as ours.
Positive points of LabCollector:
- Less expensive than other suppliers
- French company makes communication quick and simple
- Perpetual license
- System not closed, scalable and fully developed for our project (using an Illumina-NGS workflow)
- Contains supplementary modules for equipment and inventory management
- Data recovery from different equipment by parsing
Last but not least the good price of LabCollector with the value it brought to our daily lab workflow was a very positive point, being less expensive than other competitors. LabCollector stands out from the competition also with their pricing policy, as it is a perpetual license compared to an annual renting commonly offered in the LIMS market, making it a strong deal even in the long-term.
We also enjoyed many features that came with the Standard LabCollector, such as the equipment module, that allows listing all our equipments and also managing their past and future maintenance, and the inventory management, that allows managing our reagents ordering and sample storage centralizing everything we need in one place.
During our project and the implementation period of LabCollector in our lab, the LabCollector support helped us through some issues we faced, such as the saturation of our data storage in our local server, we then quickly moved the targeting folders to a larger driver. Another point is when implementing a LIMS knowing what we wanted in the beginning in relation to data parsing from equipment is not easy and understanding how it would work with the LIMS, as it can be difficult to change it during the project. LabCollector support was there to advise us on this and data parsing become much more efficient.