Abstract
BackgroundLarge clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis.ResultsTo meet the needs of clinical population studies using genome sequencing, we developed a web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation DNA sequencing technologies. Our system is referred to as MendeLIMS, is easily implemented with open source tools and is also highly configurable and extensible. MendeLIMS has been invaluable in the management of our clinical genome sequencing studies.ConclusionsWe maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases. Software is freely available for non-commercial use at http://dna-discovery.stanford.edu/software/mendelims/.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2105-15-290) contains supplementary material, which is available to authorized users.
Highlights
Large clinical genomics studies using generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps
MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases
Software is freely available for non-commercial use at http://dna-discovery. stanford.edu/software/mendelims/
Summary
Large clinical genomics studies using generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis. Due to the dramatic increase in the number of NGS clinical genomics studies, it has become increasingly important to develop adequate laboratory information managements systems (LIMS) to manage the thousands of patient samples that are subject to NGS analysis. As a general and unique solution to the needs of managing the experimental workflow for clinical genome sequencing projects, we developed MendeLIMS, a webbased, robust and flexible solution for integrating the management of clinical study samples and NGS processes. We maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu
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