Next generation sequencing (NGS) is a parallel DNA sequencing technology that is able to carry out hundreds to millions of DNA sequencing reactions in parallel, along with the analysis of the sequencing data that is being produced. Utilizing this high-throughput NGS technology, researchers can now sequence an entire human genome quickly and relatively inexpensively, allowing the utilization of NGS data in scientific research in ways that just 10 years ago would have been considered cost-prohibitive.
The ability to combine NGS-generated genomic data with clinical data, for example, has revolutionized the Life Science industry, spawning the development of personalized cancer treatments and the field of Precision Medicine. Commonly used NGS processes (e.g., whole exome sequencing, chromatin immunoprecipitation sequencing, DNA target-based sequencing, RNA sequencing, etc.) are leading to many important discoveries and innovative processes in both research and patient-centered settings.
With the ability to generate multiple terabytes of data in a single run, however, widespread use of NGS technology has led to massive datasets for researchers. Managing this data has now become a central challenge for genomics laboratories and biotechnology companies. While data storage options have become relatively inexpensive in today’s digital age, processing and analyzing these enormous datasets has become the new bottleneck.
Scientists conducting research using genomics data need to be able to effectively compare genomes across patient cohorts and retrieve the associated sample information. In this context, laboratory information management systems (LIMS) that archive and organize data in a centralized database have become a necessity for genomics labs and biotechnology companies. LIMS allow scientists to intelligently examine these massive datasets to drive research decisions.
Laboratories looking to implement a LIMS face a dizzying array of options, however. There are now several dozen LIMS vendors on the market, including LIMS that are specifically designed for genomics laboratories. In this blog, we will discuss some of the key features a LIMS serving a genomics laboratory should have and provide an overview of a LIMS selection methodology that helps to ensure you make the right choice for your unique laboratory environment.
Important Criteria for Selecting Genomics LIMS
Genomics research often involves complex, multi-step workflows that frequently need to be adjusted and can span several different laboratories. The experimental complexity of genomics research, along with the massive data volume, create unique challenges for researchers and/or laboratories looking to manage and analyze genomics data. In addition, regulatory bodies have been working to catch up with this dynamic field, and complex guidance and regulations are beginning to emerge that seek to maintain testing accuracy and reliability.
When properly implemented, a LIMS solution can dramatically improve laboratory efficiency and effectiveness, along with regulatory compliance. While system requirements that are unique to your lab should be the foundation of every LIMS selection process, there are number of selection criteria that are typically important for a genomics LIMS. Some examples include:
Easily configurable and customizable. With the cutting-edge research being performed in genomics labs, workflows, protocols, methods and technologies are constantly changing. Genomic LIMS need to be adaptable to help labs accommodate changing technologies and methodologies. Instead of having to call up the LIMS vendor every time something needs to change in the system, the lab team should be able to quickly configure the software. The LIMS should also come with a flexible application program interfaces (API) that allows a lab team with programming expertise to easily customize the system. The bottom line is that the rapid timescales associated with NGS require an easily configurable and customizable LIMS that will enable labs to avoid programming delays and make changes quickly.
Easily integrates with next generation sequencing instrumentation. Integrating instruments with LIMS is one of the primary ways that LIMS improve workflow efficiency in labs. Towards this end, any LIMS utilized by a lab with NGS equipment should integrate (generate and consume instrument files) readily with major next-generation sequencing instrumentation. In order to help automate workflows and speed analysis, the LIMS should:
- Automates the process of setting up a run – scientists specify the samples they want to use, and the LIMS automatically generates the files the sequencer needs for the run.
- Tracks the quality of sequencing data coming from the instruments – it is highly inefficient for labs to wait until the run are complete before evaluating data quality.
- Tracks results – scientists should be able to easily locate the information associated with any particular run.
A good LIMS will enable scientists to avoid having to organize and track sequencing data so they can spend more time on analysis and innovation.
User specific interfaces. NGS work involves collaboration between many different types of scientists to extract the insights that drive innovative medicines. Given each of these scientists needs access to different types of information and performs different tasks, the LIMS needs to be able to provide user specific interfaces to maximize productivity. User specific interfaces are also necessary for data security – users should only have access to the information they need to do their jobs effectively.
Comprehensive sample tracking. NGS biologics add significant complexity to sample tracking and workflows, including the need to track sample lineage and progeny over time. Given this complexity, genomics labs often struggle to effectively track the samples (and associated metadata) used to conduct a particular experiment. To be able to effectively analyze the enormous quantities of data the NGS produces, scientists need to be able to track all the granular details unique to genomics samples throughout the workflow (from sample submission to result reporting). This will allow researchers to see and interrogate sample history over its full lifecycle in a single centralized system, ultimately making it easier for scientists to set up and validate experiment runs.
Compliance Support. Given that genomic research typically involves human samples, genomics laboratories must adhere to a variety of regulations – CLIA, GDPR, HIPAA – administered by US and international agencies in addition to GxP and 21 CRF part 11. There are also frequently stringent state regulations for genetic testing, in addition to both laboratory and scientific professional organization (e.g., College of American Pathologists, Association of Molecular Pathology, American College of Medical Genetics and Genomics) guidelines that need to be integrated into laboratory operations.
As such, the LIMS solution chosen will need to have a robust set of controls that support compliance with applicable regulations and standards on data integrity, validation and privacy. Additionally, the project team needs to have the skills, knowledge and experience necessary to properly develop and apply these controls during the implementation so as to enhance and ensure regulatory compliance for your business.
LIMS Selection Methodology
While the above-mentioned selection criteria are usually applicable for a LIMS serving a genomics lab, every lab is unique, and care should be taken to apply a comprehensive methodology that ensures the best LIMS for your lab is chosen. One of the biggest mistakes companies make when selecting a LIMS is to omit the business analysis necessary to ensure you select the right LIMS for your unique laboratory. Organizations purchasing a LIMS typically have many workflows in place that incorporate manual processes and information stored in disconnected silos such as spreadsheets, emails and paper notebooks. These workflows will need to be completely revamped and optimized to take full advantage of the productivity and efficiency gains that a LIMS can offer.
The first step in any technology selection process should be thorough workflow and business analysis that serves to maximize business value for your organization. Such an analysis utilizes business analysts with domain, industry and system knowledge to document the current state of laboratory operations, as well as an optimized set of future state requirements that will encompass the flexibility necessary for genomic workflows.
Once a set of optimized future-state requirements are generated, it may also be necessary (for large organizations) to design a laboratory informatics architecture that is aligned with business goals, along with a roadmap to deployment, before engaging in a proper technology selection process for your organization. With the proper foundation laid for your selection process in this way, you ensure that the LIMS selected for your laboratory will maximize business value for your organization.
LIMS have proven to be an invaluable tool for laboratories across a wide range of industries for over 30 years now. Due to the unique demands of next generation sequencing, selecting the right LIMS for a genomics laboratory can be a challenging endeavor, however. Genomics labs typically need a flexible, scalable, regulatory-compliant, multifunctional LIMS with a low total cost of ownership (TCO) that satisfies most or all of the selection criteria described above.
While several vendors now produce LIMS specifically designed for genomics labs, some of these systems can be rigid and prescriptive about workflows. A comprehensive methodology that includes a thorough evaluation of hosting options should be followed to ensure that you select the best LIMS for your laboratory.
Astrix Technology Group has over 20 years of experience facilitating successful LIMS selections and implementations in pharmaceutical and biotech companies. Our experienced professionals have the experience and knowledge to help you select a LIMS that will allow your organization to turn data into knowledge, increase organizational efficiency, improve quality and facilitate regulatory compliance. If you would like to discuss your LIMS project an Astrix expert, please contact us for a free, no obligations consultation.