Laboratory Management for Clinical and Research NGS Labs

Transcription

1 Laboratory Management for Clinical and Research NGS Labs Introduction Few can argue that Next Generation Sequencing is having a major impact on genomics research. The progress in this field exceeds even that of computational growth according to Moore s Law, and this rapid progression will be continuing for years to come. The net result is that more labs are able to afford NGS instruments and to perform high volume sequencing. The adoption of NGS sequencers has presented new challenges in handling requests for services, preparing samples and tracking results, especially given the fluid nature of both the NGS market and the protocols for each instrument. Although it is early in the ability to understand the voluminous NGS data, there are already clinical applications for NGS, particularly in oncology. This raises the bar on laboratory operations as CLIA certification will be required, which implies more detailed tracking than in a research setting. A proper LIMS solution will address both the research and clinical settings while improving the NGS laboratory operations through increased efficiencies, quality of operations and overall throughput. Such a solution should also be able to quickly adapt to changing protocols and even new NGS technologies as they become available. NGS Workflows and the Laboratory So what is a workflow? According to Wikipedia a workflow: consists of a sequence of connected steps. It is a depiction of a sequence of operations, declared as work of a person, a group of persons, an organization of staff, or one or more simple or complex mechanisms. A laboratory s overall daily NGS workflow is an overarching construct that may itself be comprised of several sub-processes. Each of the sub-processes can be further defined as a sequence of steps that a person or group follow to achieve some end result. For NGS labs, there are common sub-

2 processes that typically comprise the overall workflow, these may include: Request for Services Sample Receiving Library Construction Sequencing Post Sequencing Processes such as Primary and Secondary Analysis A LIMS solution should be able to quickly implement this processing pipeline specific to each clients needs largely via configuration and should do this in short timeframes. Workflows in the LIMS solution should embody the lab s SOP by walking the user through each step of the process so there is very little or no training required for lab technicians to immediately begin using the system. Workflows should be able to be connected together so that one workflow can initiate another workflow, further streamlining the process and enabling workflow re-use within multiple lab overarching processes. Customer enters request for NGS service(s) from lab & registers samples that will be shipped Samples arrive at the lab from external locations Receive Samples (e.g. assess condition, barcode, record storage locations) Perform One or More QC Analyses Perform aliquots for QC When ready to process samples, pull samples from the freezer Perform Library Preparation Workflow Perform Cluster Gen and Scan Workflow Launch Primary Analysis Process (external to LIMS) Load metrics from secondary analysis into LIMS Launch Secondary Analysis Pipeline (external to LIMS) Load metrics from primary analysis into LIMS Figure 1 - A high-level example NGS workflow process

3 Consumables Tracking A key aspect of NGS process tracking is tracking consumables. A LIMS Materials Management Module should be available for detailed tracking of usage of reagent lots and their volumes in NGS and other workflows. This module should have several key features that make lab operations more efficient and traceable: Reagent inventory tracking Flexible implementation to changes in NGS process chemistry can easily be added via configuration Automatic Master Mix computations for constituent reagents in workflows Reagent volume-on-hand tracking with preset order levels and alerts Reagent validation Reagent storage location tracking Integration with back end financial systems for purchasing and receiving Process Tracking Many NGS labs want to enable electronic ordering of services via the internet. The initial stage of this tracking should begin with a web based Request Portal that enables client order entry over the internet via a secure connection. When NGS services are requested, it should support multiple NGS services for each sample (e.g. PacBio and Illumina HiSeq DNA Sequencing for Sample A ) along with other NGS instrument-specific request items. The Portal should enable these complex order types via configuration, allowing for very flexible portal configuration and rapid deployment. The Request Portal ideally enables sample pre-registration, which streamlines the request approval and sample-receiving processes as the samples already exist in the LIMS when they arrive. Once received, samples should be marked as being ready for the assigned workflows per their requested NGS service(s), and the requestor should (optionally) receive proper notifications from the LIMS of sample status changes. Importantly, the integrated process tracking should enable the requestor to see where each sample is in the processing pipeline. This reduces calls to the lab as the requestor is never in doubt as to the status of their samples.

4 Compliance In recent years, NGS has largely been a research and development technology, and it will continue to experience high growth as the cost and quality of NGS improves. In parallel, there have been some prominent stories of NGS saving lives when all other attempts to understand a person s conditions had failed, indicating the potential of NGS in clinical applications. Presently, only a few CLIA compliant NGS labs service the clinical market. In the future, this will be a very large growth area as more specific NGS clinical applications are discovered and validated. Sapio expects the clinical NGS market to experience strong growth. Key for CLIA is to have detailed utilization tracking of all consumables and equipment in relation to samples. Other possible requirements include single sign on, client inactivity timeouts, detailed audit logging, etc. The NGS LIMS solution should have experience operating in these more rigorous environments. The Mobile Lab Technician The modern NGS lab can be expansive, often spanning multiple rooms and sometimes floors. Lab technicians will need to access freezers, QC equipment, chemistry stations and sequencers requiring them to move around the lab, but also to have access to the LIMS for information retrieval (e.g. storage locations) or data entry. The ideal NGS LIMS solution moves with your lab technicians as they move around the lab. This allows lab technicians to be more efficient while reducing errors by eliminating the need for paper records and data transcription. The new tablet computing devices such as the ipad 3 now have the necessary processing power to make this possible. The LIMS solution should make optimum usage of tablet screen real estate and touch features. IT Concerns The reality is that IT groups are often understaffed and overworked. They have to support many solutions and technologies, and these evolve rapidly making it difficult to keep up with each solution s capabilities and requirements. To lessen this burden, the

5 NGS LIMS solution is ideally very easy for IT to support and deploy, requiring minimal setup and ongoing attention. The optimum LIMS should be based on leading web technologies (e.g. JavaScript/Ajax) and will run in all the leading web browsers with no extra software installation required such as browser plugins. The LIMS server technology should also be operating system agnostic giving customers the most flexibility for deployment. It should also support multiple popular databases, both free and commercial, so that customers have choices that suit their particular requirements. LIMS for NGS Summary Important NGS related capabilities to look for: Templatized and configurable workflows for rapid implementation of custom NGS library preparations and sequencing workflows Overarching process tracking that connects workflows together Reagent Materials Management Module with flexible implementation so that changes to reagents in processes can be easily accommodated with no programming required and volume-on-hand is tracked Intuitive, step by step workflows that guide lab techs through a defined process Workflow step level help to provide detailed descriptions to end users as needed Graphical request level dashboard to show progress of each sample through its process Graphical work queues Instrument status and maintenance monitoring Mobile tablet support Web based deployment and low IT burden Support for multiple DB and server technologies The combination of these features is essential for NGS Lab Management software. We invite you to view an NGS presentation of Exemplar LIMS where we demonstrate how Exemplar addresses NGS lab s needs. To schedule a detailed technical demonstration, please contact Sapio at sales@sapiosciences.com.