This is part three of our series on life in a CLIA lab. The previous two blogs in this series explored the transition from working in a research-based facility to working in a CLIA lab and bringing NGS into a Sanger Lab.
In a Bringing Next-Generation Sequencing into a Sanger Lab, I discussed implementing NGS workflows in a Sanger sequencing lab. After working through the initial challenges surrounding new equipment, developing new informatics workflows and establishing new Standard Operation Procedures (SOPs), the lab team needs to configure a laboratory information management system (LIMS) to handle new NGS workflows, assays and instrumentation. A LIMS system is the next logical step because the amount of data created by NGS instruments is too great to be tracked manually.
You have a New NGS LIMS – Now What?
You have a brand new NGS LIMS system, now the question is — what are you going to do with it? Having instrumentation up and running is only half of the equation. Next, you either need to find an “off the shelf” test where the primers for the genes are already designed, or develop a test in-house. Developing tests in-house comes with its own set of challenges.
Designing Your NGS Test(s)
When designing a test in-house, you need to begin by targeting a disease state and gene. After the target has been identified, primers will need to be designed and tested against controls. Analysis thresholds must be determined and the test must be optimized for all components involved. All of this hard work results in a unique offering for your test menu. However, an “off the shelf test” (OTS) is a time-saving alternative. With an OTS test, that discovery and development has already been completed by another lab.
Ultimately the decision of which tests to run is up to lab management. Regardless of the type of test, it still needs to be validated and SOPs need to be written. Test validation is designed to prove the test is accurate and precise, and that the results are repeatable, and reproducible. Everything involved with the test must be documented. This is generally achieved through several runs of the test using multiple trained technicians.
Tracking Test Results in Your NGS Lab
Now, you have your NGS system up and running, and a test ready to bring to market. However, there is one more very important aspect to consider – tracking. Development of a tracking system can also be a challenge. Working with an outdated tracking system forces the lab to use workarounds such as Excel spreadsheets and paper tracking. This was the case in the lab where I worked. Tracking instruments, reagents, and showing chain of custody using an Excel sheet is not optimal for a CLIA lab. It can be done, however, should there be a large market for the test, having an Excel spreadsheet for every batch can get confusing.
NGS LIMS Solutions for CLIA Labs
If you choose to move away from spreadsheets, a Laboratory Information Management System (LIMS) is the best method for a lab to handle this information. Traditional informatics solutions for CLIA labs can be unwieldy, especially when it comes to creating a new test and new system protocol. The time it takes to custom code a new system can be extensive… and while the months are slipping away, your new NGS sequencers gather dust.
A laboratory information management system which can be configured to fit new workflows is optimal for an NGS lab — especially one which is creating its own tests. Suites of applications for NGS testing available from the Thermo Fisher™ Platform for Science™ Marketplace solution cover the entire workflow process, from accessioning and sample prep to sequencing and analysis. The additional benefit of working with a LIMS system designed for NGS is the ability to find information quickly, and if necessary, determine the time and location of a problem in the sequencing run. Tracking information is useful not only for CLIA purposes but for troubleshooting as well. Laboratory Information Management Systems like the Thermo Scientific™ Core LIMS™ software give you the ability to know which instrument samples were run on, or what lot number of buffer was used is incredibly helpful for pinpointing issues.
An up-to-date and functional tracking system can also help track sequencing failures. There are some parts of the genome, such as GC rich regions, that can prove difficult to sequence on the NGS system. If you have a gene that is difficult to sequence on the NGS system what are your options? You could continue to try and sequence it on the NGS instrument, or you could turn to Sanger. It’s not uncommon for labs to perform Sanger sequencing in parallel with NGS. This is often referred to as running “Sanger confirmations” and can be used to confirm NGS findings, or as a way to deal with difficult-to-sequence regions.
With the capability to run multiple types of sequencing and to sequence several patients at once, NGS can bring flexibility to the lab. The process of bringing NGS to the CLIA lab is no different than bringing any other new piece of equipment or new test on board. A LIMS system can help ease the information burden associate with NGS, helping the lab to experience the benefits of NGS without the headaches of manual data management.