This is part two of our series on life in a CLIA lab. The first blog in this series explored the transition from working in a research-based facility to moving to a CLIA lab.
For the last two decades, Sanger sequencing was the gold standard in the clinical lab. It was perfect for the era when most genetic tests were looking for short segments of DNA or amplicons, usually for specific mutations within genes. With gene segments measuring only 100 to 500 hundred base pairs long, it was an easy task for Sanger sequencing and one at which it excels. These are the types of tests typically run on Sanger: looking for specific genes or mutations in a patient, not at their whole genome. However, what if there isn’t a specific gene or mutation connected to the disease pathway in question, and the patient’s whole genetic code needed to be analyzed? This is where Sanger sequencing has limitations.
With the current push toward personalized medicine and with more people seeking answers in their personal genomes, clinical labs need to adopt new technology that is flexible enough to handle massive amounts of sequencing data. Whole genome sequencing (WGS) and whole exome sequencing (WES) using the Sanger method are time and cost prohibitive.
Next-Generation Sequencing in the Lab
An alternative version of sequencing — Next-Generation Sequencing (NGS) is able to perform WGS, WES, and even sequence specific amplicons in a much more efficient manner than Sanger sequencing. NGS uses unique adaptors about 10 base pairs long, typically referred to as “barcodes”, that are attached to a patient sequence. This tagging allows for as many as 96 patients to be sequenced in a single sequencing run on NGS systems. This is where NGS trumps Sanger, due to efficiencies in time and expense.
Introducing NGS to a Sanger Sequencing lab
Introducing Next-Generation Sequencing to a Sanger Sequencing lab can be difficult, however the advantages far outweigh the hurdles presented during the implementation process.
It is not simply “plug and play” when it comes to bringing a new technology into a lab. In addition to bringing in new equipment, the laboratory team must develop new informatics workflows and new Standard Operation Procedures (SOPs). The laboratory Information management system keeping track of the experimental data needs to be configured to handle new NGS workflows, assays and instrumentation. Not only must the lab’s LIMS system track and store the new data, it must make the data accessible for future analysis.
CLIA in an NGS Lab
Implementing a new NGS system and ensuring the instrumentation is up and running within CLIA specifications are substantial hurdles for any lab. Before genetic tests can be run on an instrument it must go through a validation process which ensures the instrumentation is running correctly. This process is necessary for all machines in the lab associated with the sequencing process, not just the sequencer itself.
Once it is established the instruments in the lab are working to the correct specifications, reference samples are used to establish that the test will run properly on that machine. This data can also can be used to help troubleshoot in the early stages of test development. Establishing maintenance and calibration routines, writing standard operating procedures, and proper documentation are all very important to this process, not only for CLIA approval but also for future internal or external lab audits.
The preparation which goes into establishing a NGS CLIA lab seem lengthy however, once it is completed it does not need to be repeated. Establishing good practices such as maintenance schedules and proper documentation early on can ensure smooth performance and continued accuracy of machines in the future.
Once the lab has the ability to handle NGS testing the next big question is, “What tests are you going to run with it?” We will tackle test developing and tracking in an upcoming blog post.