For High-Confidence Results, Focus on Your Molecular Controls

One of the first things we learn on our journey as clinical scientists is the importance of controls in our experiments and lab workflows. But there is so much more we need to know about controls to use them well and to ensure that we are generating the best possible results—particularly when those results will be used to make decisions for patient care.

In clinical laboratories, molecular controls are widely used for diagnostic assays. They fall into three broad categories: positive and negative controls, exogenous and endogenous controls, and internal and external controls. 

Positive and negative controls are the best known and are designed to always be positive or always be negative when the assay workflow has been performed correctly. They can be incorporated at various points of the testing process and are considered most important during the analytical phase when a patient’s results are produced.

The other controls may be considered process controls, riding with the sample throughout the workflow to ensure that all steps went according to plan. An internal control that’s either endogenous or exogenous moves with the sample and can be used to confirm that preanalytical phases of the assay worked properly, while an external control remains separate from the sample but can be processed in parallel to verify that the workflow produced high-confidence results.

For the most reliable results—and the clearest path for troubleshooting if an issue does arise—many clinical lab teams often use these controls in combination. Introducing controls as early as possible in the process, even at the point of sample collection, gives the most comprehensive view of how reliably an entire workflow performed.

Of course, the confidence you get from using controls is based on choosing the right controls. To ensure the best results, controls should behave as much as possible like the sample being tested, and should match the type of molecule (DNA or RNA). They should also perform consistently across runs, operators, and labs.

In an ideal world, controls would come from the same material being tested—perhaps human cell lines, human reference materials, or previously tested clinical samples. However, ensuring a steady supply of exactly the right materials is a real challenge in clinical labs. In addition, residual clinical samples for infectious diseases can put lab workers at risk from the pathogen.

For these reasons, it often makes sense to choose synthetic controls. They are manufactured in highly controlled environments with rigorous QC testing to ensure lot-to-lot consistency. They are designed to match the native analyte, offering safer testing conditions without sacrificing reliability. 

Synthetic controls can also be produced in “armored” versions in which the analyte of interest is surrounded by a protective capsule, giving the control excellent stability so it can be used from the point of sample collection all the way through to analysis without degradation. Because of their protective coating, armored controls are a particularly good match in assays for viral pathogens.

As clinical diagnostic assays have gotten more complex, so too has the process for choosing the best controls. Incorporating high-quality controls at the earliest point and monitoring them throughout the workflow can help to ensure reliable patient results from even the most finicky assays.