Public health officials, as well as scientists and researchers working in academia and the healthcare industry, have to remain vigilant against emerging diseases. That’s crucial for maintaining diagnostic capabilities, tracking the spread of novel outbreaks of diseases, and paving the way for new therapies.
The more information we have about the location of a disease outbreak and the nature of its severity, the better we can formulate a coordinated response. One of the tools scientists are now investigating for addressing the looming threat of infectious diseases is next generation sequencing.
When it comes to molecular diagnostic approaches, researchers want to see if they can use next generation sequencing for diseases spreading through the population.
What Is Next Generation Sequencing?
Next generation sequencing or NGS is a way to sequence vast amounts of DNA fragments in parallel. It represents an advance beyond polymerase chain reaction (PCR), which scientists need to know what organisms they are targeting first, using the appropriate primers for these targets. NGS systems do not require advanced knowledge of the DNA under consideration.
As software and computer technology continues to advance and become more powerful, the promise of NGS increases too. It depends on rapid analysis to identify which organisms when searching for pathogens in a sample.
So, when a patient comes to a doctor and the physician doesn’t know the cause without testing, being able to look for multiple causes simultaneously in the lab would help to speed up diagnosis and get the patient on the path of treatment.
How Can Scientists Use Next Generation Sequencing for Disease Diagnostics in a Clinical Setting?
Inside a clinical environment, technicians specializing in microbiology can use NGS to conduct whole genome sequencing, as well as metagenomic NGS and targeted NGS, including Amplicon Sequencing. They obtain a specimen, fragment it and randomly amplify the genomic material. Then, it’s time to sequence it, such as by looking for an illuminated fluorescence signal or by detecting pH changes as the sample incorporates investigatory nucleotides. Using high-speed software, you can rapidly identify what’s in the fragments.
If doctors encounter an unknown pathogen in patients, they can apply NGS to sequence a microbe’s genome, to type and identify it. In situations where a disease is known to resist conventional treatments, it’s useful to identify resistance markers in problematic bacteria, such as Mycobacterium tuberculosis complex members.
Advantages and Limitations of NGS for Diagnostics
A major advantage of NGS for diagnosis is the rapid speed at which technicians can run tests. That’s especially critical if you are looking at a possible pandemic.
The ability to scan genetic sequences in parallel allows researchers to plow through huge amounts of data. And the fact that you don’t need to know the organism ahead of testing makes it more versatile.
One clear limitation of NGS when considering the technology for disease diagnosis is that the technology is still in the early stages of development. While it’s used in some reference and commercial labs, it is not yet approved for widespread use.
For one, there is not enough technical ability in the industry for this to be deployed, and instrumentation is not widely available for labs to adopt. And American Association for Clinical Chemistry notes that the medical industry does not yet have formal guidelines to validate, interpret and evaluate the quality of testing yet.
Lack of standardization for these uses means NGS technology is not quite ready for widespread usage.
Awaiting FDA Approval
Currently, there are no NGS-based tests to diagnose infectious disease, for use in pre-market studies, according to the American Association for Clinical Chemistry.
At the moment, some tests based on NGS technology to detect pathogens are permitted in certain reference and commercial labs under Clinical Laboratory Improvement Amendments (CLIA). More studies will need to be finished before the Food and Drug Administration can consider authorizing its use. The potential of using next generation sequencing will be borne out as scientists devise studies and publish results.
