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When it comes to applying genomic sequencing in diagnostic medicine, increasing evidence is demonstrating that whole exome sequencing (WES) can sometimes fall short. This is a particular issue when analyzing large segments of DNA from patients and can adversely impact a physician's diagnosis.An alternative to WES is the utilization of a smaller, more targeted genetic test that analyzes a specific panel of genes known to be associated with a certain pathology. These tests are less of a financial burden on healthcare systems and patients and can offer highly accurate results. Targeted NGS is enabling this testing approach, and we're seeing increased adoption of NGS in the clinical diagnostics space.

But what barriers still exist to the full implementation of NGS, and how can we remove them? Technology Networks recently spoke with Luca Quagliata, Ph.D., Global Director of Medical Affairs for Thermo Fisher Scientific, to learn more.Molly Campbell (MC): How is genome sequencing currently utilized in the oncology diagnostics space? What are its limitations?Luca Quagliata (LQ): Sequencing of DNA and RNA is currently used in routine molecular testing for two purposes. Firstly, they are used with the aim of supporting a diagnostic decision, i.e. differential diagnosis (such as PIDGFA mutation status in gastrointestinal stromal cancer. More commonly, they are adopted to complement a pathology report by adding information related to a clinically relevant genomic variant (e.g. mutations in the EGFR gene) that are directly associated with any specific approved drug treatment (for example, BRAF inhibitors for V600E BRAF mutated melanoma patients).Some of the major limitations of genomic testing are related to quality of the starting material for testing (generally known as pre-analytic issues, e.g. tissue fixation), the ability of a given sequencing method to generate usable results (not every sequencing approach is born equal), the capability of interpreting the results (e.g. is the observed genomic variant a pathogenic alteration or is simply benign?) and finally the economic aspect. Who should pay for the test?MC: Why does WES commonly fail to adequately analyze large segments of DNA?LQ: As above mentioned, not all sequencing methods are born equal, WES can be performed using a variety of library preparation kits, possibly leading to substantially different results.1 Unfortunately, no universally accepted standard has been established for WES, especially for oncology applications.Generally, one of the most common issue is related to the sequencing depth, also known as coverage. High coverage allows to gain higher confidence in the generated results, as the genomic examined regions are analyzed multiple times, thus increasing the robustness of the data. However, high coverage comes at the cost of increasing sequencing price. Plus, even in the absence of any financial constraints, increasing coverage indefinitely is simply not possible due to technical limitations, i.e. the input material will define the maximal reachable coverage.

Furthermore, it is well established that, in certain situations, even pushing the coverage a 100-fold higher does not generate any tangible benefit in terms of data analysis output. Finally, a variety of alignment and calling algorithms can be deployed to identify large DNA segments rearrangements. Once again, no standard is strictly defined, thus the varying ability of different algorithms will greatly impact the final result. To conclude, while robust approaches are in place for single nucleotide variants (SNV) or multiple nucleotide variants (MNP), as well as insertions and deletions (INDEL), this is not the case when applying WES to study large DNA segments. Nowadays, microarray-based investigations are very popular for assessment of large genomic rearrangements.MC: Why is a targeted test more suitable in the diagnostics space?LQ: Targeted NGS is most commonly used for routine diagnostics because:

MC: NGS is becoming increasingly easier for patients to access and costs are rapidly declining. In your opinion, will we reach a stage where a genetic test is as common as, say, having a blood test when you visit your healthcare provider?LQ: While the price of NGS, meaning reagents related costs to perform the test, is undoubtedly going down, one should not forget that the largest fraction of NGS cost is generated by the human labor necessary to carry out the analysis. Thus, any technological approach that will reduce human intervention in the process will be the most effective in compressing the overall sequencing cost to enable true democratization of NGS.At Thermo Fisher Scientific, we recently made a significant step in this direction with the launch of the Ion Torrent Genexus System, the first research NGS solution that automates the entire specimen to report workflow in a single day with only two touch points.Having said that, there is no doubt that sequencing will eventually become as common as performing a classical blood check. The question is, rather, when will it happen?

In my opinion, that will largely depend not exclusively on the reduction of the overall NGS cost, but rather our ability to expand our understanding of the genomic variants clinical implications. As for now, only a limited fraction of variants can be clearly classified and associated with either a clinical condition or a drug treatment benefit. In my view, it is rather a matter of knowledge than merely a problem of costs. We use blood testing not only because it is easy and cheap, but because we can generate valuable and meaningful information through it.MC: The number of individuals undergoing direct-to-consumer genetic testing at home is on the rise. In your opinion, what impact is this having on the use of genetic testing in the clinical spaceLQ: Direct-to-consumer (DTC) genetic testing is an interesting recent phenomenon that in my view poses several questions, mainly regarding the quality of the results it provides. Several regulatory agencies have expressed concerns and are now acting with the aim of monitoring this market. In this initial and still immature phase of DTC, I strongly advocate for the implementation of a regulatory framework that should be considered not a barrier to wide genomic testing access but rather a safeguard.Should that framework be implemented, then DTC market expansion will have a positive effect on the use of genetic testing in the clinical space, as an audience of genetic-educated patients will also inevitably push physicians toward the adoption of genomics in medicine.

Should the DTC genetic market be given complete freedom, I am concerned that it would negatively impact genetic testing in the clinical space, as people might be easily convinced that managing this kind of data is simplistic, and thus the value of a controlled and professionally regulated testing approach will lose value. I think of this in relation to the "Dr Google self-medication" phenomenon.MC: What challenges still exist in the use of NGS in diagnostics?LQ: Overall NGS data generation and interpretation is still perceived as being extremely complex. Furthermore, while we are witnessing an increase in policy coverage for NGS testing, reimbursement remains a practical issue as well as NGS results being restricted to very specific indications. Finally, limited medical education and awareness regarding the value of genetic testing remains high in the healthcare community, with a substantial knowledge gap between physicians working at large academic centres and those working in the community setting. It will take a shared collective effort to remove the above-mentioned barriers to allow broad adoption of NGS in routine diagnostics. No single company, as large as it could be, can achieve such results.

We at Thermo Fisher Scientific are on the front-line supporting precision medicine through partnering with a variety of major stakeholders in the field, from patient advocacy groups to medical associations and Pharma.

Luca Quagliata, Ph.D., Global Director of Medical Affairs for Thermo Fisher Scientific, was speaking to Molly Campbell, Science Writer, Technology Networks.References:

1. Clinical Exome Studies Have Inconsistent Coverage, Clinical Chemistry, Volume 66, Issue 1, January 2020, Pages 199206.

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Removing the Barriers to Broad Adoption of NGS in Diagnostics - Technology Networks

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