The challenges of bringing next-generation sequencing to patients

29 Jul 2020

Prof Kurt Zatloukal. Image: Sissi Furgler Fotografie

Prof Kurt Zatloukal spoke to about genome sequencing and the difference between research and healthcare settings.

Medical genomics and next-generation sequencing may be a major game changer in healthcare and diagnostics. By using the knowledge of an individual’s genomic make-up to identify those with higher risks of certain conditions, it could enable healthcare professionals to intervene at earlier stages.

Couple this with pharmacogenetic testing, which shows how a person’s genes affect their body’s response to certain medicines, and the way in which patients are treated in the future could be life changing.

With this in mind, there are currently two projects in the EU each receiving approximately €11m in funding as part of the Horizon 2020 framework, which aim to bring next-generation sequencing into routine diagnostics and closer to the patient.

Prof Kurt Zatloukal is a professor of pathology at the Medical University of Graz in Austria, which is a consortium partner on one of the two EU-funded projects. The project in which he is involved, Instand-NGS4P, is looking at ways to better provide access to next-generation sequencing for cancer patients and meet with regulatory requirements.

Zatloukal, who recently spoke at a genomic medicine webinar hosted by Genuity Science, talked to about the challenges that come with bringing next-generation sequencing to routine healthcare.

“I think sequencing has a tremendous success story from sequencing the first human genome to what we can do today,” he said. “But what is interesting is even though there is this remarkable success in research, still not many patients benefit from next-generation sequencing in routine healthcare outside of research programmes.”

The difference in regulations

Zatloukal said one of the biggest roadblocks to bringing next-generation sequencing into routine healthcare is the additional regulations of diagnostics that lie outside of research. “It’s quite a challenge that such complex and advanced technologies fulfil these regulatory requirements.”

In Europe, this means complying with the In Vitro Diagnostic Regulation (IVDR), which came into force in May 2017. Manufacturers of currently approved in-vitro diagnostic medical devices have until May 2022 to meet the requirements of the IVDR, which means that these regulations must be considered when bringing next-generation sequencing from research to routine diagnostics.

Additionally, as with most innovations, GDPR comes into play, because when you’re dealing with genetic information, you’re handling “a very sensitive category” of data. “When you have a certain amount of genetic information, it gets unique for a person so it’s a very powerful identifier,” said Zatloukal.

“This reduces our opportunities to anonymise genetic data. We have to work mostly with identifiable data, therefore GDPR fully applies.”

He also flagged the challenge of exchanging genetic information internationally. “If we collect genetic data from European citizens and we transfer that data outside of Europe, we have to guarantee there is adequacy in the protection outside of Europe, which sounds really obvious but it’s not easy to do and implement.”

While transferring data outside of the EU has been a challenge in many industries, Zatloukal noted that individual states in the US as well as other countries are starting to follow the European example when it comes to data protection, adding that it’s often “driven by the interest of the citizens”.

Zatloukal also believes that the scientific community working within next-generation sequencing can sometimes be unaware of the differing requirements when it comes to moving from the research domain to routine diagnostics. “If they want to translate their knowledge and the technology developed in a research domain to routine healthcare, they also have to consider what are these regulatory requirements, otherwise, this translation will not be efficient.”

The health economic benefits

Outside of the regulatory considerations, another challenge facing the advances in next-generation sequencing is showing the health economic benefit of applying these techniques, since it will be the healthcare systems that will have to pay for it in the end.

While the benefits of applying genomics appear huge on paper, the sheer volume of information and data that is produced can almost hinder these benefits when it comes to routine healthcare and, critically, how it will factor into medical decisions.

Zatloukal said there needs to be enough clinical evidence to show how a genetic variant should be considered when actually treating a patient.

“This makes a huge difference between applying next-generation sequencing in research or doing it in routine healthcare. In the end, you need what is called a clinical performance test, where you can really show that considering a certain genetic variant in the decision-making really shows benefits for the patient.”

The information gap

Another key challenge Zatloukal spoke about was how the information at the end of the research will translate in the medical profession, especially in such a new and rapidly developing field.

“There’s a huge challenge with how to train the medical professionals and how to use this information properly and I think it has to be approached from two sides,” he said.

“On the one hand, to make the information really explainable to them so they have all the background information [and] they can take the responsibility as a medical doctor for making a decision,” he said. “And then we must not forget the patient themselves, therefore we are also working very closely with the patient advocacy groups.

‘You have to define the user needs before you design something’

“You have to explain this information, and if there’s not a basic understanding, it’s almost impossible in the context of routine healthcare to really explain what genetic testing is about, what are the consequences, what are the possible risks. If you have a good basic understanding, then you can do it in a healthcare setting. But without that basis, it’s mission impossible.”

He also spoke about the importance of improving health literacy with the general public to increase awareness of how these technologies can help with improving their health.

“There’s a general overestimation to some extent of genetic information,” he said. “Genetic make-up is [just] one component that determines health or disease. It’s also the environment and it’s the lifestyle, it’s the nutrition, it’s the microbiome, so there are many factors that all act together and define an individual’s health or disease status.”

The need for communication

Similar to the information gap, Zatloukal also cited the need for two-way communication between the scientific community and the medical community due to the different needs and regulations when it comes to transitioning technology from one area to the other. He added that pharmacogenetic testing is an example of this challenge, as it’s still only available for a limited number of medicines.

“The science behind pharmacogenetic testing is very well established, but still it’s essentially not used and this, for me, is an example of the gap between scientific evidence, technical feasibility and lack of translation in routine healthcare,” he said.

“If you design an interface, you need the user. You have to define the user needs before you design something. And it’s not only the medical professionals, it’s the patients as well. And I think this is very important to be aware of.”

He added that early engagement of key users is critical, and that includes both medical professionals and patients. “Don’t forget the patients. They are also users, they are the end users. They should be involved from the very beginning.”

Jenny Darmody is the editor of Silicon Republic