Paradigm shift in genomics: Technology and investment

MedTech & Diagnostics News: The vision of a portable device capable of sequencing a patient’s entire genome at the bedside, delivering a diagnosis within an hour is becoming a reality.

Professor Zornitza Stark, clinical geneticist and researcher at the Murdoch Children’s Research Institute in Melbourne, reflected on a pivotal patient case from a decade ago, where it took six months to obtain sequencing results and reach a diagnosis. Today, such a process could be expedited to a matter of days, or even hours, altering the trajectory of a child’s life through timely diagnosis and treatment.

She highlighted the multifaceted challenges accompanying this paradigm shift, stating, “It’s all very well to speed up the test to be done in under 10 hours, but if it takes 3 weeks for that child to even access the test, you’re not really going to get the full benefit.”

Overcoming obstacles such as workforce capacity, education, health system costs and infrastructure, and ensuring equality of access and data interpretation consistency, remain critical.

Nearly a decade ago, Professor Stark and her team at Australian Genomics and the Victorian Clinical Genetics Services embarked on a mission to establish a national rapid sequencing network in Australia. Their efforts have garnered recognition and support, with rapid genomic testing in critically ill newborns and children now endorsed as standard of care by the Human Genetics Society of Australasia and funded by state governments in Victoria and Western Australia.

While Illumina continues to dominate clinical-sequencing programs globally, emerging platforms pose viable alternatives, potentially democratising rapid sequencing.

Stephen Kingsmore, a pioneer in rapid-sequencing at the Rady Children’s Institute for Genomic Medicine in San Diego, California expressed enthusiasm for the AVITI instrument from Element Biosciences, heralding its potential with per-base accuracy rivalling or surpassing that of Illumina, at a fraction of the investment.

“You buy three instruments and the instruments are relatively inexpensive, about $250,000 each – and you’ll get $200 genomes,” he said. By comparison, sequencing a full genome cost roughly $10,000 just a decade ago. “That is going to be quite transformative.”

Furthermore, scientists are exploring sequencing-based ‘liquid biopsies,’ leveraging technologies like RNA sequencing to expedite cancer detection, monitoring, and treatment assessment.

A team led by computational biologist Martin Smith at the University of New South Wales in Sydney, has shown that RNA sequencing with the MinION could shorten the time for leukaemia profiling of blood samples from days to minutes.

“Five minutes was enough for most of the samples to get above 90% classification – that’s only 30,000 reads,” said Mr Smith. “The algorithm could distinguish 11 subtypes of acute lymphoblastic leukaemia on a standard laptop, and Smith says that a similar approach could be applied to other time-critical conditions, including sepsis, infections and autoimmune-disease flare-ups.”

However, technological innovation is only part of the equation in clinical diagnostics. Dr Ahmad Abou Tayoun at the Al Jalila Children’s Specialty Hospital in Dubai, United Arab Emirates, underscored the necessity of integrating these advancements into clinical practice seamlessly.

“The bottleneck is really to get the doctors to be familiar with the fact that it’s available and when to order it. And of course, making sure that when they get the results, they can act on them,” he explained.

“We need something we can do on millions of samples per year for less than $1,000, and maybe less than $500,” stated Stephen Kingsmore, a rapid-sequencing pioneer at the Rady Children’s Institute for Genomic Medicine in San Diego, California. “We have to think about automation on a completely different scale.”

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