Need for (Diagnostic) Speed

How fast is fast? “Rapid” genome sequencing typically takes a few weeks – not fast enough for many patients. To bring new meaning to the term, researchers have developed a fast DNA sequencing approach that reduces diagnostic time to just a few hours (1). When the team achieved their fastest genome sequencing time – five hours and two minutes – they knew they had created something groundbreaking. “It was just one of those amazing moments where the right people suddenly came together to achieve something amazing,” said senior author Euan Ashley (2). “It really felt like we were approaching a new frontier.”

The time taken to diagnose that case was seven hours and 18 minutes – offering a significant improvement for patients in intensive care units awaiting diagnosis to begin treatment. To achieve the super-fast sequencing speeds, the team enlisted the help of researchers from Oxford Nanopore Technologies, who built a machine made up of 48 flow cells to sequence all the cells simultaneously.

But not everything was smooth sailing. “We weren’t able to process the data fast enough,” said Ashley (2). “We had to completely rethink and revamp our data pipelines and storage systems.” To solve this, graduate student Sneha Goenka redirected the data to a cloud-based storage system that could handle the required computational power and analyze the data in real time. Each genome was then scanned for disease-causing errors and compared against known disease-causing variants.

Word of the test is already gaining traction around campus. “I know people at Stanford have heard we can make a genetic diagnosis in a few hours and they’re excited about it,” said Ashley (2). “Genetic tests just aren’t thought of as tests that come back quickly, but we’re changing that perception.”

What’s next in their quest for faster diagnostics? Ashley has ambitious plans. “I think we can halve it again. If we’re able to do that, we’re talking about being able to get an answer before the end of a hospital ward round. That’s a dramatic jump (2).”

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References

1. JE Gorzynski et al., Circ Genom Precis Med, [Online ahead of print] (2022). PMID: 35133172.
2. H Armitage (2022). Available at: https://stan.md/3C8SKJG.

About the Author(s)

Liv Gaskill

During my undergraduate degree in psychology and Master’s in neuroimaging for clinical and cognitive neuroscience, I realized the tasks my classmates found tedious – writing essays, editing, proofreading – were the ones that gave me the greatest satisfaction. I quickly gathered that rambling on about science in the bar wasn’t exactly riveting for my non-scientist friends, so my thoughts turned to a career in science writing. At Texere, I get to craft science into stories, interact with international experts, and engage with readers who love science just as much as I do.

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