Standford Scientist Set New Record for Sequencing and Diagnosing Patient

Researchers at Stanford University set a Guinness World Record for the fastest DNA sequencing technique that sequenced a human genome in just 5 hours and 2 minutes.

The new ultra-rapid genome sequencing approach developed by Stanford Medicine scientists and their collaborators was used to diagnose rare genetic diseases in an average of eight hours.

“A few weeks is what most clinicians call ‘rapid’ when it comes to sequencing a patient’s genome and returning results,” said Euan Ashley, professor of medicine, genetics, and biomedical data science at Stanford.

Ashley and his colleagues developed a mega-sequencing approach that allowed them to rapidly diagnose patients. In one case they were able to make a diagnosis in just more than seven hours.

The approach is described in a paper in the January 12 issue of The New England Journal of Medicine. Ashley is the senior author of the paper. Postdoctoral scholar John Gorzynski is the lead author.

Over a period of less than six months, the team enrolled and sequenced the genomes of 12 patients, five of whom received a genetic diagnosis from the sequencing information in about the time it takes to round out a day at the office.  The team’s diagnostic rate is about 42 percent, which they noted is about 12 percent higher than the average rate for diagnosing patients with undiagnosed conditions.

“It was just one of those amazing moments where the right people suddenly came together to achieve something amazing,” Ashley said. “It really felt like we were approaching a new frontier.”

To achieve the rapid sequencing Ashley contacted colleagues at Oxford Nanopore Technologies, who had built a machine composed of 48 sequencing units known as flow cells. The idea was to sequence just one person’s genome using all flow cells simultaneously. The mega-machine approach was a success, although genomic data overwhelmed the lab’s computational systems at first.

The team was able to funnel the data straight to a cloud-based storage system where computational power could be amplified enough to sift through the data in real time. From start to finish, the team sought to accelerate every aspect of sequencing a patient’s genome.

The approach also made use of long-read sequencing, which preserves long stretches of DNA composed of tens of thousands of base pairs, provides more detail for scientists scouring the sequence for errors.

Not only is it easier to detect mutations that occur over a large piece of the genome, it is also much faster.

Now, the team is optimizing its system to reduce the time even further. Ashley believes they can still cut the time it takes in half.

Author: Rare Daily Staff