The Record Breakers
Euan Ashley and Team Crack Difficult Medical Cases with Rapid Gene Sequencing
When a three-month-old patient arrived at Stanford’s pediatric emergency department with epileptic seizures, the cause was a mystery. Standard diagnostic techniques like electroencephalography and magnetic resonance imaging of the brain gave few clues. An epilepsy gene panel had been ordered, but it could take two weeks to get results, with no guarantee of finding any significant variants.
That’s when Euan Ashley, MB ChB, DPhil, and his team went to work. Using nanopore genome sequencing, in just under eight and a half hours they made a definitive diagnosis of CSNK2B-related disorder, also known as Poirier–Bienvenu neurodevelopmental syndrome.
As reported in the New England Journal of Medicine, “This result halted further planned diagnostic testing, facilitated disease-specific counseling and prognostication, and aided in management of epilepsy by providing insight about reported seizure types and treatment response to common antiseizure medications.”
Another article, in Circulation: Genomic and Precision Medicine, describes how Ashley’s team used rapid genetic sequencing to determine within hours that 13-year-old Matthew Kunzman's heart failure was the result of a genetic condition. The finding enabled Matthew to receive a transplanted heart just three weeks later.
Solving medical mysteries is nothing new for Ashley, professor of cardiovascular medicine, of genetics, and of biomedical data science.
“That's very much how we view our work, particularly with undiagnosed diseases, because they’re very often mystery cases that have been going on for months or years that no one has been able to solve, and we use DNA sequencing to try to solve the case,” says the director of the Stanford Center for Inherited Cardiovascular Disease and one of the principal investigators at the Stanford Center for Undiagnosed Diseases, which is part of the Undiagnosed Diseases Network of the National Institutes of Health (NIH).
While solving medical mysteries using genome sequencing is very much what Ashley has been doing over the past several years, what’s novel about his recent work is the speed at which the sequencing can be performed.
“Some of our patients, especially little babies with really grave conditions in the critical care units of our hospitals, need answers faster than we can currently give them, and we can’t wait around for weeks for an answer. We want to get information in hours,” he says.
"These are often mystery cases that no one has been able to solve, and we use DNA sequencing to try to solve the case.
Finding answers fast depends on several factors, beginning with the old-fashioned process of drawing a sample of the patient’s blood in the critical care unit and getting that sample to the lab as soon as possible. Ashley’s team found a way to shave a few minutes even at that stage: Team lead and postdoctoral scholar John Gorzynski, DVM, PhD – who is an ultra endurance runner – volunteered to sprint from the patient's bedside to the lab carrying the vial of blood.
But technology is what’s really made the difference in getting answers quickly. In trying to expedite the process of genome sequencing, the team looked at how fast they could extract the DNA out of the blood, how fast they could get it onto the sequencer, and how fast the sequencing machine could analyze the data.
“Using a gene sequencer from Oxford Nanopore Technologies in England allows us to produce the data for an entire genome in one to two hours. The analysis of that data relies on computing power, and we devised hardware upgrades to get the data off of the sequencer and into the cloud (computer) as fast as possible. Because ultimately, we have to take that list of six billion data points in one genome, turn it into a list of four and a half million data points (which is the variations we each have from each other), and then finally condense it into a short list of 20 or 30 variants. Among that short list is the smoking gun for any individual patient,” Ashley explains.
As discussed in the sidebar, they have perfected their technique to the point of setting a record for fastest DNA sequencing.
High-throughput and the Heart
Ashley, a self-proclaimed “technology geek,” was drawn to medicine as the child of a doctor and a midwife. At age 16, he became fascinated with genetics while reading Richard Dawkins’s The Selfish Gene.
After completing medical school at the University of Glasgow and a medical residency and a doctorate in molecular physiology at the University of Oxford, Ashley came to Stanford in 2002 for a four-year fellowship in cardiovascular medicine.
“While Stanford was a mecca for computer science, back then not much was being done with high-throughput data. Little did I know that coming here would give me such an opportunity to combine my computer nerd personality and my fascination with the heart,” he confesses.
The timing couldn’t have been better for the physician with side interests in computers and genetics.
“Before this genome sequencing technology came along, genetic testing wasn't particularly relevant to cancer, cardiovascular disease, and other diseases responsible for the greatest number of deaths in our society. But when you sequence a genome, you get information about every single disease that there is. The accessibility of this information has had a huge impact on the diagnosis and treatment of the most common diseases in our society, and those are the diseases that the Department of Medicine treats,” he explains.
Among many colleagues, Ashley cites two in the Department of Medicine who have been particularly instrumental in his genomics work. Matthew Wheeler, MD, assistant professor of cardiovascular medicine, is Ashley’s “right hand” in the Center for Undiagnosed Diseases. Wheeler is another principal investigator and serves as the operational leader of the center.
Jason Hom, MD, clinical associate professor of internal medicine, also plays a major role at the center. “Of course, our team is diverse, and we have experts in genomics, bioinformatics, genetic counseling, and more. We also have one physician who sees most of the adult patients in the clinic, and Jason is that lead physician,” Ashley says.
Setting a World Record
Euan Ashley and his team of record-breakers. Photo by Steve Fisch.
It seems odd to include Guiness World Record and precision medicine in the same sentence, but Euan Ashley’s work has made that possible. On February 16, 2022, a representative from Guinness World Records came to Stanford to present a certificate attesting that:
The fastest DNA sequencing technique was achieved in 5 hr 2 min by Euan Ashley (USA and UK) and the ultra-rapid genome team at Stanford University, Stanford, California, USA on 16 March 2021. This record was validated with benchmarks from the Genome in a Bottle consortium, hosted by the National Institute of Standards and Technology. Euan and the ultra-rapid genome team sequenced a human genome using an Oxford Nanopore PromethIon-48 machine.
School of Medicine leadership has also shown great support for Ashley’s activities. When the NIH was making final decisions about which seven locations would serve as clinical sites in the Undiagnosed Diseases Network, School of Medicine Dean Lloyd Minor, MD, and Department of Medicine Chair Robert Harrington, MD, made presentations on behalf of Stanford. When a drop in funding from the NIH threatened a financial shortfall for the Center for Undiagnosed Diseases, the Department of Medicine contributed dollars and physical space to keep the program afloat.
In another show of support, the Department of Medicine enabled Ashley to create the Stanford Center for Inherited Cardiovascular Disease in 2009. In 2021, it became the first such center in the nation to use genome sequencing while continually searching for clues to the causes of patients’ heart diseases.
“In the past, we were limited by the genetic panels we could run as we sought integrated care for patients with inherited cardiovascular disease. But now we have a patient’s entire genome available. At first, we focus on the key genes that we understand today could cause the patient’s disease. But with the entire genome in their medical record now, if we need to go later to look at newly discovered genes for unsolved cases, there is no need for a new test: we already have the data,” Ashley says.
That work is having a positive effect in another area. Later in 2022, Stanford will be one of the first clinical centers in the nation to use genomics to help prevent disease.
“This is something Bob Harrington’s been a strong supporter of, and, along with two other broad categories of genomics, it is central to the Department of Medicine’s mission,” Ashley says, identifying the three categories as:
- "Undiagnosed or rare genetic disease, which is undifferentiated and could be any organ or any system. We use genomics to try to solve mystery disease.
- “Inherited heart diseases, which are often the cause of sudden death in families. We’re now using genomes in our clinical center here to diagnose diseases that are not quite as mysterious, because we can look at the heart and see that it looks abnormal, but the underlying molecular cause remains unknown. So, we use the genome for that.
- “Preventive genomics, where we use the genome to help us predict who is at risk for heart attack and implement individualized care to try to prevent future heart attacks on a broader scale.”
For the Patients and their Families
Ashley has said that by his teen years he was drawn to a career as a physician geneticist. But today, as an established expert in both fields, what drives his pursuit of the science of precision medicine? As he says in his book, The Genome Odyssey – Medical Mysteries and the Incredible Quest to Solve Them:
“Our patients and their families never escape what the genome brought to their lives, and we can never tire in our pursuit of understanding their genomes more fully, finding ways to treat their diseases more effectively, and, when our efforts fail, hugging them more tightly and assuring them that we will not rest until we come together upon a brighter day."