Studies could lead to new prognostic biomarkers and clinical laboratory diagnostics for cancer
Might fungi be involved in human cancers? Two separately published studies have found fungal DNA in various cancers in the human body. However, the researchers are unclear on how the fungi got into the cancer cells and if it is affecting the cancers’ pathology. Nevertheless, these discoveries could lead to utilizing tumor-associated fungal DNA as clinical laboratory diagnostics or prognostic biomarkers in the fight against cancer.
“The finding that fungi are commonly present in human tumors should drive us to better explore their potential effects and re-examine almost everything we know about cancer through a ‘microbiome lens,’” said Ravid Straussman, MD, PhD (above), a principal investigator at Weizmann Institute of Science and one of the authors of the study in a UCSD press release. These findings could lead to new clinical laboratory diagnostics and prognostic biomarkers. (Photo copyright: Weizmann Institute of Science.)
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Microbiome Key to Cancer Biology and Detection
To perform their research, the team examined 17,401 samples of patient tissues, blood, and plasma across 35 different types of cancers in four independent cohorts. They discovered fungal DNA and cells in low abundances in many human cancers.
“The existence of fungi in most human cancers is both a surprise and to be expected,” said biologist Rob Knight, PhD, founding Director of the Center for Microbiome Innovation and Professor of Pediatrics and Computer Science and Engineering at UC San Diego in a UCSD press release. “It is surprising because we don’t know how fungi could get into tumors throughout the body. But it is also expected because it fits the pattern of healthy microbiomes throughout the body, including the gut, mouth and skin, where bacteria and fungi interact as part of a complex community.”
The main highlights of this study include:
Fungi detected in the different cancer types were often intracellular.
Multiple fungal-bacterial-immune ecologies were detected across tumors.
Intratumoral fungi stratified clinical outcomes, including immunotherapy response.
Cell-free fungal DNA found in both healthy and cancer patients in early-stage disease.
Fungi found on the human body appear as either environmental fungi, such as yeasts and molds, and commensal fungi, which live either on or inside the body. Both are typically harmless to most healthy people and can provide some benefits, such as improving gut health, but they may also be a contributing factor in some disease.
The researchers found that there were notable parallels between specific fungi and certain factors, such as age, tumor subtypes, smoking status, immunotherapy responses, and survival measures.
“These findings validate the view that the microbiome in its entirety is a key piece of cancer biology and may present significant translational opportunities, not only in cancer detection, but also in other biotech applications related to drug development, cancer evolution, minimal residual disease, relapse, and companion diagnostics,” said Gregory Sepich-Poore, MD, PhD, one of the study’s authors and co-founder and chief analytics officer at biotechnology company Micronoma, in the UCSD press release.
New Clinical Laboratory Tests to Identify Fungal Species in Cancer
Researchers from Duke University and Cornell University uncovered compelling evidence of fungi in multiple cancer types and focused on a detected link between Candida and gastrointestinal cancers.
They found that “several Candida species were enriched in tumor samples and tumor-associated Candida DNA was predictive of decreased survival,” according to their paper.
Their analysis of multiple body sites revealed tumor-associated mycobiomes in fungal cells. The researchers found that fungal spores known as blastomyces were associated with tumor tissues in lung cancers, and that high rates of Candida were present in stomach and colon cancers.
The Duke/Cornell researchers hope their work can provide a framework to develop new tests that can distinguish fungal species in tumors and predict cancer progression and help medical professionals and patients chose the best treatment therapies.
“These findings open up a lot of exciting research directions, from the development of diagnostics and treatments to studies of the detailed biological mechanisms of fungal relationships to cancers,” said Iliyan Iliev, PhD, Associate Professor of Microbiology and Immunology in Medicine, Weill Cornell Medicine, and one of the authors of the study, in a Weill news release.
More research is needed to determine if fungal DNA plays a role in disease pathology or if its presence does not have any causal link.
“It’s plausible that some of these fungi are promoting tumor progression and metastasis, but even if they aren’t, they could be very valuable as prognostic indicators,” Iliev said.
The insights gleaned from these two studies will be of particular interest to microbiologists, clinical laboratory professionals, and anatomic pathologists. Additional research could answer questions about how and if fungi infect tumors and if such fungi is a factor that increases cancer risk and outcomes.
Technologies developed by Pääbo to sequence Neanderthal DNA are being widely used in many clinical laboratory settings, including to study infectious disease outbreaks
Pääbo is considered to be the founder of paleogenetics. This field of science studies the past through examination of preserved genetic material found in remains of ancient organisms. It was his development of pioneering technologies that allowed for the genomic sequencing of Neanderthal DNA.
“[Pääbo’s] work has revolutionized our understanding of the evolutionary history of modern humans,” said German electrochemist Martin Stratmann, PhD, President of the Max Planck Society for the Advancement of Science (MPG), in a press release. “Svante Pääbo, for example, demonstrated that Neanderthals and other extinct hominids made a significant contribution to the ancestry of modern humans.”
“The thing that’s amazing to me is that you now have some ability to go back in time and actually follow genetic history and genetic changes over time,” Svante Pääbo, PhD (above), director of the Max Planck Institute for Evolutionary Anthropology, stated in a news conference, Reuters reported. “It’s a possibility to begin to actually look on evolution in real time, if you like.” Development of modern clinical laboratory techniques for identifying and tracking disease outbreaks have already evolved due to these findings. (Photo copyright: Max Planck Institute for Evolutionary Anthropology.)
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Comparing Neanderthal DNA to That of Modern Humans
Back in the mid-1990s, Pääbo and a team of researchers decoded relatively short fragments of mitochondrial DNA of a Neanderthal male. They discovered through their analysis that the DNA from the Neanderthal varied considerably from the genome of contemporary humans. This validated the belief that modern humans are not direct descendants of the Neanderthals.
Pääbo’s research team found nearly all (99.9%) of the Neanderthal DNA they studied to be heavily colonized by bacteria and fungi. That required them to create solutions for assembling the short components of mitochondrial DNA like a huge puzzle.
To accomplish this, the team had to:
Work under clean room conditions to prevent the accidental introduction of their own DNA into their experiments.
Establish more efficient extraction methods to enhance the output of Neanderthal DNA.
Generate complex computer programs that could compare the ancient DNA fragments with reference genomes of both humans and chimpanzees.
“Neanderthals are the closest relatives of humans today” said Pääbo in the press release. “Comparisons of their genomes with those of modern humans and with those of apes enable us to determine when genetic changes occurred in our ancestors. In the future, it could also be clarified why modern humans eventually developed a complex culture and technology that enabled them to colonize almost the entire world.”
Pääbo’s team succeeded in reconstructing their first version of the Neanderthal genome in 2010. Their comparisons between the genomes of Neanderthal and modern humans proved that the two groups had produced common offspring about 50,000 years ago and that this genetic contribution did influence human evolution.
The genome of modern non-African people still contains about 2% Neanderthal DNA.
“We have found around 30,000 positions in which the genomes of almost all modern humans differ from those of Neanderthals and great apes,” Pääbo added. “They answer what makes anatomically modern humans ‘modern’ in the genetic sense as well. Some of these genetic changes may be the key to understanding what distinguishes the cognitive abilities of today’s humans from those of now extinct hominids.”
Those with Neanderthal DNA More Susceptible to Severe COVID-19 Infection
Pääbo’s research also found that Neanderthal DNA may have affected the immune systems of modern people. During the COVID-19 pandemic, his work verified that individuals who carry a gene variant inherited from Neanderthals are more prone to severe forms of the illness than those who do not have that gene variant.
“We can make an average gauge of the number of the extra deaths we have had in the pandemic due to the contribution from the Neanderthals,” Pääbo said in a 2022 lecture, Reuters reported. “It is quite substantial, it’s more than one million extra individuals who have died due to this Neanderthal variant that they carry.”
Pääbo’s research team continues to develop new methods for reconstructing DNA fragments that are even more biodegraded, and which present in smaller amounts. Their ultimate goal is to investigate even older DNA and genetic material that is scarce due to climate conditions.
The DNA technologies pioneered by Pääbo to sequence Neanderthal DNA are being used widely in many clinical laboratory and research settings today. They include forensic science and the ability to collect DNA from human remains hundreds of years old to identify infectious disease outbreaks and study how today’s human genome has adopted new mutations.
Judge will decide the restitution Holmes must pay to defrauded Theranos investors at future court date; Ex-COO Ramesh “Sunny” Balwani to be sentenced next month
Clinical laboratory leaders and anatomic pathologists who closely followed the fraud trial of Elizabeth Holmes may have wondered how the Theranos founder and ex-CEO would be punished for her crimes. Now we know.
Late into the four-hour sentencing hearing, Holmes tearfully spoke, according to a twitter post by NBC reporter Scott Budman, who was in the courtroom. “I am devastated by my failings,” Holmes said. “I have felt deep pain for what people went through because I have failed them … To investors, patients, I am sorry.”
Davila ordered Holmes to surrender to authorities on April 27 to begin her time behind bars. She is free until that time. Her upcoming prison term caps off one of the biggest downfalls ever of an American entrepreneur.
Elizabeth Holmes (above), founder and former CEO of Theranos, the now defunct clinical laboratory company, as she enters the federal courthouse in San Jose, Calif., prior to her sentencing on Friday. In January, Holmes was convicted on three counts of wire fraud and one count of conspiracy. Last summer, Theranos’ former CLIA laboratory director, pathologist Adam Rosendorff, MD, expressed remorse over his testimony which led to Holmes’ defense team requesting a new trial. The judge denied that request and allowed the sentencing of Holmes to proceed as scheduled. (Photo copyright: Jim Wilson/The New York Times.)
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Defense Lawyers Plan to Appeal
Dean Johnson, JD, a California criminal defense lawyer, told NBC Bay Area News during live coverage of the hearing on Friday that Holmes’ defense team will appeal her conviction.
“I have no doubt there will be an appeal in this case,” Johnson said.
Judge Edward Davila, who oversaw Holmes’ trial and sentencing hearing in US District Court in San Jose, Calif., estimated that the total loss for Theranos investors was $121 million. Investors had committed funds to support the company’s flawed Edison blood testing technology. A separate restitution hearing for Holmes will be scheduled for a later date.
Beyond the sentencing, Holmes, 38, will be saddled by infamy for the rest of her life, with her past reputation as a charismatic innovator ruined.
“The judge [said] evidence shows Elizabeth Holmes was leader of the company, but not necessarily the leader of the criminal acts,” Budman tweeted. Those words clearly pointed to Balwani, who Holmes’ defense team had painted as exerting control over her and the company.
Prosecutors Sought a Stiffer Sentence for Holmes
Prosecutors had asked Davila to sentence Holmes to 15 years in prison, arguing that her conviction represented “one of the most substantial white collar offenses Silicon Valley or any other district has seen,” according to NBC Bay Area News, which cited court documents. The government also wanted her to pay $803 million in restitution.
Holmes’ defense team, however, wished for no prison time at all, instead asking that Holmes serve time under house arrest. “If a period of confinement is necessary, the defense suggests that a term of 18 months or less, with a subsequent supervised release period that requires community service, will amply meet that charge,” her lawyers wrote in a court filing.
Prior to the sentencing, Davila received 130 letters supporting Holmes and asking for leniency, NPR reported. Among them was a note from William “Billy” Evans, Holmes’ partner.
“If you are to know Liz, it is to know that she is honest, humble, selfless, and kind beyond what most people have ever experienced,” Evans wrote, NPR reported. “Please let her be free.”
Holmes and Evans have a 16-month-old son together, and she is pregnant with the couple’s second child. Her first pregnancy caused her trial to be rescheduled. Prior to last week’s sentencing, some reporters covering the trial speculated that because Holmes was the mother of an infant—and now pregnant again—the judge might be more lenient in sentencing. The 11-year, four-month sentence indicates that the judge was not much influenced by that factor.
Last Minute Pitch for New Trial Failed
Holmes’ legal wranglings continued until the very end.
However, Rosendorff later told the court that he stood by his testimony about problems with Theranos’ blood testing technology.
In denying the request for a new trial, Davila wrote, “The court finds Dr. Rosendorff’s statements under oath to be credible,” according to The Washington Post.
From Teen Founder to Disgraced Entrepreneur
Holmes founded Theranos in 2003 at age 19 while she was attending Stanford University as a chemical engineering major. She dropped out of Stanford as a sophomore to focus on her new company.
Theranos claimed its technology—known as Edison—could perform diagnostics tests using a finger prick and a micro-specimen vial instead of a needle and several Vacutainers of blood. The company said it could return results to patients and clinicians in four hours for about half of the cost of typical lab test fees.
However, the promise of this technology began to unravel in 2015 following an investigative article by The Wall Street Journal that revealed the company ran only a handful of tests using its technology, instead relying on traditional testing for most of its specimen work.
Following The Journal’s exposé, the Centers for Medicare and Medicaid Services (CMS) sanctioned Theranos and Holmes in 2016. Meanwhile, the US Securities and Exchange Commission (SEC) investigated Holmes for raising hundreds of millions from investors by exaggerating or making false statements about the company’s technology and financial performance.
In 2018, the US Department of Justice (DOJ) indicted Holmes and Balwani, and Theranos closed shortly after.
Fortunately, the Theranos saga has not stunted investment in healthcare technology startups. Spending was in the tens of billions in 2021, although that number has dropped this year as the COVID-19 pandemic has waned, according to TechCrunch. Nevertheless, it is safe to assume that healthcare tech investors are scrutinizing scientific data from startups more thoroughly because of the Theranos fraud case.
Meanwhile, the saga of Theranos continues to leave a bad taste in the mouths of many clinical laboratory managers and pathologists. That’s because, during the peak period of adulation and spectacular news coverage about Elizabeth Holmes and her plans to totally disrupt the clinical laboratory industry, hospital and health system CEOs believed that they would be able to downsize their in-house medical laboratories and obtain lab tests from Theranos at savings of 50% or more. Consequently, during the years 2013 through the end of 2015, some hospital lab leaders saw requests for capital investment in their labs denied or delayed.
One example of how hospital CEOs embraced news of Theranos’ blood testing technology took place at the Cleveland Clinic. Elizabeth Holmes did such a good job selling the benefits of the Edison technology, then-CEO, Toby Cosgrove, MD, placed Theranos at number three on its list of top ten medical innovations for 2015.
In later years, Cosgrove admitted that no one at Cleveland Clinic or its pathologists were allowed to examine the analyzers and evaluate the technology.
It was for these reasons that the demise of Theranos was welcomed by many hospital lab administrators and pathologists. The fact that two of Theranos’ senior executives have been convicted of fraud validates many of the serious concerns that medical laboratory professionals had at that time, but which most major news reporters and media ignored and failed to report to the public.
Epidemiologists warn that elderly and other individuals may be at high-risk for co-infection by strains of both SAR-CoV-2 and influenza
As of October, the influenza (flu) season has begun in North America. With the COVID-19 pandemic still prevalent, clinical laboratories must be prepared not only for increased demand for SARS-CoV-2 tests, but also for an increased number of orders for flu tests as well. In fact, virologists are sounding the alarm that some patients may present with an uncommon double infection of both viruses.
The potential for contracting the co-infection was dubbed “flurona” by the Israeli Outbreak Management Advisory Team in 2020. The Israeli Team coined the term flurona to describe the potential of contracting both COVID-19 and influenza after two young Israeli pregnant women were diagnosed with influenza and COVID-19. Since then, cases of co-infections have been confirmed in multiple countries around the world, according to The Washington Post.
The symptoms of influenza and COVID-19 are extremely similar. According to the Centers for Disease Control and Prevention (CDC), symptoms for both influenza and COVID-19 include fever, cough, chills, sore throat, and body aches. However, without a clinical laboratory test it is nearly impossible to distinguish one virus from the other.
Therefore, during this cold and flu season, clinical laboratory testing will be extremely important. And though co-infection with COVID-19 and the flu is rare, lab leaders should be on the lookout for spikes in testing.
“Co-infection is rare with COVID-19 and the flu, or COVID-19 and other types of infections that you might get as far as upper respiratory infections, because COVID-19 tends to take over,” Stephen McMullan, MD, a Mayo Clinic family medicine physician, told Mayo Clinic News. “Once COVID-19 is in your body, it’s going to be the predominant virus, but there are some rare cases where we have seen people getting both COVID-19 and the flu. So, it is possible, but it’s certainly not common.” Clinical laboratories should prepare for a spike in viral infections this winter that could indicate flurona. (Photo copyright: Mayo Clinic.)
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What Exactly Is a Flurona?
Although it is possible—albeit rare—to contract the flu and COVID-19 at the same time, flurona does not appear to be a “twindemic,” nor is it a distinct disease or a mutation of the two viruses, The Washington Post reported.
“The name seems to suggest that the viruses have somehow combined—and that’s not the case. It’s just that a person may get infected with two respiratory viruses at the same time or in short succession,” epidemiologist Judith O’Donnell, MD, Director, Department of Infection Prevention and Control, and Section Chief, Division of Infectious Diseases at Penn Presbyterian Medical Center, told an NPR affiliate in Pittsburg.
“It’s rare, but it’s not surprising that during a typical influenza season—which here in the northern hemisphere is right now during the winter months—that you will see multiple respiratory viruses circulating at the same time, and that people can get infected with more than one respiratory virus at the same time,” she added.
Though flurona may not be a hybrid virus, that does not mean it is of no concern.
“Although a low proportion of COVID-19 patients have influenza co-infection, the importance of such co-infection, especially in high-risk individuals and the elderly, cannot be ignored,” wrote the authors of a study published in Frontiers of Medicine titled, “COVID-19 and Influenza Co-infection: A Systematic Review and Meta-Analysis.”
Did COVID-19 Lockdowns, Social Distancing Cause Flurona?
According to the Washington Post, the US had record lows of influenza during the 2020-2021 flu season, however this was likely due to lockdown measures. With lockdown measures and social distancing even less prevalent this flu season, there is a risk of individuals being at risk for multiple respiratory viruses.
“We’re all a little bit more back together than we were a year ago,” McMullan told Mayo Clinic News. “The kids are back in school, and we have more events that people are attending, which could explain why we’re seeing flu cases rise.”
Thus, clinical laboratories should prepare for not only a higher number of flu tests, but also COVID-19 tests as well. That is because patients will not be able to distinguish which virus they are sick with based on symptoms alone. Further, because COVID-19 and the flu have similar symptoms, individuals may seek out multiple tests, or test for one virus and not the other.
McMullan asserts that a co-infection of the flu and COVID-19—though rare—is not impossible. For the best chance to avoid both diseases he suggests high-risk individuals “Get vaccinated against COVID-19, including your booster if eligible, and make sure to get your flu vaccine, continue to do the same strategies to protect yourself and others, such as wearing a mask in high-risk situations, washing your hands, and staying home if you feel ill.”
Meanwhile, clinical laboratory managers will want to track developments during this flu season. For example, flurona may be uncommon at this time, but emerging variants of SARS-CoV-2 and different strains of influenza might increase the number of patients diagnosed as infected with both COVID-19 and influenza.
As the number of Hospital at Home programs increase, clinical laboratories will want to develop programs for collecting samples from patients where they live
Shortages of nurses and hospital staff, combined with pressure to lower the cost of care, are encouraging more institutions to implement hospital-in-the-home programs. One such project involves Oregon Health and Science University (OHSU), which last November began a Hospital at Home (HaH) program that enables certain patients to receive hospital-level care in the comfort of their own homes. Clinical laboratories servicing these programs will need to develop specimen collection and testing services in support of these patients.
The OHSU program can provide healthcare for eight patients simultaneously, and it has treated more than 100 patients at home since its inception. Although this number is only a small segment of OHSU’s 576 bed capacity, it does affect the overall healthcare provided by the hospital.
Under the program, basic services, such as the monitoring of vital signs—as well as some clinical laboratory work and routine imaging studies—are performed in the patient’s home. Individuals are transported to OHSU for more complex imaging or other procedures.
“Every patient we have in Hospital at Home is one who is not waiting in the emergency room or a hallway for a bed to become available in the hospital,” said Matthias Merkel, MD, PhD (above), Senior Associate Chief Medical Officer, Capacity Management and Patient Flow at OHSU, in a press release. In the same way clinical laboratories support telehealth programs, medical laboratories will need procedures for collecting specimens and testing patients participating in Hospital at Home programs as well. (Photo copyright: Oregon Health and Science University.)
OHSU’s HaH program utilizes advances in technology to connect at-home patients with physicians and nurses around the clock via a smart tablet. In addition, participating patients receive real-time monitoring and at least two daily in-person visits from nurses and paramedics that have been contracted by OHSU.
“It’s a better experience for patients, plus it increases our system’s capacity to provide care for all the people who need it,” said Darren Malinoski, MD, Chief Clinical Transformation Officer and Professor of Surgery at OHSU in the press release. “It allows us to make good on our promise to take care of the state as best we can.”
The current eligibility criteria to participate in OHSU’s Hospital at Home program include:
Patient must be over the age of 18.
Patient’s primary residence must be within a 25-mile radius of the OHSU hospital.
Inpatient hospitalization is initially required.
Patient must have a diagnosis that can be managed remotely, such as COVID-19, pneumonia, cellulitis, congestive heart failure, urinary tract infections, or pyelonephritis.
Malinoski feels that OHSU’s HaH program is ready to expand. In fact, he is so confident in it he enrolled his own 83-year-old mother as one of its first patients. While undergoing treatment for lung cancer, a routine clinical checkup exposed evidence of toxicity in her blood. Typically, she would have been directly admitted to the hospital for monitoring, but instead she was entered into the HaH program.
“It was unbelievable,” stated Lesley Malinoski in the press release. “I had the feeling of being well taken care of. I was in my own home. I could cook, I could rest—anything I wanted and still have all this care.”
“They didn’t just come in and run out,” she continued. “I felt like a celebrity.”
HaH programs around the country were made possible through a federal waiver granted by the federal Centers for Medicare and Medicaid Services (CMS) in November 2020 in response to the COVID-19 pandemic.
According to the American Hospital Association (AHA), “this care delivery model has been shown to reduce costs, improve outcomes, and enhance the patient experience.”
Prior to the waiver, there were only about two dozen hospitals across the US that had HaH programs. However, as of May 20, 2022, 227 hospitals in 35 states had received a HaH waiver from CMS. This number represents nearly 4% of all hospitals in the country, according to Health Affairs.
In “Two US Studies Show Home-based Hospital Care Lowers Costs while Improving Outcomes and Patient Satisfaction,” we reported on a hospital-based home care program that involved 323 patients at Presbyterian Healthcare Services in Albuquerque, N.M. We surmised that significant growth in the number of patients treated in home-based hospital care programs would directly affect hospital-based clinical laboratories and pathology groups. Among other things, it would reduce the volume of inpatient testing while increasing the number of outpatient/outreach specimens.
And in “Australia’s ‘Hospital in the Home’ Care Model Demonstrates Major Cost Savings and Comparable Patient Outcomes,” Dark Daily saw that wider adoption of that country’s Hospital in the Home (HITH) model of patient care would directly affect pathologists and clinical laboratory managers who worked in Australia’s hospital laboratories. We reported that more HITH patients would increase the need to collect specimens in patient’s homes and transport them to a local clinical laboratory for testing, and that because they are central to the communities they serve, hospital-based medical laboratories would be well-positioned to provide this diagnostic testing.
OHSU’s overall experience with their Hospital at Home program demonstrates that such a model can be a highly successful and cost-effective method of providing patient care. It is probable that in the future, more medical institutions will create similar programs in an effort to effectively serve as many patients as possible while ensuring shorter hospital stays and rendering better healthcare outcomes. As this happens, it will give hospital-based medical laboratories an opportunity to deliver value in home-based patient care.
And in less than eight hours, they had diagnosed a child with a rare genetic disorder, results that would take clinical laboratory testing weeks to return, demonstrating the clinical value of the genomic process
In another major genetic sequencing advancement, scientists at Stanford University School of Medicine have developed a method for rapid sequencing of patients’ whole human genome in as little as five hours. And the researchers used their breakthrough to diagnose rare genetic diseases in under eight hours, according to a Stanford Medicine news release. Their new “ultra-rapid genome sequencing approach” could lead to significantly faster diagnostics and improved clinical laboratory treatments for cancer and other diseases.
“A few weeks is what most clinicians call ‘rapid’ when it comes to sequencing a patient’s genome and returning results,” said cardiovascular disease specialist Euan Ashley, MD, PhD (above), professor of medicine, genetics, and biomedical data science, at Stanford University in the news release. “The right people suddenly came together to achieve something amazing. We really felt like we were approaching a new frontier.” Their results could lead to faster diagnostics and clinical laboratory treatments. (Photo copyright: Stanford Medicine.)
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Need for Fast Genetic Diagnosis
In their NEJM paper, the Stanford scientists argue that rapid genetic diagnosis is key to clinical management, improved prognosis, and critical care cost savings.
“Although most critical care decisions must be made in hours, traditional testing requires weeks and rapid testing requires days. We have found that nanopore genome sequencing can accurately and rapidly provide genetic diagnoses,” the authors wrote.
To complete their study, the researchers sequenced the genomes of 12 patients from two hospitals in Stanford, Calif. They used nanopore genome sequencing, cloud computing-based bioinformatics, and a “custom variant prioritization.”
Their findings included:
Five people received a genetic diagnosis from the sequencing information in about eight hours.
Diagnostic rate of 42%, about 12% higher than the average rate for diagnosis of genetic disorders (the researchers noted that not all conditions are genetically based and appropriate for sequencing).
Five hours and two minutes to sequence a patient’s genome in one case.
Seven hours and 18 minutes to sequence and diagnose that case.
How the Nanopore Process Works
To advance sequencing speed, the researchers used equipment by Oxford Nanopore Technologies with 48 sequencing units called “flow cells”—enough to sequence a person’s whole genome at one time.
The Oxford Nanopore PromethION Flow Cell generates more than 100 gigabases of data per hour, AI Time Journal reported. The team used a cloud-based storage system to enable computational power for real-time analysis of the data. AI algorithms scanned the genetic code for errors and compared the patients’ gene variants to variants associated with diseases found in research data, Stanford explained.
According to an NVIDIA blog post, “The researchers accelerated both base calling and variant calling using NVIDIA GPUs on Google Cloud. Variant calling, the process of identifying the millions of variants in a genome, was also sped up with NVIDIA Clara Parabricks, a computational genomics application framework.”
Rapid Genetic Test Produces Clinical Benefits
“Together with our collaborators and some of the world’s leaders in genomics, we were able to develop a rapid sequencing analysis workflow that has already shown tangible clinical benefits,” said Mehrzad Samadi, PhD, NVIDIA Senior Engineering Manager and co-author of the NEJM paper, in the blog post. “These are the kinds of high-impact problems we live to solve.”
In their paper, the Stanford researchers described their use of the rapid genetic test to diagnose and treat an infant who was experiencing epileptic seizures on arrival to Stanford’s pediatric emergency department. In just eight hours, their diagnostic test found that the infant’s convulsions were attributed to a mutation in the gene CSNK2B, “a variant and gene known to cause a neurodevelopmental disorder with early-onset epilepsy,” the researchers wrote.
“By accelerating every step of this process—from collecting a blood sample to sequencing the whole genome to identifying variants linked to diseases—[the Stanford] research team took just hours to find a pathogenic variant and make a definitive diagnosis in a three-month-old infant with a rare seizure-causing genetic disorder. A traditional gene panel analysis ordered at the same time took two weeks to return results,” AI Time Journal reported.
New Benchmarks
The Stanford research team wants to cut the sequencing time in half. But for now, the five-hour rapid whole genome sequence can be considered by clinical laboratory leaders, pathologists, and research scientists a new benchmark in genetic sequencing for diagnostic purposes.
Stories like Stanford’s rapid diagnosis of the three-month old patient with epileptic seizures, point to the ultimate value of advances in genomic sequencing technologies.
