NIH program could lead to new diagnostic biomarkers for clinical laboratory tests across a more diverse segment of US population
In another milestone in the US National Institutes of Health’s (NIH) plan to gather diverse genetic information from one million US citizens and then use that data to inform clinical care in ways consistent with Precision Medicine, the NIH’s All-of-Us Research Program announced in a news release it has “begun returning personalized health-related DNA results” to more than 155,000 study participants.
In addition, those participants who request them will receive genetic reports that detail whether they “have an increased risk for specific health conditions and how their body might process certain medications.”
The All-of-Us program, which began enrolling people in 2018, is one of the world’s largest—if not the largest—project of its kind. It could result in more than a million human whole genome sequences to drive medical research and speed discoveries. Study findings, for example, may produce new biomarkers for clinical laboratory tests and diagnostics.
In 2020, the All-of-Us program “had begun releasing genetic results for ancestry and a small number of nonclinical genetic traits,” according to GenomeWeb. Now, the program is taking on the greater challenge of sharing health-related genetic test results directly with its participants.
“We really wanted to make sure that we are providing a responsible return to our participants,” Anastasia Wise, PhD, All-of-Us Program Director for the Genetic Counseling Resource, told GenomeWeb. “They might get information that’s unexpected,” she explained.
So far, about 10,000 people received the NIH’s invitation and 56% have shown interest in receiving their genetic test results, GenomeWeb noted.
“Knowledge is powerful,” said Josh Denny, MD (above), Chief Executive Officer, NIH All-of-Us Research Program, in an NIH news release. “By returning health-related DNA information to participants, we are changing the research paradigm, turning it into a two-way street—fueling both scientific and personal discovery that could help individuals navigate their own health,” he added. The NIH’s research could lead to new clinical laboratory precision medicine diagnostics for chronic diseases across a more diverse segment of the US population. (Photo copyright: National Institutes of Health.)
Two Types of Genetic Health Reports
Study participants who provided a blood sample and gave their consent to receiving genomic information may also receive a Hereditary Disease Risk report that includes 59 genes and genetic variants linked to serious and “medically actionable” health conditions.
About 3% to 5% of participants will have findings suggesting a high risk for a genetic disease such as breast and ovarian cancers as indicated by BRCA1 and BRCA2 genes, Medical Xpress reported.
“I kind of shudder to think about what could happen if I hadn’t known this [finding that she has the BRCA2 gene],” said Rachele Peterson, All-of-Us Chief of Staff, who spoke to the Associated Press about her receiving own Hereditary Disease Risk report.
Participants can also choose to receive an All-of-Us Medicine and Your DNA report with insights on seven genes that affect how specific medications are metabolized. This pharmacogenetics report is important for those who could learn, for example, that they have a 50% to 60% greater risk of a second heart attack when they continue to take the standard medication, as opposed to a different medication, Medical Xpress noted.
“The information on metabolizing medication can be particularly important for people who need treatment after a heart attack,” Josh Denny, MD, Chief Executive Officer, NIH All-of-Us Research Program, told Medical Xpress.
“Such transparency of genetic information about a massive group—as well as the genetic information on individuals—can be used to improve patient care and clinical outcomes,” said Robert Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report.
“The program provides a roadmap for other healthcare organizations to follow. And this is useful strategic knowledge for clinical laboratory leaders to understand and incorporate into their plans to support precision medicine with genetic testing and whole human genome sequencing,” Michel added.
Rich Genetic Data Across a More Diverse Population
As to its goal to reflect national diversity, NIH reported about 80% of All-of-Us participants reside in communities that have been unrepresented in medical research, and that 50% are part of a racial or ethnic minority group.
By combining this information into a single database, the MVP promises to advance knowledge about the complex links between genes and health, according to an MVP news release.
Researchers tapping All-of-Us and MVP data may ultimately produce enlightening and impactful study findings, which could enable clinical laboratories to perform new diagnostic precision medicine tests that identify diseases early and save lives.
Clinical laboratory scientist who aided in the investigation compared DNA test results with publicly available genetic information
In an interesting twist in the solving of crime, genetic test results—along with help from a clinical laboratory scientist (CLS) turned amateur genealogist—guided relatives of Melissa Highsmith to her whereabouts after she was allegedly kidnapped as a toddler over half a century ago. According to The Guardian, the CLS helped locate Melissa by “interpreting the key DNA results and mining publicly available records.”
Highsmith’s abduction was one of the oldest missing person cases in the country and demonstrates how clinical laboratory skills can be applied outside the laboratory to help solve other problems—in this case, helping a family search for a kidnapped daughter—using genetic testing technologies that until recently were not available to the general public.
Thanks to a 23andMe at-home DNA test—and a tenacious clinical laboratory scientist/amateur genealogist—Melissa Highsmith (shown above at time of kidnapping and today) has been reunited with her birth family. This shows how genetic testing is being used in remarkable ways outside of the clinical laboratory. (Photo copyright: Highsmith family/People.)
Thanksgiving Reunion
Back in 1971, Melissa’s mother, Alta Apantenco, placed an advertisement in a local newspaper in Fort Worth, Texas, to hire a babysitter to care for her 21-month-old daughter. Apantenco hired Ruth Johnson to babysit her daughter without meeting the woman in person. Because Apantenco had to be at work, the child was handed over to Johnson by Apantenco’s roommate. The babysitter then allegedly abducted Melissa and disappeared with her.
Melissa’s family reported her missing to the police and searched for the snatched baby for more than 51 years. The family even organized a Facebook page called “Finding Melissa Highsmith” and sought outside assistance from the National Center for Missing and Exploited Children (NCMEC) in locating their lost relative, according to the New York Post.
The police and the FBI also got involved in the case, but few leads emerged over the decades.
Then, in September of 2022, Melissa’s family received a new lead regarding her location based on her father’s 23andMe DNA test results. Those results, along with a birthmark and date of birth, confirmed that Melissa was alive and well and residing in the Charleston, South Carolina area.
Over Thanksgiving weekend, Melissa was reunited with her mother, her father Jeffrie Highsmith, and two of her four siblings at a church in Fort Worth. She hopes to meet her remaining two siblings over the Christmas holidays.
“I can’t describe my feelings. I’m so happy to see my daughter that I didn’t ever think I would see again,” Apantenco told Saint Paul, Minnesota, television station KSTP.
“I couldn’t stop crying,” said Melissa’s sister Victoria Garner in a family statement. “I was overjoyed, and I’m still walking around in a fog trying to comprehend that my sister [was] right in front of me and that we found her,” The Guardian reported.
Clinical Laboratory Scientist Aids in the Investigation
The 23andMe test results alerted the family to the existence of a few unknown relatives that could be connected to the DNA of Melissa’s father. The family then contacted a genealogist and clinical laboratory scientist from Minnesota named Lisa Jo Schiele to help them interpret the results and potentially locate the missing woman. Schiele compared the DNA results with public records to help find Melissa Highsmith.
“I was able to use what we call traditional genealogy to find marriage records and things like that to find where Melissa was right now,” Schiele told KSTP. “At first glance, you look at these matches, but I’m like, ‘Holy cow, is this too good to be true?’ I’m very happy to help them navigate all of this.”
One of Melissa’s sisters, Sharon Highsmith, stated that her mother experienced deep feelings of guilt after Melissa’s abduction and had even faced accusations that she had something to do with the disappearance of her daughter.
“My mom did the best she could with the limited resources she had. She couldn’t risk getting fired, so she trusted the person who said they’d care for her child,” Sharon said in a family statement. “I’m grateful we have vindication for my mom,” The Guardian reported.
“I keep having to pinch myself to make sure I’m awake,” Melissa, who now resides in Fort Worth, told KSTP.
“It’s a miracle,” Apantenco said.
“A Christmas miracle,” Melissa added.
Due to the statute of limitations, which expired 20 years after Melissa turned 18, the babysitter who allegedly took Melissa cannot be criminally prosecuted.
“I’m angry our family was robbed for 51 years,’’ Melissa told Fort Worth news station WFAA.
This remarkable story illustrates how clinical laboratory skills combined with genetic testing results can be used outside of medical laboratory testing purposes to aid in solving criminal cases and other mysteries involving missing people.
Further advances in DNA testing combined with genetic databases that include DNA from greater numbers of people could result in more reunions involving missing persons who were identified because of genetic matching.
Researchers at the university suggested their findings could lead to new genetic tests that could be offered by medical laboratories
New research conducted at the University of Utah suggests that clinical laboratories may someday be able to deploy genetic tests to indicate whether a couple has a higher-than-average risk of stillbirth.
This is yet another example of how researchers are cracking DNA’s code to understand how certain gene variants may affect the healthcare of offspring. The knowledge produced by this research, as confirmed by additional studies, may lead to genetic markers that medical laboratories can use to diagnose the risk of stillbirth using the parent’s DNA.
“Stillbirth is one of those problems that is so tragic and life-changing,” said study co-author Jessica Page, MD (above). “It is especially frustrating when you don’t have a good answer for why it happens. This knowledge may give us the opportunity to change how we risk stratify people and reduce their risk through prevention.” Should this research be validated, clinical laboratories may soon have new genetics tests to help doctors identify risk for stillbirth. (Photo copyright: Intermountain Healthcare.)
Can Stillbirth be Prevented?
Jessica Page, MD, an assistant professor in the Department of Obstetrics and Gynecology at the University of Utah School of Medical and co-author of the 2022 study, was lead author of a 2018 study that estimated nearly one-fourth of stillbirths are preventable.
“Stillbirth rate reduction has been slow in the US and we think many stillbirths may be potentially preventable,” she said in a university press release. “This is motivating us to look for those genetic factors so we can achieve more dramatic rate reduction.”
According to the press release, the University of Utah researchers found that stillbirth “can be inherited and tends to be passed down through male members of the family. That risk preferentially comes from the mother’s or father’s male relatives—their brothers, fathers, grandfathers, uncles, or male cousins. But the odds of a couple losing a baby to stillbirth are even greater when the condition comes from the father’s side of the family.”
The researchers made this discovery by analyzing data from the Utah Population Database (UPDB), which contains information on eight million people who were born in the state or have other connections there. The database is maintained by the Huntsman Cancer Institute at the University of Utah. It includes genealogical information and health records that allowed the researchers to trace incidence of stillbirths across multiple generations of families.
The researchers examined 9,404 stillbirth cases between 1978 and 2019, along with 18,808 live births that served as controls. They identified 390 multi-generational families with high numbers of stillbirths. Within that group, they looked at incidence of stillbirth among first-, second-, and third-degree relatives of stillborn babies. They then compared those numbers with data from unaffected families.
“We were able to evaluate multigenerational trends in fetal death as well as maternal and paternal lineages to increase our ability to detect a familial aggregation of stillbirth,” said genetic epidemiologist Tsegaselassie Workalemahu, PhD, lead author of the study. “Not many studies have examined inherited genetic risk for stillbirth because of a lack of data. The Utah Population Database allows for a more rigorous evaluation than has been possible in the past.”
Workalemahu described the research as “an important step toward identifying specific genes that increase the risk of stillbirth, which could one day lead to better diagnosis and prevention,” according to the university press release.
One caveat, the press release notes, is that Utah’s population is disproportionately of northern European descent. “Future studies will need to determine whether the trends hold true among people of different races and ethnicities,” it stated.
Call for More Testing
The University of Utah study is part of a larger effort to gain a greater understanding of the causes of stillbirths.
The story notes that “more than 20,000 pregnancies in the US end in stillbirth,” and in one in three of those cases, the cause is not determined.
Drucilla Roberts, MD, an obstetric and perinatal pathologist at Massachusetts General Hospital (MGH), told ProPublica that at a minimum, “the placenta should definitely be evaluated in every stillbirth.” But citing CDC data, the story notes that this is done in only 65% of stillbirths, and autopsies are performed in less than 20%.
“Experts blame the low rates on several factors,” the story states. “Because an autopsy often is performed in the days following a stillbirth, doctors and nurses have to ask families soon after they receive news of the death if they would like one. Many families can’t process the loss, let alone imagine their baby’s body being cut open. What’s more, many doctors aren’t trained in the advantages of an autopsy, or in communicating with parents about the exam.”
One consequence, ProPublica notes, is that clinicians are ill-equipped to advise patients on how to reduce risk in future pregnancies. The story describes the case of Karen Gibbins, MD, a maternal-fetal medicine specialist and an assistant professor of obstetrics and gynecology at the Oregon Health and Science University (OHSU) in Portland.
An Opportunity for Pathologists
Gibbins’ son was stillborn in 2018. She asked for an autopsy and learned that her son “had a rare disease caused by her antibodies attacking the cells in his liver,” the story states. When she became pregnant again, her doctor prescribed antibody infusions and she later gave birth to a healthy son. “If we had not had that autopsy, my third child would have died as well,” she told ProPublica.
This parent’s comment about the value of the autopsy done after her son’s stillbirth identifies an opportunity for the pathology profession. For several decades, health plans have become ever more reluctant to pay for autopsies. Yet, pathologists know the value that autopsies can provide.
The immediate value comes from revealing useful insights about all the health conditions of the deceased. The long-term value comes from the ability to gather the findings across a large number of autopsies that can contribute to new knowledge about health conditions that physicians use to improve the diagnoses of different health conditions.
Thus, with the publication of this peer-reviewed study about the connection between genetic variations and stillbirth, there is the opportunity for some of the nation’s pathology societies to advocate for funding a pilot program to fund more autopsies of stillborn babies, specifically to add more knowledge about the role of gene mutations as a causative factor in stillbirths.
OIG warns that without adequate clinical laboratory testing healthcare organizations could see more deaths and increased spending
Clinical laboratory leaders and pathologists know that lab test volume decreased dramatically during the early months of the COVID-19 pandemic. That was primarily because community lockdowns stopped people from seeing their doctors for the standard range of chronic health conditions, many of which require clinical laboratory tests for diagnosis and chronic disease management.
• 24% reduction in Medicare Part B test volumes in March • 53% in April • 30% in May
The decline of Medicare patients visiting clinical laboratories continued through the balance of 2020. During the first 10 months of the pandemic—March through December 2020—Medicare beneficiaries who pursued lab testing decreased by about 9% compared to the same 10-month period in 2019, according to a news release.
This is a strong indicator that the government’s response to the pandemic had a measurable effect on clinical laboratory testing volume among all age groups, especially among the elderly.
“The cumulative decline in lab test volume across all client labs for [March 9 to April 12] was just over 40%. But in that time, some of our lab customers were hit with a decline of maybe 50% to 60% in test volume,” Kyle Fetter (above), COO, XIFIN, told The Dark Report in 2020. Clinical laboratory testing that originates from a routine patient visit to a doctor—such as blood testing—may have been affected the most, Fetter explained. (Photo copyright: XIFIN.)
Clinical Laboratory Tests Key to Well-being of Patients with Chronic Conditions
The OIG study was limited to Medicare beneficiaries and thus did not provide information about testing fall-off among people who have private health insurance. But in “From Mid-March, Labs Saw Big Drop in Revenue,” Dark Daily’s sister publication The Dark Report reported early in 2020 on a 40% decline in test volumes and the pandemic’s varying effects on clinical labs, anatomic pathology (AP) groups, and AP subspecialties.
The OIG’s Report in Brief on its study recognized that medical laboratory testing is critical to helping healthcare providers manage chronic conditions that affect patients’ well-being and increase their healthcare costs.
“Lab tests are important for beneficiaries with chronic medical conditions, which are associated with hospitalizations, billions of dollars in Medicare costs, and deaths,” the OIG said.
“The information may be useful to stakeholders involved in ensuring that beneficiaries avoid the potential bad outcomes that may result from missing or delaying appropriate care,” the report noted.
Overall, 23.7 million Medicare beneficiaries received medical laboratory tests during the first 10 months of the pandemic, down 2.4 million from 26.1 million in 2019, the OIG reported.
Overall Medicare lab test volume and spending also declined during the reported period:
Part B clinical laboratory tests for Medicare beneficiaries decreased 15% from 419.9 million tests in 2019 to 358.4 million tests in the first 10 months of the pandemic.
Medicare spending for these tests decreased 16% from $6.6 billion in 2019 to $5.5 billion during the first 10 months of the pandemic.
“OIG’s audit of Part B clinical laboratory tests, reimbursed under the Clinical Laboratory Fee Schedule (CLFS) is a useful benchmark for how Medicare beneficiaries received fewer lab tests during the pandemic, especially during the early months,” said Robert Michel, Editor-in-Chief of Dark Daily and The Dark Report.
Medical Laboratory Tests That Were Down Most During COVID-19
The following 10 clinical laboratory tests experienced a 10% or more decline in Medicare beneficiaries seeking them during the pandemic period as compared to pre-pandemic, according to the OIG report:
Comprehensive urine culture test fell 16% to three million Medicare patients.
Uric acid level blood down 13% to 1.9 million Medicare beneficiaries.
Evaluation of antimicrobial drug decreased 17% to 1.74 million Medicare patients.
Folic acid level down 12% to 1.73 million Medicare beneficiaries.
Urinalysis manual test plunged 28% to 1.4 million Medicare patients.
Beyond Medicare, Clinical Laboratory Test Volume Dropped 40%
OIG was not the only organization to analyze medical laboratory testing volume during the pandemic’s early phase.
The Dark Report correlated data tracked by XIFIN, a San Diego-based health information technology (HIT) company providing revenue cycle management services to clinical laboratories and pathology groups. XIFIN’s collected data showed a steep drop in routine test volume as COVID-19 testing ramped up.
“Starting in the third week of March, we saw medical laboratories suffer a sharp drop in routine testing. But at about the same time, many labs began to offset those revenue losses with testing for the novel coronavirus,” Kyle Fetter, XIFIN’s then Executive Vice President and General Manager of Diagnostic Services told The Dark Report in 2020. Fetter is now XIFIN’S Chief Operating Officer.
“Over four weeks beginning March 9, we saw a cumulative drop of over 40% in test volume from all of our lab clients,” he added.
According to XIFIN’s data, lab specialty organizations experienced the following drop in routine testing during the period March 9 to April 16, 2020:
58% at clinical laboratories.
61% at hospital outreach laboratories.
52% at molecular and genetic testing laboratories.
44% at anatomic pathology (AP) groups.
70% to 80% at AP dermatology and other AP subspecialties.
Many medical laboratories are still recovering from the COVID-19 pandemic’s effects on testing volume.
Notably, the OIG’s report acknowledges the importance of adequate clinical laboratory testing and declares that—without these essential lab tests to manage some healthcare conditions—the healthcare industry could see increased morbidity, deaths, and Medicare spending.
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.)
.
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.
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.)
.
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.
