Research in the UK and US into how rapid WGS can prevent deaths and improve outcomes for kids with rare genetic diseases may lead to more genetic testing based in local clinical laboratories
Genetic scientists with the National Health Service (NHS) in England have embarked on an ambitious plan to offer rapid whole genome sequencing (rWGS) for children and babies with serious illnesses, as part of a larger initiative to embrace genomic medicine in the United Kingdom (UK).
The NHS estimates that the plan will benefit more than 1,000 children and babies each year, including newborns with rare diseases such as cancer, as well as kids placed in intensive care after being admitted to hospitals. Instead of waiting weeks for results from conventional tests, clinicians will be able to administer a simple blood test and get results within days, the NHS said in a press release.
The press release notes that about 75% of rare genetic diseases appear during childhood “and are responsible for almost a third of neonatal intensive care deaths.”
Here in the United States, pathologists and clinical laboratory managers should see this development as a progressive step toward expanding access to genetic tests and whole genome sequencing services. The UK is looking at this service as a nationwide service. By contrast, given the size of the population and geography of the United States, as this line of medical laboratory testing expands in the US, it will probably be centered in select regional centers of excellence.
“This strategy sets out how more people will be empowered to take preventative action following risk-based predictions, receive life-changing diagnoses, and get the support needed to live with genomically-informed diagnoses alongside improved access to cutting-edge precision [medicine] treatments. It also outlines how the NHS will accelerate future high-quality genomic innovation that can be adopted and spread across the country, leading to positive impacts for current and future generations,” the NHS wrote.
“This global first is an incredible moment for the NHS and will be revolutionary in helping us to rapidly diagnose the illnesses of thousands of seriously ill children and babies—saving countless lives in the years to come,” said NHS chief executive Amanda Pritchard (above) in a press release announcing the program. (Photo copyright: Hospital Times.)
New Rapid Whole Genome Sequencing Service
The NHS announced the plan following a series of trials last year. In one trial, a five-day old infant was admitted to a hospital in Cheltenham, Gloucester, with potentially deadly levels of ammonia in his blood. Whole genome sequencing revealed that changes in the CPS1 gene were preventing his body from breaking down nitrogen, which led to the spike in ammonia. He was given life-saving medication in advance of a liver transplant that doctors believed would cure the condition. Without the rapid genetic test, doctors likely would have performed an invasive liver biopsy.
Using a simple blood test, the new newborn genetic screening service in England is expected to benefit more than 1,000 critically ill infants each year, potentially saving their lives. “The rapid whole genome testing service will transform how rare genetic conditions are diagnosed,” explained Emma Baple, PhD, Professor of Genomic Medicine at University of Exeter Medical School and leader of the National Rapid Whole Genome Sequencing Service in the press release. “We know that with prompt and accurate diagnosis, conditions could be cured or better managed with the right clinical care, which would be life-altering—and potentially life-saving—for so many seriously unwell babies and children,” Precision Medicine Institute reported.
According to The Guardian, test results will be available in two to seven days.
Along with the new rWGS testing service, the NHS announced a five-year plan to implement genomic medicine more broadly. The provisions include establishment of an ethics advisory board, more training for NHS personnel, and an expansion of genomic testing within the existing NHS diagnostic infrastructure. The latter could include using NHS Community Diagnostics centers to collect blood samples from family members to test for inherited diseases.
UK’s Longtime Interest in Whole Genome Sequencing
The UK government has long been interested in the potential role of WGS for delivering better outcomes for patients with genetic diseases, The Guardian reported.
In 2013, the government launched the 100,000 Genomes Project to examine the usefulness of the technology. In November 2021, investigators with the project reported the results of a large pilot study in which they analyzed the genomes of 4,660 individuals with rare diseases. The study, published in the New England Journal of Medicine (NEJM) titled, “100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care—Preliminary Report,” found “a substantial increase in yield of genomic diagnoses made in patients with the use of genome sequencing across a broad spectrum of rare disease.”
The study’s findings suggest that use of WGS “could save the NHS millions of pounds,” The Guardian reported.
Whole Genome Sequencing System for Newborns in the US
“This NBS-rWGS [newborn screening by rapid whole genome sequencing] system is designed to complement the existing newborn screening process and has the potential to eliminate the diagnostic and therapeutic odyssey that many children and parents face,” Kingsmore said in a press release. “Currently, only 35 core genetic disorders are recommended for newborn screening in the United States, but there are more than 7,200 known genetic diseases. Outcomes remain poor for newborns with a genetic disease because of the limited number of recommended screenings. With NBS-rWGS, we can more quickly expand that number and therefore potentially improve outcomes through precision medicine.”
A more recent 2023 study which examined 112 infant deaths at Rady Children’s Hospital found that 40% of the babies had genetic diseases. In seven infants, genetic diseases were identified post-mortem, and in five of them “death might have been avoided had rapid, diagnostic WGS been performed at time of symptom onset or regional intensive care unit admission,” the authors wrote.
“Prior etiologic studies of infant mortality are generally retrospective, based on electronic health record and death certificate review, and without genome information, leading to underdiagnosis of genetic diseases,” said Christina Chambers, PhD, co-author of the study, in a press release. “In fact, prior studies show at least 30% of death certificates have inaccuracies. By implementing broad use of genome sequencing in newborns we might substantially reduce infant mortality.”
Pioneering work with whole genome sequencing for newborns, such as that being conducted by the clinical laboratory and genetic teams at Rady Children’s Hospital and the UK’s NHS, could allow doctors to make timely interventions for our most vulnerable patients.
“The SDPR will consolidate geographically fragmented EMR, PAS, and LIMS systems to create a detailed lifelong patient record and deliver cost savings,” NSW Health said in a news release.
NSW Health is the largest public health system in Australia with more than 220 public hospitals, 16 Local Health Districts, and three Specialty Networks. NSW Health Pathology operates more than 60 pathology laboratories (clinical laboratories in the US) and has 150 patient service centers.
“While this initiative will provide untold benefits to all the patients of NSW, we are excited about its potential for improving the health outcomes of our regional patients,” said Andrew Montague (above), former Chief Executive, Central Coast Local Health District in a press release. “By enabling greater collaboration across all local health districts and specialty health networks, the Single Digital Patient Record will provide clinicians with even better tools to keep the patient at the center of everything we do.” This project is more market evidence of the trend to bring clinical laboratory test results from multiple lab sites into a single data repository. (Photo copyright: Coast Community News.)
Cloud-based Realtime Access to Patient Records
Australia has a population of about 26 million and New South Wales, a state on the east coast, is home to more than eight million people. Though the scale of healthcare in Australia is much smaller than in the US, this is still a major project to pull patient data together from all the NSW hospitals, physicians’ offices, and other healthcare providers such as clinical laboratories and pathology practices.
With the change, NSW clinicians will benefit from a cloud–based system offering up real-time access to patients’ medical records, NSW Health Pathology Chief Executive Tracey McCosker told ITnews.
“Patients and our busy staff will benefit from clinical insights gained from the capture of important new data. Our work in pathology is vital to the diagnostic process and developing a statewide laboratory information management system will ensure we provide the best possible services,” McCosker told ITnews.
The KLAS Research report, “US Hospital Market Share 2022,” states that Epic, located in Verona, Wisconsin, has the largest US electronic health record (EHR) market share, Healthgrades noted. According to KLAS:
NSW Health’s decision to engage Epic came after a process involving 350 clinicians, scientists, and technical experts, Zoran Bolevich, MD, Chief Executive of eHealth NSW and NSW Health’s Chief Information Officer, told ITnews.
NSW Health’s Goal for Statewide Digital Patient Record
It was in December 2020 when NSW Health announced its plan to create the SDPR.
“Our vision is to be able to provide a single, holistic, statewide view of every patient—and for that information to be readily accessible to anyone involved in the patient’s care,” Bolevich said in the news release.
The SDPR, according to NSW Health, will address the following:
Challenges:
Current systems not connected statewide.
Inaccessible patient data.
Duplicative data collection.
Gaps in decision-making.
Goals:
Improve health outcomes.
Create patient centricity.
Leverage insights.
NSW’s government has already invested more than $106 million in the SDPR, Healthcare IT News reported.
Other Large EHR Rollouts
NSW Health is not the only large organization to take on such an ambitious project of creating a large-scale digital patient record. And not always to a successful conclusion.
The US Department of Veterans Affairs (VA)—also intent on EHR modernization—recently announced it is suspending roll-out of the Oracle Cerner EHR at VA centers until June 2023 to address technical issues affecting appointments, referrals, and test results.
Four VA centers in Washington, Oregon, and Ohio already went live with the system in 2022.
“We are delaying all future deployments of the new EHR while we fully assess performance and address every concern. Veterans and clinicians deserve a seamless, modernized health record system, and we will not rest until they get it,” said Deputy Secretary of Veterans Affairs Donald Remy, JD, in a news release.
For its part, Oracle Cerner wrote federal lawmakers noting the importance of continuing the project, which will move the VA away from its former VistA health information system.
“Modernization requires change and some short-term pain for the long-term benefits of a modern technology infrastructure,” noted Oracle Cerner Executive Vice President Ken Glueck in the letter, Becker’s Health IT reported. “A modernization project of this scale and scope necessarily involves time to untangle the decades of customized processes established in support of VistA, which inevitably involves challenges.”
NSW Health’s goal is to build a single repository of health information—including lab test results from multiple clinical laboratory sites. When finished NSW Health expects that sharing patient data will contribute to producing better healthcare outcomes.
However, the VA’s experience—and several other similar attempts at large-scale electronic patient record installations—suggest the work ahead will not be easy. But for NSW Health, it may be worth the effort.
Clinical laboratories could play a key role in helping users collect their samples correctly, interpret results, and transfer flu test data to their health records
Clinical laboratories may have another opportunity to provide service to their clients and the physicians who treat them. With the success of at-home COVID-19 testing, consumer demand for self-tests is changing and advances in diagnostic technology now make it feasible to make more influenza (flu) tests available for consumers to buy and use at home.
At-home tests for SARS-CoV-2 can be found at pharmacies all across America. But that’s not the case with tests for influenza.
Should self-test flu kits eventually become available and common, clinical laboratories could offer the service of helping consumers understand:
that the test was conducted correctly (specimen collection and analysis),
“Home flu testing would ensure that those who do need and receive antiviral medication for influenza are the ones who need it the most,” and that “we are making our treatment decisions based on data,” infectious disease specialist Christina Yen, MD (above), University of Texas Southwestern Medical Center, told STAT News. At-home flu self-tests could also bring opportunities for clinical laboratories to provide service to healthcare consumers and the physicians who treat them. (Photo copyright: UT Southwestern Medical Center.)
Pros and Cons of Consumers Doing At-home Influenza Testing
According to the federal Centers for Disease Control and Prevention (CDC), COVID-19 and influenza are both upper respiratory illnesses with similar symptoms. So, why don’t we have more at-home flu tests available? Partly because at-home testing is a relatively new phenomenon in modern healthcare.
“It’s really rare, and it’s really new that people are allowed to know about what’s happening inside their body without a physician in the middle,” Harvard epidemiologist Michael Mina, MD, PhD, told STAT News. The article uses the example of at-home pregnancy tests. Despite a prototype for an at-home pregnancy test being created in 1967, it took another decade before an over-the-counter pregnancy test became available to the public.
“The general thinking was, ‘How could a woman possibly know what to do if she found out she was pregnant on her own without a doctor in the room?’ That is a ridiculous concern because women have been doing that for millions of years,” Mina added.
So, why be cautious when it comes to giving patients the option of at-home flu testing?
There are some cons to at-home influenza tests. Average citizens are not clinical laboratory professionals. They might obtain too little sample for an accurate reading or read the results incorrectly. Then, there is the possibility for false-negatives or false-positives.
An at-home test user is not likely to consider the possibility of a false result, however clinicians look at the situation with more nuance. If the patient was still symptomatic or in a high-risk community, the provider could administer a more sensitive medical laboratory test to confirm the previous test results.
“In a Facebook post from mid-November with hundreds of responses, concertgoers compared symptoms and positive test results, many of those from tests taken at home. But those data weren’t added to state public health tallies of COVID’s spread,” STAT News noted.
The larger concern is that samples obtained by at-home self-test users are not submitted for genomic sequencing. This could lead to incomplete data and delay identifying new variants of the coronavirus in communities.
Another barrier to at-home flu testing is that rapid influenza diagnostic testing can be unreliable. In 2009, the rapid influenza tests could only detect the H1N1 influenza virus in a mere 11% of samples, STAT News reported. Because of this, the FDA now requires manufacturers to test their rapid tests against eight different strains that change every year depending upon which strains are prevalent. This could present a problem if individuals use leftover tests from the previous flu season.
Do Pros of At-home Testing Outweigh the Cons?
At-home testing is convenient and makes testing more accessible to patients who may not be able to get to a clinic. Being able to test at home also encourages individuals to take precautions necessary to stop the spread of whichever illness they may have. Given the similarities in symptoms between influenza and COVID-19, people could benefit from having tools at home that correctly identify their illness.
At-home COVID-19 tests are here to stay, and at-home influenza tests may be on the way soon. Clinical laboratories could play an important role in educating the public on the correct handling of these tests.
Retail giant now has primary care clinics at stores in five states, but the rollout has not gone smoothly
Healthcare is increasingly being driven by consumerism and one clear sign of this trend is Walmart’s ambitious plan to open health clinics at its retail locations. The retail giant set its plans in motion in 2019 with its first primary care site in a suburban Atlanta store, however, the rollout since then has presented certain challenges.
Nevertheless, the trend of placing nearly full-service primary care clinics in retail locations continues. Clinical laboratories in these areas need strategies to serve customers accessing healthcare through these new channels, particularly as Walmart and the national retail pharmacy chains continue to expand the clinical services offered in their retail stores.
“Consumer engagement is a huge part of healthcare, [yet it is also a] gap for us in healthcare,” cardiologist and Walmart VP of Health and Wellness Cheryl Pegus, MD, told Modern Healthcare. “Healthcare is incredibly complicated,” she added. “And where we are in healthcare today is not in having great treatments. It’s not in having evidence-based medicine. It’s understanding how we engage consumers.”
The company also entered the telehealth business with last year’s acquisition of multispecialty telehealth provider MeMD.
“Telehealth offers a great opportunity to expand access and reach consumers where they are and complements our brick-and-mortar Walmart Health locations,” said Pegus in a Walmart new release announcing the acquisition. “Today people expect omnichannel access to care and adding telehealth to our Walmart healthcare strategies allows us to provide in-person and digital care across our multiple assets and solutions.”
Currently, Walmart Health centers only operate in Georgia, Florida, Illinois, and Arkansas. But telehealth enables Walmart “to provide virtual healthcare across the country to anyone,” Pegus said. With both offerings, “we’re really attempting to allow people to get healthcare the way they need it without disrupting the rest of their life.” Many users of these services are Walmart “associates,” she added, using the company’s term for its retail employees.
“In this country, about 25% of people don’t have a primary care physician,” cardiologist Cheryl Pegus, MD (above), Walmart’s VP of Health and Wellness, told Medscape. “So, your options for being able to solve in real time something that will help you, they’re quite limited. What we’re trying to do is give those options. We’re not trying to take away emergency rooms, or healthcare systems, or existing primary care. We’re asking, how do we expand that infrastructure so that people get care when they need it?” And this includes clinical laboratory testing, radiology, and telehealth services as well. (Photo copyright: Walmart.)
Large Portfolio of Healthcare Offerings
Pegus joined Walmart (NYSE:WMT) in December 2020 to oversee a portfolio that now includes more than 4,700 pharmacies and 3,400 Vision Centers, in addition to the telehealth operation and the Walmart Health centers. She was previously chief medical officer at Walgreens and Cambia Health Solutions and worked in private practice as a cardiologist.
The retail giant opened its first Walmart Health center in Dallas, Ga., an Atlanta suburb, in September 2019, followed by additional centers in Georgia, Arkansas, and Illinois.
Earlier this year, it opened five new clinics in northern and central Florida with plans for at least four more in the Jacksonville, Orlando, and Tampa areas, according to a press release. Each health center is adjacent to a Walmart retail location.
These centers offer a range of primary care medical services, including:
physicals,
injury care,
immunizations,
radiology, and
care for chronic health conditions.
Pictured above is one of the first health clinics established by Walmart. This location is in a western Atlanta suburb. Note that the services advertised include more than just primary care. Also offered are “labs and X-ray,” along with dental, hearing, optometry, and counseling. Clinical laboratory managers and pathologists may want to monitor whether consumers embrace primary care delivered from clinics located in retail stores. (Photo copyright: Georgia Health News.)
As Dark Daily reported in May 2020, the Walmart Health centers also offer clinical laboratory testing at cut-rate prices, such as:
$10 for a lipid test,
$10 for Hemoglobin A1c, and
$20 for a strep test.
On the Walmart Health website, patients can enter their Zip code to view a list of Walmart Health clinics in their area, including links to price lists.
Walmart’s Expansion into Healthcare Not Without Problems
However, the company’s expansion into healthcare has not gone smoothly. In 2018, the Walmart board signed off on a plan to open 4,000 health centers by 2029, Insider reported. By the end of 2021, Walmart expected to have 125 health centers in operation, but as of June 2022, the Walmart Health website listed only 25 locations, mostly in Georgia.
Citing anonymous sources, Insider reported problems that include “leadership changes, competing business priorities brought on by the coronavirus pandemic, and the complexity of scaling a massive healthcare operation.”
In Sept. 2021, Insider further reported that the clinics were experiencing operational difficulties including hidden fees and billing problems. One culprit, the story suggested, was the company’s electronic health record (EHR) software. That same month, Walmart announced it would adopt the Epic health records system, beginning with the opening of new clinics in Florida locations.
Pegus’ arrival at Walmart appears to be part of a management shakeup. In January 2022, Insider reported that she had assembled a new executive team, with David Carmouche, MD, Senior VP, Omnichannel Care Offerings, overseeing the health centers and telehealth operations. By then, the original executives leading the rollout of the health centers had all left, Insider reported. Carmouche was previously an executive VP with Ochsner Health in New Orleans.
Partnership with Quest Diagnostics
Meanwhile, in January, Walmart announced a deal with Quest Diagnostics that allows consumers to order more than 50 lab tests through The Wellness Hub on Walmart.com, which is separate from the Walmart Health website. The tests cover “general health, digestive health, allergy, heart health, women’s health, and infectious disease,” according to a press release announcing the partnership.
Consumers can order at-home test kits for certain conditions or set up appointments for tests at Quest Patient Service Centers. The tests on the Walmart/QuestDirect website include:
COVID-19 Active Infection ($119+)
COVID-19 Antibody Test ($69)
Cholesterol Panel ($59)
Complete Blood Count ($59)
Comprehensive Metabolic Panel ($49)
CRP Inflammation Marker ($59)
Diabetes Management ($69+)
Diabetes Risk ($99+)
Food Allergy Test Panel ($209)
Chickenpox ($59)
The website also offers a combined Basic Health Profile with CBC, CMP, cholesterol panel, and urinalysis for $149. “Each purchase is reviewed and, if appropriate, ordered by a licensed physician,” the press release states.
What does all this mean for clinical laboratories? “They need to recognize that the Millennials and Gen Zs are driving a consumer revolution in healthcare,” said Robert Michel, Publisher and Editor-in-Chief of Dark Daily and its sister publication The Dark Report.
“Walmart was early to recognize and respond to this, in part because it employs 1.3 million Americans, many of whom are Gen Y and Gen Z and quick to use telehealth and similar virtual health services,” he added.
Clinical laboratory leaders need to understand this trend and develop strategies to attract and serve new patients who are willing to access healthcare virtually, while still needing to provide blood and other specimens for the lab tests ordered by their providers.
Should their research result in new ways to identify and diagnose disease, doctors and clinical laboratories would do confirmatory testing and then initiate a precision medicine plan.
Dan Roden, MD, Senior Vice President for Personalized Medicine at VUMC and Senior Author of the Circulation study, said in a VUMC news release that the findings support the growing use of genetic information in clinical care.
“The questions we asked were: How many people who had no previous indication for cardiac genetic testing had pathogenic or likely pathogenic variants, and how many of those people actually had a phenotype in the electronic health records?” he explained.
Arrhythmia More Common than Previously Thought
The VUMC researchers drew data for their reports from the eMERGE Phase III study, which investigated the feasibility of population genomic screening by sequencing 109 genes across the spectrum of Mendelian diseases—genetic diseases that are caused by a mutation in a single gene—in more than 20,000 individuals. The scientists returned variant results to the participants and used EHR and follow-up clinical data to ascertain patient phenotypes, according to a Northwestern University Feinberg School of Medicine news release.
The research team looked specifically at the 120 consortium participants that had disease-associated pathogenic or likely pathogenic (P/LP) variants in the arrhythmia-associated genes. An analysis of the EHR data showed that 0.6% of the studied population had a variant that increases risk for potentially life-threatening arrhythmia, and that there was overrepresentation of arrhythmia phenotypes among patients, the VUMC news release noted.
The research team returned results to 54 participants and, with clinical follow-up, made 19 diagnoses (primarily long-QT syndrome) of inherited arrhythmia syndromes. Twelve of those 19 diagnoses were made only after variant results were returned, the study’s authors wrote.
Carlos G. Vanoye, PhD, Research Associate Professor of Pharmacology at Northwestern University (NU), said the study suggests arrhythmia genes may be more common than previously thought.
“A person can carry a disease-causing gene variant but exhibit no obvious signs or symptoms of the disease,” he said in the NU news release. “Because the genes we studied are associated with sudden death, which may have no warning signs, discovery of a potentially life-threatening arrhythmia gene variant can prompt additional clinical work-up to determine risks and guide preventive therapies.”
“The take-home message is that 3% of people will carry a pathogenic or likely pathogenic variant in a disease-causing gene and many others will carry variants of uncertain significance,” said Dan Roden, MD (above), Senior Vice President for Personalized Medicine at VUMC and Senior Author of the Circulation study in the VUMC news release. “We can use genetic testing, electronic health record phenotypes, and in vitro technologies to evaluate and find people who have unrecognized genetic disease and save lives by making earlier diagnoses.” Clinical laboratories will play a key role in making those early diagnoses and in managing personalized medical treatment plans. (Photo copyright: Vanderbilt University.)
Variants of Uncertain Significance
According to the NU news release, the scientists determined the functional consequences of the variants of uncertain significance they found and used that data to refine the assessment of pathogenicity. In the end, they reclassified 11 of the variants: three that were likely benign and eight that were likely pathogenic.
In the JAMA Oncology study, the VUMC scientists and other researchers conducted a phenome-wide association study to find EHR phenotypes associated with variants in 23 hereditary cancer genes. According to the VUMC news release, they identified 19 new associations:
The VUMC study findings could improve disease diagnosis and management for cancer patients and help identify high-risk individuals, the researchers noted in their published report.
In an editorial published in Circulation, titled, “First Steps of Population Genomic Medicine in the Arrhythmia World: Pros and Cons,” the professors noted that using genomic information in the case of potentially lethal inherited arrhythmia syndromes could be “lifesaving,” but questioned the benefits of reporting such secondary findings when patients are undergoing genome sequencing for other indications such as cancer.
“The likelihood that these ‘genetic diagnoses’ are translated into clinical diagnoses have not been completely evaluated,” they wrote. “In addition to the challenge of accurately identifying disease-causing genetic variants, defining the penetrance of such variants is critical to this process, i.e., what proportion of individuals in the general population with apparently pathogenic variants will develop the associated phenotype? If penetrance is low for particular gene/phenotype combinations, the costs associated with clinical screening and the psychological effects on individuals informed that they have potentially life-threatening variants may outweigh the benefits of the few new clinical diagnoses.”
These latest studies provide further evidence of the value of big data in healthcare and offer another lesson to clinical laboratories and pathologist about the future role data streaming from clinical laboratories and pathology assays may have in the growth of personalized medicine.
