All-of-Us program is free to participants and provides data to more than 800 research studies for cancer, COVID-19, Alzheimer’s, and other diseases; findings will lead to new biomarkers for clinical laboratory tests
It is hard to say no to free. At least that is what the National Institutes of Health (NIH) is counting on to help increase the size and diversity of its database of genetic sequences. The NIH’s All-of-Us Research Program is offering free genetic testing for all participants in the program, as well as free wearable Fitbits for those selected to provide lifestyle and behavior data.
Many pathologists and clinical laboratory managers know that this group of researchers hope to build a database of more than one million genetic sequences to better understand “how certain genetic traits affect underrepresented communities, which could greatly affect the future of customized healthcare,” CBS affiliate 8 News Now reported.
“Customized healthcare” is a euphemism for precision medicine, and genetic sequencing is increasingly playing a key role in the development of personalized diagnostics and therapeutics for cancer and other deadly diseases.
In “VA’s ‘Million Veterans Program’ Research Study Receives Its 100,000th Human Genome Sequence,” Dark Daily described how the NIH’s All-of-Us program was launched in 2018 to aid research into health outcomes influenced by genetics, environments, and lifestyle. At that time, the program had biological samples from more than 270,000 people with a goal of one million participants.
Matthew Thombs, Senior Project Manager of Digital Health Technology at Scripps Research in La Jolla, Calif., joined the All-of-Us program after losing a family member “to a condition I believe could have been managed with changes to their lifestyle,” he told 8 News Now.
“What we are building will empower researchers with the information needed to make such conclusions (about possible need to change lifestyles) and forever alter how diseases are treated,” he added. “I hope that what we are doing here will help my son grow up in a world where healthcare is more of a priority, and many of the ailments we see today are things of the past.”
Such genetic testing could discover biomarkers for future personalized clinical laboratory diagnostics and drug therapies, a key aspect of precision medicine.
Scripps Research Integrates Mobile Health Technology into All-of-Us Program
A critical aspect of the NIH’s research is determining how people’s behavior combined with their genetics may predispose them to certain diseases. Nonprofit research institution Scripps Research is working with the NIH’s All of Us Research Program to enroll and collect biological samples from one million US residents.
In addition, Scripps is fitting study participants with wearable mobile health devices to capture data on their habits and lifestyles.
“Until now, the treatment and prevention of disease has been based on a ‘one-size-fits-all’ approach, with most therapeutics tailored for the ‘average patient’. However, advances in genomic sequencing, mobile health technologies, and increasingly sophisticated informatics are ushering in a new era of precision medicine. This new approach takes into account differences in people’s genes, environment, and lifestyles giving medical professionals resources to design targeted treatments and prevention strategies for the individual,” Scripps states on its website.
Can wearable fitness devices and related data contribute to research on genetics and healthcare outcomes? Scripps aims to find out. It has fitted 10,000 people in the All-of-Us program with Fitbit devices (Fitbit Charge 4 tracker or Fitbit Versa 3 smartwatch) at no cost. Since February, Scripps has distributed 10,000 Fitbit wearable devices through the All-of-Us program.
“By sharing information about their health, habits, and environment, participants will help researchers understand why people get sick or stay healthy,” the Scripps website adds.
The Scripps researchers plan to analyze how the people use the wearable devices. They are also accumulating data about participants’ physical activity, heart rate, sleep, and other health metrics and outcomes “as part of the broader All of Us program,” a Scripps news release explained.
“This is the first time All of Us is distributing devices to participants. Our goal is to better understand how participants engage during research studies in order to continually improve user experience and participation. We also expect to learn more about how wearable data may inform the personalization of healthcare,” said Julia Moore Vogel, PhD, Director of The Participant Center at the All of Us Research Program at Scripps Research, in the news release.
All-of-Us Program Records ‘Significant Progress in Participant Diversity’
As of June, the NIH has enrolled 386,000 participants into the All-of-Us program, with 278,000 consenting to all of the program’s steps. Eighty percent of biological samples in the collection are from people in communities that have been under-represented in previous biomedical research an NIH new release noted. According to the NIH, that gives the All-of-Us research program “the most diverse dataset.”
What will all this research ultimately bring to clinical laboratories? Who knows? Nevertheless, if federal institutions like the NIH and non-profit research companies like Scripps believe precision medicine is worth investing in, then the All-of-Us program is worth watching.
A diverse database of a million genetic sequences combined with lifestyle and behavioral data may lead to new and improved personalized diagnostics and drug therapies.
Since all Americans have access to free COVID-19 vaccines, many pathologists and clinical lab managers will ask if this test is even necessary. Some experts say “maybe”
Here’s another example of genetic test developers who are willing to push boundaries and sell a diagnostic test directly to consumers that has some diagnostic experts and pathologists challenging its clinical validity.
The test was developed by molecular diagnostics company Genetic Technologies Ltd. (NASDAQ:GENE) of Melbourne, Australia, and, according to an article in Science, is an at-home saliva test that “combines genetic data with someone’s age, sex, and pre-existing medical conditions to predict their risk of becoming extremely ill from COVID-19.”
In a non-peer-reviewed preprint, titled, “Development and Validation of a Clinical and Genetic Model for Predicting Risk of Severe COVID-19,” Genetic Technologies’ Chief Scientific Officer Richard Allman, PhD, and Senior Biostatistician and the study’s first author, Gillian Dite, PhD, wrote, “Using SARS-CoV-2 positive participants from the UK Biobank, we developed and validated a clinical and genetic model to predict risk of severe COVID-19. … Accurate prediction of individual risk is possible and will be important in regions where vaccines are not widely available or where people refuse or are disqualified from vaccination, especially given uncertainty about the extent of infection transmission among vaccinated people and the emergence of SARS-CoV-2 variants of concern.”
But since every American already has access to free COVID-19 vaccines, one wonders why this test would be launched in the US?
Determining Risk for COVID-19 Infection
Can a genetic test predict an individual’s risk of contracting a SARS-CoV-2 infection that would require hospitalization or cause death? Genetic Technologies and its US partner, Infinity BiologiX (IBX) of Piscataway, N.J., believe so.
According to a Genetic Technologies news release, the saliva test, which reportedly costs $175, enables a “leading-edge risk assessment that estimates your personal risk of severe disease,” IBX says on its website.
The at-home saliva-based test, which is intended for people age 18 and older, gives a risk score for contracting a serious COVID-19 case based on genetic and clinical information, IBX stated in its own news release.
The two companies partnered with Vault Health, a “virtual platform for telemedicine and diagnostics” developer, to distribute, and sell the COVID-19 Serious Disease Risk Test in the US.
Is There a Place for Genetic COVID-19 Risk Test in the US?
“Alongside existing treatment options and vaccines, we believe this test will enable more insightful decisions for states, workplaces, and individuals,” said Simon Morriss, Genetic Technologies’ CEO, in the news release.
Meanwhile, some experts are uncertain about predictive types of testing for the SARS-CoV-2 coronavirus. “I think it’s premature to use a genetic test to predict a person’s likely COVID-19 severity. We don’t understand exactly what these genetic variants mean or how they affect disease,” epidemiologist Priya Duggal PhD, a professor in the Genetics Epidemiology Division at the Johns Hopkins University School of Public Health, told Science.
According to Science, “The test debuts in a regulatory gray zone …. The two companies did not seek [FDA] approval for validity because, [Genetic Technologies Chief Scientific Officer Richard Allman] says, the test is not a direct-to-consumer product that falls under its review. After a customer receives results from IBX’s federally-approved labs, they can consult with a ‘telehealth’ physician.”
“We are uniquely and strategically positioned with our partners to deliver the test and provide remote telehealth services and reporting, utilizing our extensive array capability and capacity across a number of platforms,” Grimwood said in the IBX news release.
However, Science reported that “Several geneticists who reviewed the company’s preprint” said “the test needs to be validated in other, more diverse populations than one detailed in the UK Biobank, and they wonder whether its predictions are reliable for people infected with new SARS-CoV-2 variants.”
“It’s a good start, but by no means is it calibrated or validated sufficiently to say this is a test I would take, or my wife should take,” cancer geneticist Stephen Chanock, MD, Director of the Division of Cancer Epidemiology and Genetics at the National Cancer Institute, National Institutes of Health, told Science.
The question remains unanswered as to why a genetic risk test for SARS-CoV-2 and its variants is needed in the United States. Nevertheless, clinical laboratory leaders and pathologists may want to monitor these developments for new biomarkers and COVID-19 diagnostics.
Following a nearly two-year disruption due to the SARS-CoV-2 pandemic, pathologists and clinical laboratory professionals once again have an opportunity to gather and learn from each other
It is good news that the daily number of new cases of COVID-19 continue declining here in the United States. That fact, and the growing number of vaccinations, have encouraged state and federal officials to lift many restrictions on business and social activities.
Clinical laboratories are watching a big drop in the daily number of COVID-19 tests they perform, even as routine test volumes climb and more patients show up in doctors’ offices for the typical mix of ailments and health conditions.
It’s true that many familiar routines are back. But it is also true that things are not exactly the way they were pre-pandemic. And that’s the rub. Going forward, what should medical laboratory managers and pathologists expect to be the “post-pandemic normal” in how patients access care and how providers deliver clinical services? How will healthcare in this country be different from what it was pre-pandemic?
Preparing Clinical Lab Leaders for What Comes Next
These questions and more will be front and center when the Executive War College on Lab and Pathology Management returns on Nov. 2-3, 2021, at the Hyatt Riverwalk Hotel in San Antonio. The theme of this first live gathering since the spring of 2019 will be “Preparing Your Clinical Laboratory and Pathology Group for Post-Pandemic Success.”
“Today, lab managers have the interesting challenge of understanding the new opportunities they can use to advance their labs, both clinically and financially,” stated Robert L. Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report, and founder of the Executive War College. “It isn’t that the pandemic changed healthcare in fundamental ways. Rather, it is that the pandemic accelerated changes that were underway before the outbreak began.
“That’s true of telehealth as well, for example,” he continued. “Once the nation was locked down, utilization of virtual physician visits and telehealth services skyrocketed. Today, national surveys confirm that as many as 50% of all patients and physicians have used a telehealth service, are comfortable with this type of appointment, and are ready to continue to use virtual office visits.
“Another trend accelerated by the pandemic is patient self-testing at home,” Michel added. “Government health officials saw the benefit of clearing for clinical use different specimen collection systems and COVID-19 test methods designed for use by consumers in the comfort of their home. Today, consumers can choose from multiple specimen collection products and SARS-CoV-2 tests designed for in-home use. Clinical laboratory managers should consider this development to be a consumer home-test baseline. Federal officials have created a regulatory pathway that will make it easier and faster for federal regulators to clear other types of diagnostic tests for consumer home use.”
What if the FDA Approves More Consumer At-Home Tests?
There are implications to each of the two trends described above. In the case of telehealth, if patients see their doctors virtually and the doctors order medical tests, how do clinical laboratories access these patients to collect the specimens needed to do this testing?
Similarly, if, in coming years, the federal Food and Drug Administration (FDA) increases the number of diagnostic test specimen-collection kits that consumers can use from home, how should local clinical laboratories position themselves to receive those kits and perform those tests?
These are two examples of important questions to be answered at sessions scheduled for the Executive War College in San Antonio on Nov. 2-3. Case studies by innovative lab leaders will address topics ranging from high-level strategy to daily management, operations, marketing, and managed care contracting.
Attendance Limited at This Fall’s Executive War College
At the first live edition of the Executive War College since May 2019, attendees will notice one significant difference from earlier years. By design, and for the safety and well-being of attendees, the number of attendees will be limited to 300. The hotel follows the Centers for Disease Control and Prevention (CDC) guidelines and is prepared to adjust those numbers as CDC guidance evolves. Thus, those interested in attending this year’s conference are advised to register early to guarantee their place and avoid being disappointed.
Suggestions for session topics and speakers are welcome and can be sent to info@darkreport.com. Conference details, session topics, and speakers will be updated regularly at www.executivewarcollege.com.
So, register today because seating is limited at the 2021 Executive War College Presents “Preparing Your Clinical Laboratory and Pathology Group for Post-Pandemic Success.” To ensure your place at this valuable conference, click HERE or place this URL (https://dark.regfox.com/2021-ewc-presents) into your browser.
The rapid diagnostic test costs less than $5 per unit and can be adapted for other diseases, the developers say, which opens a slew of possibilities for clinical laboratories
Just as the SARS-CoV-2 coronavirus spurred deployment of new vaccine technology based on messenger RNA (mRNA), the COVID-19 pandemic also could prove to be a watershed for in vitro diagnostics (IVD) innovation in ways that benefit clinical laboratories.
A Penn Medicine news release noted that “The RAPID technology … transforms the binding event between the SARS-CoV-2 viral spike protein and its receptor in the human body, the protein ACE2 (which provides the entry point for the coronavirus to hook into and infect human cells), into an electrical signal that clinicians and technicians can detect. That signal allows the test to discriminate between infected and healthy human samples. The signal can be read through a desktop instrument or a smartphone.”
Though still in its early stages, the technique potentially offers dramatically lower costs and faster results than traditional RT-PCR (reverse transcription polymerase chain reaction) molecular tests. Moreover, the RAPID technology might be useful for identifying other types of biomarkers and could be the basis for diagnostic tests that help reduce the cost-per-test in medical laboratory testing while providing comparable sensitivity and specificity to existing methodologies.
Clinical trials began on January 5, 2021, and the Penn Medicine researchers say the IVD test technology can be applied to other infectious diseases, which, if proven accurate, would be a boon to clinical laboratory testing.
Diagnostic Test Results in Four Minutes for Less than $5/Test
According to the news release, the RAPID 1.0 (Real-time Accurate Portable Impedimetric Detection prototype 1.0) biosensor test costs less than $5 and can deliver results in four minutes. The researchers reported overall accuracy of 87.1% on (139) nasal swab samples and 90% on (50) saliva samples.
The technology uses electrodes that can be mass-produced at low cost on commercially-available screen printers, the researchers said. Results can be read on electronic devices connected to a PC or smartphone.
Does Penn Medicine’s RAPID 1.0 Test Replace Traditional RT-PCR Testing?
In their published study, the Penn Medicine researchers cited the need for “fast, reliable, inexpensive, and scalable point-of-care diagnostics.”
RT-PCR tests, they said, “are limited by their requirement of a large laboratory space, high reagent costs, multistep sample preparation, and the potential for cross-contamination. Moreover, results usually take hours to days to become available.”
Researchers who have studied the SARS-CoV-2 coronavirus know that it uses a spike-like protein to bind to angiotensin-converting enzyme 2 (ACE2) receptors on the surfaces of human cells.
As described in Penn Medicine’s published study, the biosensor contains ACE2 and other biochemical agents anchored to an electrode. When the SARS-CoV-2 coronavirus attaches to the ACE2, the biosensor transforms the chemical reaction into an electrical signal that can be measured on a device known as a potentiostat.
The researchers tested their RAPID 1.0 technology with two commercially available potentiostat models:
The researchers initially developed the electrode as a printed circuit board, which is relatively expensive. To reduce costs, they constructed a version that uses filter paper as the main component. The researchers noted that one screen printer in a lab can produce 35,000 electrodes per day, including time needed to incorporate the chemical elements. “However, it must be noted that these steps can be fully automated into a production line for industrial purposes, drastically reducing time requirements,” they wrote.
The test can be performed at room temperature, they added, and total cost per unit is $4.67. Much of that—$4.50—is for functionalizing the ACE2 recognition agent. The cost for the bare electrode is just seven cents.
“The overall cost of RAPID may be further reduced through recombinant production of ACE2 and ACE2 variants,” the researchers said, adding that the RAPID 1.0 test can detect the SARS-CoV-2 coronavirus at low concentrations correlating to the earliest stages of the COVID-19 disease.
Testing Penn Medicine’s RAPID 1.0 Test
The researchers evaluated the technology in blinded tests with clinical samples from the Hospital of the University of Pennsylvania. The evaluation included 139 nasal swab samples, of which 109 were determined to be COVID-19 positive by RT-PCR tests and clinical assessments. Among these, the RAPID test successfully detected the SARS-CoV-2 coronavirus in 91 samples, for a sensitivity rate of 83.5%. One sample was from a patient diagnosed with the highly contagious SARS-CoV-2 Alpha variant B.1.1.7, which the test correctly identified as positive.
Among the 30 samples determined to be COVID negative, the RAPID test scored a specificity rate of 100%, meaning no false positives. Overall accuracy, including sensitivity and specificity, was 87.1%.
The researchers also analyzed 50 saliva samples: 13 COVID-positive and 37 COVID-negative. The test correctly identified all 13 positive samples but produced five false-positives among the 37 negative samples, for a specificity rate of 86.5%. The researchers speculated that this could be due to interactions between ACE2 and other biomolecules in the saliva but suggested that performance “will improve when using fresh saliva samples at the point-of-care.”
Are There Other Applications for the RAPID Test?
The Penn Medicine news release said the RAPID technology can be adapted to detect other viruses, including those that cause Influenza and sexually-transmitted diseases.
Robert Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report, said the test points to one silver lining in the COVID-19 pandemic. “Researchers around the world intensified their work to find ways to identify the SARS-CoV-2 virus that are faster, cheaper, and more accurate than the diagnostic technologies that existed at the time of the outbreak. In this regard, the COVID-19 pandemic may have accelerated the development and refinement of useful diagnostic technologies that will disrupt long-established methods of testing.”
Marcelo Der Torossian Torres, PhD, postdoctoral researcher at Penn Medicine and lead author of the study, said in the news release, “Quick and reliable tests like RAPID allow for high-frequency testing, which can help identify asymptomatic individuals who, once they learn they are infected, will stay home and decrease spread.
“We envision this type of test being able to be used at high-populated locations such as schools, airports, stadiums, companies—or even in one’s own home,” he added.
Clinical laboratory managers may want to stay current on the development and possible commercialization of the RAPID 1.0 (Real-time Accurate Portable Impedimetric Detection prototype 1.0) biosensor test by the research team at Penn Medicine.
This is yet another example that dogs can be highly accurate screeners for disease. But are they ready to be included in clinical laboratory diagnostic tests?
Thailand researchers have trained dogs to screen for COVID-19 infections in humans, despite the country’s “spicy and flavorful cuisine,” the AP reported. This is just the latest example of a country using dogs to identify individuals who are infected with the SARS-CoV-2 coronavirus. Clinical laboratory managers and pathologists have seen other examples of dogs being trained to identify different diseases or health conditions.
In fact, dogs have been shown to be highly accurate at spotting disease in humans and the practice is becoming common worldwide. But could dogs achieve the required clinical accuracy and reproducibility in detecting disease for the procedure to be translated into clinical practice?
Smelling Disease as a Clinical Laboratory Diagnostic
Clinical laboratory professionals are quite familiar with the concept of the human body producing volatile chemicals that can serve as biomarkers for disease or illness. Dark Daily has previously reported on multiple breath/aroma-based diagnostic clinical laboratory tests going as far back as 2013.
But it is in the use of dogs to spot COVID-19 infections in humans where this type of breath/aroma-based diagnostic test research is making a notable impact.
“Even if this approach were not warranted as a clinical diagnostic procedure, trained dogs could be deployed at airports, train stations, sporting events, concerts, and other public places to identify individuals who may be positive for SARS-CoV-2, the coronavirus that causes the COVID-19 illness,” we wrote. “Such an approach would make it feasible to ‘screen’ large numbers of people as they are on the move. Those individuals could then undergo a more precise medical laboratory test as confirmation of infections.”
According to the researchers, individuals with a COVID-19 infection emit a unique odor that is present in sweat samples. The six Labrador retrievers used in the research were able to detect the presence of COVID-19 with an impressive 95% accuracy rate in more than 1,000 samples presented to them, the AP reported.
To perform the study, the scientists placed sweat samples in metal containers and allowed the dogs to sniff each sample. If no trace of the infection was present, the dogs simply walked past the container. If the disease was detected in a particular sample, the dogs would sit down in front of the container.
Would Spicy Food Interfere with Dogs’ Ability to Detect COVID-19?
The head of the research team, Professor Kaywalee Chatdarong, PhD, noted that other countries also have been using canines to detect the presence of COVID-19. She did have some concerns that the utilization of dogs for this purpose may not work in Thailand due to their often-spicy cuisine. However, since the samples used were from students and faculty at the university, as well as people from the surrounding area, the cuisine did not seem to affect the study results, the AP reported.
Thailand is facing a surge in COVID-19 cases with recent clusters reported at construction sites, crowded neighborhoods, and large markets. The research team plans to use the canines in mobile units in communities suspected of being hotspots for the disease.
A major plus of using dogs to sniff out the disease from sweat samples is the ability to test people who may not be able to get out of their homes to be tested.
“People can simply put cotton balls underneath their armpits to collect sweat samples and send them to the lab,” Suwanna Thanaboonsombat, a volunteer who collects samples and brings them to the clinical laboratory for testing, told the AP. “And the result is quite accurate.”
According to the US Centers for Disease Control and Prevention (CDC), dogs can become infected with the SARS-CoV-2 coronavirus. However, their chances of transmitting the disease to humans is extremely low. Nevertheless, to ensure the dogs do not become infected with COVID-19 themselves, the researchers designed the sample containers to avoid contact between the samples and the dogs’ noses.
Living Animals Come with Limitations
While dogs can provide a quick and inexpensive method of testing for COVID-19, they do have limitations.
“5 p.m. is their dinner time. When it’s around 4:50, they will start to be distracted. So, you can’t really have them work anymore,” Chatdarong told the AP. “And we can’t have them working after dinner either because they need a nap. They are living animals and we do have to take their needs and emotions into consideration. But for me, they are heroes and heroines.”
Using Dogs to Detect COVID-19 in Other Countries
Last fall, the Helsinki Airport in Finland announced it would use a team of trained dogs to detect the presence of COVID-19 among visitors to the airport to ensure the health and safety of its customers and their families, and to help prevent the spread of SARS-CoV-2 in Finland.
“We are among the pioneers. As far as we know no other airport has attempted to use canine scent detection on such a large scale against COVID-19,” said Airport Director Ulla Lettijeff in a Finavia press release. “This might be an additional step forward on the way to beating COVID-19.”
In addition to being “man’s best friend,” dogs serve valuable purposes in the medical community. Their strong sense of smell may render them useful in the detection of and fight against illnesses, including COVID-19.
Whether the performance and accuracy of individual dogs can be validated with acceptable quality control (QC) procedures remains to be seen. Medical laboratory managers and pathologists understand the challenges presented with demonstrating accuracy and reproducibility with this method of diagnostic testing. That obstacle has prevented research outcomes from being translated into clinical practice.