University of Alberta researchers developed CIDER-Seq tool and protocols for the study, which they have made freely available to all scientists
Here’s another promising new technology which, given more research into effectiveness and safety, may soon lead to improved clinical laboratory cancer diagnostics. Oncology research scientists have focused much attention on understanding the role of extrachromosomal circular DNA (eccDNA) in human cancer. Now, a new gene sequencing method may help expand their knowledge about that and other circular DNA found in the genomes of bacteria, viruses, and other cells.
University of Alberta (UA) researchers have invented a new way for sequencing circular DNA, according to a recent study published in the journal Nature Protocols. As with any new technological method, this new tool—called CIDER-Seq—will need to be time-tested, but it does hold promise for providing valuable insights into the role these “mysterious loops” play not only in human disease, but in agricultural viruses as well.
A New Tool for Understanding DNA
DNA is considered “circular” when it has a closed loop with no ends. It differs from “linear” DNA chromosomes found in human cell nuclei. Circular DNA include:
Devang Mehta, PhD (above), Postdoctoral Fellow in the University of Alberta’s Department of Biological Sciences, and lead author of the UA study, describes the breakthrough in his team’s on-going work researching the role of eccDNA molecules. “We devised a new molecular biology method and a new bioinformatics algorithm to finally obtain full-length sequences of eccDNA,” he said in a news release. “Our method finally allows us to sequence these molecules completely and gives us and other researchers a tool to better understand what they actually do in the cell.” (Photo copyright: ecrLife.)
According to the UA study, circular DNA enrichment sequencing (CIDER-Seq) “is a technique to enrich and accurately sequence circular DNA without the need for polymerase chain reaction amplification, cloning, and computational sequence assembly.”
CIDER-Seq uses DNA sequencing technology from Pacific Biosciences, Inc. (PacBio) of Menlo Park, Calif. PacBio (NASDAQ:PACB) is an American biotechnology company founded in 2004 that develops and manufactures gene sequencing systems.
Understanding Circular DNA in Any Human or Plant Cell, Including Cancer
Because many viruses that infect crops have circular DNA, Mehta believes the new tool may be particularly helpful to agricultural scientists. His team of researchers, he noted in the UA news release, used an earlier version of CIDER-Seq to study crop plants in Kenya which were genetically engineered to resist circular DNA viruses.
“Our key advance is that, through our method, scientists can finally gain an unbiased, high-resolution understanding of circular DNA in any type of cell. With our invention of CIDER-Seq, we can start to begin to understand the function of these mysterious circular DNAs in human and plant cells,” Mehta said.
However, this technological advance may be equally welcomed by researchers investigating the role of eccDNA in human cancer. Though both healthy and diseased cells may contain circular DNA, the New York Times noted that the “mysterious loops” are “surprisingly common in cancer cells and play a bigger role in many types of cancers than was previously recognized.” The article goes on to state that until now there have not been effective methods for sequencing circular DNA.
In Clinical Chemistry, a panel of eccDNA experts discussed the critical role circular DNA plays in cancer, referred to as extrachromosomal DNA (ecDNA). “Importantly, in cancer cells, ecDNAs seem to be more transcriptionally active than their chromosomal counterparts and have been suspected to confer growth and survival advantage to cancer cells,” the article states.
According to the New York Times, scientists first discovered the existence of circular DNA in the 1960s when “little clumps of DNA” were detected alongside chromosomes. Today, researchers believe circular DNA is more common in the human genome than first realized and could be linked to a variety of conditions and diseases, not solely to cancer.
CIDER-Seq Research May Lead to New Clinical Laboratory Biomarkers
Birgitte Regenberg, PhD, Associate Professor in Ecology and Evolution at the University of Copenhagen, pioneered methods for detecting circular DNA. She told the New York Times, “I think we’re just opening our eyes up.”
Though she says the research has been “cancer-centered,” Regenberg maintains the role circular DNA plays in human biology may prove to be much broader.
“It’s like when a horse has blinders: The blinders focus the science, but they also prevent some things from being understood,” she said.
Clinical laboratory leaders should keep an eye on the use of CIDER-Seq technology. It may lead to the development of new biomarkers for cancer and other diseases.
In the absence of a “gold standard,” researchers are finding a high frequency of false negatives among SARS-CoV-2 RT-PCR tests
Serology tests designed to detect antibodies to the SARS-CoV-2 coronavirus that causes the COVID-19 illness have been dogged by well-publicized questions about accuracy. However, researchers also are raising concerns about the accuracy of molecular diagnostics which claim to detect the actual presence of the coronavirus itself.
“Diagnostic tests, typically involving a nasopharyngeal swab, can be inaccurate in two ways,” said Steven Woloshin, MD, MS, in a news release announcing a new report that “examines challenges and implications of false-negative COVID-19 tests.” Woloshin is an internist, a professor at Dartmouth Institute, and co-director of the Geisel School of Medicine at Dartmouth.
“A false-positive result mistakenly labels a person infected, with consequences including unnecessary quarantine and contact tracing,” he stated in the news release. “False-negative results are far more consequential, because infected persons who might be asymptomatic may not be isolated and can infect others.”
Woloshin led a team of Dartmouth researchers who analyzed two studies from Wuhan, China, and a literature review by researchers in Europe and South America that indicated diagnostic tests for COVID-19 are frequently generating false negatives. The team published their results in the June 5 New England Journal of Medicine (NEJM).
For example, one research team in Wuhan collected samples from 213 hospitalized COVID-19 patients and found that an approved RT-PCR test produced false negatives in 11% of sputum samples, 27% of nasal samples, and 40% of throat samples. Their research was published on the medRxiv preprint server and has not been peer-reviewed.
The literature review Woloshin’s team studied was also published on medRxiv, titled, “False-Negative Results of Initial Rt-PCR Assays for COVID-19: A Systematic Review.” It indicated that the rate of false negatives could be as high as 29%. The authors of the review looked at five studies that had enrolled a total of 957 patients. “The collected evidence has several limitations, including risk of bias issues, high heterogeneity, and concerns about its applicability,” they wrote. “Nonetheless, our findings reinforce the need for repeated testing in patients with suspicion of SARS-Cov-2 infection.”
Another literature review, published in the Annals of Internal Medicine, titled, “Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction–Based SARS-CoV-2 Tests by Time Since Exposure,” estimated the probability of false negatives in RT-PCR tests at varying intervals from the time of exposure and symptom onset. For example, the authors found that the median false-negative rate was 38% if a test was performed on the day of symptom onset, versus 20% three days after onset. Their analysis was based on seven studies, five of which were peer-reviewed, with a total of 1330 test samples.
Doctors also are seeing anecdotal evidence of false negatives. For example, clinicians at UC San Diego Health medical center treated a patient with obvious symptoms of COVID-19, but two tests performed on throat samples were negative. However, a third test, using a sample from a bronchial wash, identified the virus, reported Medscape.
Sensitivity and Specificity of COVID-19 Clinical Laboratory Tests
The key measures of test accuracy are sensitivity, which refers to the ability to detect the presence of the virus, and specificity, the ability to determine that the targeted pathogen is not present. “So, a sensitive test is less likely to provide a false-negative result and a specific test is less likely to provide a false-positive result,” wrote Kirsten Meek, PhD, medical writer and editor, in an article for ARUP Laboratories.
“Analytic” sensitivity and specificity “represent the accuracy of a test under ideal conditions in which specimens have been collected from patients with either high viral loads or a complete absence of exposure,” she wrote. However, “sensitivity and specificity under real-world conditions, in which patients are more variable and specimen collection may not be ideal, can often be lower than reported numbers.”
In a statement defending its ID Now molecular point-of-care test, which came under scrutiny during a study of COVID-19 molecular tests by NYU Langone Health, Northwell Health, and Cleveland Clinic, according to MedTech Dive, Abbott Laboratories blamed improper sample collection and handling for highly-publicized false negatives produced by its rapid test. An FDA issued alert about the test on May 14 noted that Abbott had agreed to conduct post-market studies to identify the cause of the false negatives and suggest remedial actions.
Issues with Emergency Use Authorizations
In their NEJM analysis, Woloshin et al point to issues with the FDA’s process for issuing Emergency Use Authorizations (EUAs). For example, they noted variations in how manufacturers are conducting clinical evaluations to determine test performance. “The FDA prefers the use of ‘natural clinical specimens’ but has permitted the use of ‘contrived specimens’ produced by adding viral RNA or inactivated virus to leftover clinical material,” they wrote.
When evaluating clinical performance, manufacturers ordinarily conduct an index test of patients and compare the results with reference-standard test, according to the Dartmouth researchers. For people showing symptoms, the reference standard should be a clinical diagnosis performed by an independent adjudication panel. However, they wrote, “it is unclear whether the sensitivity of any FDA-authorized commercial test has been assessed in this way.” Additionally, a reference standard for determining sensitivity in asymptomatic people “is an unsolved problem that needs urgent attention to increase confidence in test results for contact-tracing or screening purposes.”
“To truly determine false negatives, you need a gold standard test, which is essentially as close to perfect as we can get,” Stephen Rawlings, MD, PhD, (above), a resident physician of internal medicine and infectious diseases fellow at UC San Diego’s Center for AIDS Research (CFAR), who has been working on SARS-CoV-2 test validation since March. “But there just isn’t one yet for coronavirus,” he told Medscape. (Photo copyright: University of California, San Diego.)
Continued adherence to current measures, such as physical distancing and surface disinfection.
Development of highly sensitive and specific tests or combinations of tests to minimize the risk of false-negative results and ongoing transmission based on a false sense of security.
Improved RT-PCR tests and serological assays.
Development and communication of clear risk-stratified protocols for management of negative COVID-19 test results.
“These protocols must evolve as diagnostic test, transmission, and outcome statistics become more available,” they wrote.
Meanwhile, clinical laboratories remain somewhat on their own at selecting which COVID-19 molecular and serology tests they want to purchase and run in their labs. Complicating such decisions is the fact that many of the nation’s most reputable in vitro diagnostics manufacturers cannot produce enough of their COVID-19 tests to meet demand.
Consequently, when looking to purchase tests for SARS-CoV-2, smaller medical laboratory organizations find themselves evaluating COVID-19 kits developed by little-known or even brand-new companies.
Urinary tract infection (UTI) is the second most common type of infection in the US, accounting for 10.5 million office visits per year and 50 percent of all Medicare hospital admissions. UTI is among the most common cause of bacterial infections in long-term care facility residents.
Effective treatment of a UTI is reliant upon the accurate identification of the pathogens and the correct choice of antibiotics. Although culture-based clinical laboratory testing methods remain the gold standard for diagnosing UTI in both research and clinical laboratories, the clinical utility of such methods continues to be called into question.
This white paper provides insights on the status of clinical utility of rapid molecular testing for UTI, describes settings where molecular testing for UTI is of high value to improving outcomes, details experiences of successful early adopters of this technology.
Find these, and many more business-critical insights in this White Paper:
Learn why a large number of Gram-negative and especially Gram-positive organisms cannot grow in typical culture-based testing conditions, leading to false negatives and missed organisms in a polymicrobial UTI
See a comparison study of traditional urine culture testing to multiplex polymerase chain reaction (PCR) molecular testing, run in parallel, showing that the molecular method found six additional polymicrobial cases for every one found using urine cultures
How, in addition to higher detection rates, PCR can provide results in as little as 6 hours, and may facilitate more appropriate and efficacious treatment that improves clinical care and outcomes
Why insurers and other payers are now acknowledging molecular diagnostic testing, which includes deoxyribonucleic acid-(DNA) or ribonucleic acid-(RNA) based analysis, and much more
White Paper Table of Contents
Chapter 1: Problems and Limitations of Culture-Based Testing for UTI in Contrast to Molecular Testing
Chapter 2: Recent Clinical Trials Focused on UTI Diagnostics Using Rapid Molecular Testing
Chapter 3: Reimbursement Trends and Cost Versus Value in Molecular Testing for UTI
CONCLUSION
Molecular tests are becoming more routine as diagnostic tools, with many now covered by Medicare and commercial insurers. Advantages of molecular tests based on PCR technology include their ability to identify uropathogens traditionally missed by culture-based tests.
Driven by urgent, unmet analytical and clinical care needs, the adoption of the rapid molecular test—particularly RT-PCR for urinary tract infection control and treatment—has important implications.
Find out how this innovative testing strategy could benefit your lab by downloading your FREE copy of “Molecular Testing for Urinary Tract Infection (UTI)” below.
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Coronavirus informatics companies are drawing clinical laboratory test data out of the shadows and into the light and compiling it into critical bioinformatics resources
What better example do we have that clinical laboratory test data is critical to population health than the current COVID-19 pandemic? Medical laboratory scientists, bioinformatics developers, and government healthcare leaders are using lab test data to track the disease’s rate of infection, and through information system dashboards, they are mapping and managing the spread of SARS-CoV-2, the coronavirus that causes the COVID-19 illness.
One such example is the CV19 Lab Testing Dashboard developed by hc1 in Indianapolis, which “integrates SARS-CoV-2 testing data from more than 20,000 testing locations across the country, updating every four hours with information on the number of tests performed and the number of positive and negative results along with demographic information like the gender and age of patients being tested,” noted an article by 360Dx titled, “SARS-CoV-2 Pandemic a Test Case for Role of Lab Data in Population Health.”
“This pandemic is putting a spotlight on how important lab data is,” Brad Bostic, Founder, Chairman, and CEO of hc1, told the Indianapolis Business Journal (IBJ). His bioinformatics firm developed the CV19 dashboard, which draws on data created by a healthcare coalition of commercial and health system clinical laboratories that use the company’s High-Value Care Platform for lab testing.
The CV19 Lab Testing dashboard is free and provides a Local Risk Index that enables public health and government agencies, and healthcare providers, to monitor escalation of infection rate at the county level and predict the need for resources, noted an hc1 news release.
“We can offer insights [about the outbreak] seven to 14 days ahead of when emergency rooms and intensive care units get bogged down,” Bostic told the IBJ.
The hc1 dashboard provides healthcare providers with:
Test data collected from 20,000 locations covering 50 states and 90% of counties;
Information updates within minutes of SARS-CoV-2-PCR test results;
Test data that are quickly shared through an intuitive interface;
Geographic maps of test results that enable insight on COVID-19 infection rates at single county or Public Use Microdata Area level;
Number of tests per day, as well as positive and negative results; and
Displays of positivity rates and aggregated demographic information, such as gender and age.
Geisinger Health Uses Dashboard, Clinical Lab 2.0
The use of medical laboratory tests results in pursuit of population health also illustrates the value of the Clinical Lab 2.0 model, noted 360Dx.
According to 360Dx, Geisinger Health System, a leader in Clinical Lab 2.0, employs informatics tools for population-centric (as opposed to patient-focused) analysis of its SARS-CoV-2 testing. The Pennsylvania-based healthcare system uses lab testing dashboards to:
Review laboratory results in aggregate;
See positivity rates per county; and
Note amount of testing from sites.
“We needed to make sure that everyone could see the amount of testing that was being done, where that testing was coming from, and the results of that testing in a much [clearer] way. We began by setting up dashboards,” Jordan Olson, MD (above), a clinical pathologist and Geisinger’s Division Chief of Clinical Pathology, Informatics and Quality, told 360Dx. [Photo copyright: Cardinal Health/Whitehat Communications.)
Clinical Lab 2.0, a Project Santa Fe initiative, is a “business model leveraging longitudinal data to produce actionable clinical insight driving better outcomes for patients, providers, and stakeholders,” states the nonprofit organization’s website.
Sonora Quest Laboratories in Arizona also uses a dashboard to support its front-line healthcare workers to mitigate the spread of COVID-19, stated a news release.
“Most data flowing into public sector sites is eight to 14 days old, which in the case of COVID-19, is too told to react. Public health action requires the most immediate data possible, including test orders and results as soon as they appear,” said Meghan Shapiro Hunter, Vice President of Operations, Hospital Laboratories, Sonora Quest Laboratories, in the news release.
Other Informatics Technology Tracking COVID-19 Pandemic
Medial EarlySign develops AlgoMarkers that “perform algorithmic processing of lab results, clinical, and EHR data to provide condition-specific, post-analytical, personalized patient risk assessment scores to physicians, population health managers, and healthcare teams,” according to the medical informatics company’s website.
Headquartered in Israel, Medial worked with Maccabi Healthcare Services to develop an AlgoMarker that clinical laboratories, healthcare systems, and life sciences companies can use to spot trends in COVID-19 patients and make disease predictions based on risk, gender, co-morbidities, and medications, noted 360Dx.
Medial EarlySign also developed AlgoMarker algorithms to foresee influenza complications. According to a news release, the algorithms work by flagging people according to:
medical parameters,
demographics,
hospital admissions,
medications,
smoking history,
past diagnoses, and
chronic conditions.
Clinical Laboratory Data Enters the Spotlight
For some time now, medical laboratory data have been supporting positive outcomes and improving patient health from behind the curtain, so to speak. However, that appears to be changing fast as bioinformatics and medical informatics companies compile data in compelling dashboards aimed at helping public officials and healthcare providers manage the spread of COVID-19.
Pathologists, clinical laboratory leaders, and informatics specialists may want to explore use of dashboards to support their population health and COVID-19 testing efforts.
Current events have highlighted the critical role of the hospital laboratory as the primary source of diagnostic information. And with legislation such as PAMA (Protecting Access to Medicare Act) reducing reimbursement, hospital laboratories must determine the best direction in defining the role of the laboratory and its value to the hospital or health system.
Unfortunately, the laboratory’s critical role in determining diagnoses and treatments also makes it vulnerable to abuse. Studies estimate that from 10% to 25% of all hospital-performed laboratory tests in the inpatient setting are not indicated. Additionally, an increasingly complex, ever-expanding set of diagnostic test options necessitates heightened awareness in order to choose the right laboratory test at the right time.
Laboratory stewardship responds to these problems by establishing a true collaboration and partnership between the organization’s clinical leadership and the laboratory, to the benefit of both.
This white paper – the third in a three-part series developed in collaboration with Mayo Clinic Laboratories and Change Healthcare – provides frontline perspective and commentary from experts and physicians on the application and value of decision support in the laboratory. It also includes early-adopter proof points from hospital laboratories that have successfully implemented third-party decision support to achieve their stewardship goals, including EHR interventions and ongoing monitoring of utilization.
This series aims to help clinical laboratory professionals like you understand the risks and requirements, as well as the clinical and financial benefits, of implementing a clinical decision support (CDS) system.
Find these, and many more business-critical insights in this White Paper:
Learn to define your lab’s specific stewardship goals and measure progress toward them using robust analytics tools, in order to compare provider behavior against evidence-based guidelines and equip your lab with the means to take control of test utilization
Understand clinically-grounded guidelines that you can apply in your lab to help address the now-prevalent problem of too much data and information for providers to consume, the result to the benefit of both patients and providers
Hear how one midwestern hospital identified that B-type natriuretic peptide (BNP) was frequently over-ordered on their wards, and the steps they took that led to a decline of 33%-43% in inappropriate BNP orders
Find out why looking at data at the facility level, then at the department level, then at the provider level is of greatest benefit to your lab, and much more
White Paper Table of Contents
Chapter 1: Taking Control of Test Utilization to Curb Clinical Laboratory Waste
Chapter 2: Reducing Variation in Laboratory Testing and Care Delivery
Chapter 3: Data from Lab Test Stewardship Using Third-Party Clinical Decision Support in the Hospital Laboratory
Case Study 1
Case Study 2
Case Study 3
CONCLUSION
A laboratory test stewardship program requires organizational attention, physician champions, meaningful data, and dedicated IT resources to enact changes—with decision support vital to driving a strategic stewardship initiative.
Moreover, as you, as a thought leader pursue the creation of a value-based laboratory, instead of a commoditized service, you will soon identify overutilization and inappropriate lab testing as areas to target for process improvement and cost savings, thus boosting your lab’s value and reinventing your role in your lab’s organization.
Learn what you need to know about these value-enhancing strategies by downloading your FREE copy of “Case Studies in Clinical Laboratory Test Stewardship” below.
Download the White Paper now by completing the form below.
Access to some white papers may require registration. In exchange for providing this free content, we may share your information with the companies whose content you choose to view. By accessing the white paper, you’re agreeing to our Terms of Service and Privacy Policy.
This is another example of technology companies working to develop medical laboratory testing that consumers can use without requiring a doctor’s order for the test
Here’s new technology that could be a gamechanger in the fight against COVID-19 if further research allows it to be used in patient care. The goal of the researchers involved is to enable individuals to test for the SARS-CoV-2 coronavirus from home with the assistance of a smartphone app enhanced by artificial intelligence (AI).
Such an approach could bypass clinical laboratories by allowing potentially infected people to confirm their exposure to the coronavirus and then consult directly with healthcare providers for diagnosis and treatment.
The at-home test is being developed through a partnership between French pharmaceutical company Sanofi and San Jose, Calif.-based Luminostics, creator of a smartphone-based diagnostic platform that “can detect or measure bacteria, viruses, proteins, and hormones from swabs, saliva, urine, and blood,” according to the company’s website.
Users who wish to self-test collect a specimen from their nose via a swab and then insert that swab into a device attached to a smartphone. The device uses chemicals and nanoparticles to examine the collected sample. If the individual has the virus, the nanoparticles in the specimen glow in a way visible to smartphone cameras. The device generates data and AI in the smartphone app processes a report. The app informs the user of the results of this COVID-19 test, and it also enables the user to connect to a doctor directly through telehealth video conferencing to discuss a diagnosis.
“This partnering project could lead to another important milestone in Sanofi’s fight against COVID-19,” said Alan Main, Sanofi’s Executive Vice President, Consumer Healthcare, and Chair of the Global Self-Care Federation, in a press release. “The development of a self-testing solution with Luminostics could help provide clarity to individuals—in minutes—on whether or not they are infected.” (Photo copyright: Global Self-Care Federation.)
According to the press release, the diagnostic platform is composed of:
an iOS/Android app to instruct a user on how to run the test, capture and process data to display test results, and then to connect users with a telehealth service based on the results;
a reusable adapter compatible with most types of smartphones; and
consumables for specimen collection, preparation, and processing.
The COVID-19 test results are available within 30 minutes or less after collecting the sample, notes the Sanofi press release. Advantages cited for having a fast, over-the-counter (OTC) solution for COVID-19 testing include:
easy access and availability;
reduced contact with others, which lowers infection risk; and
timely decision-making for any necessary treatments.
The two companies plan to have their COVID-19 home-testing application available for the public before the end of the year, subject to government regulatory clearances. They intend to make their OTC solution available through consumer and retail outlets as well as ecommerce sites.
Can Sound Be Used to Diagnose COVID-19?
Another smartphone app under development records the sound of coughs to determine if an individual has contracted COVID-19. Researchers at the Swiss Federal Institute of Technology Lausanne (École Polytechnique Fédérale de Lausanne or EPFL) in Switzerland created the Cough-based COVID-19 Fast Screening Project (Coughvid), which utilizes a mobile application and AI to analyze the sound of a person’s cough to determine if it resembles that of a person infected with the SARS-CoV-2 coronavirus.
The inspiration for this project came from doctors who reported that their COVID-19 patients have a cough with a very distinctive sound that differs from other illnesses. The cough associated with COVID-19, according the EPFL website, is a dry cough that has a chirping intake of breath at the end.
“The World Health Organization (WHO) has reported that 67.7% of COVID-19 patients exhibit a ‘dry cough,’ meaning that no mucus is produced, unlike the typical ‘wet cough’ that occurs during a cold or allergies. Dry coughs can be distinguished from wet coughs by the sound they produce, which raises the question of whether the analysis of the cough sounds can give some insights about COVID-19. Such cough sounds analysis has proven successful in diagnosing respiratory conditions like pertussis [Whooping Cough], asthma, and pneumonia,” states the EPFL website.
“We have a lot of contact with medical doctors and some of them told us that they usually were able to distinguish, quite well, from the sound of the cough, if patients were probably infected,” Tomas Teijeiro Campo, PhD, Postdoc Researcher with EPFL and one of the Coughvid researchers, told Business Insider.
The Coughvid app is in its early developmental stages and the researchers behind the study are still collecting data to train their AI. To date, the scientists have gathered more than 15,000 cough samples of which 1,000 came from people who had been diagnosed with COVID-19. The app is intended to be used as a tool to help people decide whether to seek out a COVID-19 clinical laboratory test or medical treatment.
“For now, we have this nice hypothesis. There are other work groups working on more or less the same approach, so we think it has a point,” said Teijeiro Campo. “Soon we will be able to say more clearly if it’s something that’s right for the moment.”
With additional research, innovative technologies such as these could change how clinical laboratories interact with diagnosticians and patients during pandemics. And, if proven accurate and efficient, smartphone apps in the diagnosis process could become a standard, potentially altering the path of biological specimens flowing to medical laboratories.
