Nearly 100,000 patients submitted saliva samples to a genetic testing laboratory, providing insights into their disease risk
Researchers at Mayo Clinic have employed next-generation sequencing technology to produce a massive collection of exome data from more than 100,000 patients, offering a detailed look at genetic variants that predispose people to certain diseases. The study, known as Tapestry, was administered by doctors and scientists from the clinic’s Center for Individualized Medicine and produced the “largest-ever collection of exome data, which include genes that code for proteins—key to understanding health and disease,” according to a Mayo Clinic news release.
For our clinical laboratory professionals, this shows the keen interest that a substantial portion of the population has in using their personal genetic data to help physicians identify their risk for many diseases and types of cancer. This support by healthcare consumers is a sign that labs should be devoting attention and resources to providing these types of gene sequencing services.
As Mayo explained in the news release, the exome includes nearly 20,000 genes that code for proteins. The researchers used the dataset to analyze genes associated with higher risk of heart disease and stroke along with several types of cancer. They noted that the data, which is now available to other researchers, will likely provide insights into other diseases as well, the news release notes.
“What we’ve accomplished with the Tapestry study is a blueprint for future endeavors in medical science,” said gastroenterologist and lead researcher Konstantinos Lazaridis, MD (above), in the news story. “It demonstrates that through innovation, determination and collaboration, we can deeply advance our understanding of DNA function and eventually other bio-molecules like RNA, proteins and metabolites, turning them into novel diagnostic tools to improve health, prevent illness, and even treat disease.” Some of these newly identified genetic markers may be incorporated into new clinical laboratory assays. (Photo copyright: Mayo Clinic.)
How Mayo Conducted the Tapestry Study
One notable aspect of the study was its methodology. The study launched in July 2020 during the COVID-19 pandemic. Since many patients were quarantined, researchers conducted the study remotely, without the need for the patients to visit a Mayo facility. It ran for five years through May 31, 2024. The news release notes that it’s the largest decentralized clinical trial ever conducted by the Mayo Clinic.
The researchers identified 1.3 million patients from the main Mayo Clinic campuses in Minnesota, Arizona, and Florida who met the following eligibility criteria:
Participants had to be 18 or older,
they had to have internet and email access, and
be sufficiently proficient in speaking and reading English.
More than 114,000 patients consented to participate, but some later withdrew, resulting in a final sample of 98,222 individuals. Approximately two-thirds were women. Mean age was 57 (61.9 for men and 54.3 for women).
“It was a tremendous effort,” said Mayo Clinic gastroenterologist and lead researcher Konstantinos Lazaridis, MD, in the news release. “The engagement of such a number of participants in a relatively short time and during a pandemic showcased the trust and the dedication not only of our team but also of our patients.”
He added that the researchers “learned valuable lessons about some patients’ decisions not to participate in Tapestry, which will be the focus of future publications.”
Three Specific Genes
Enrolled patients were invited to visit a website, where they could view a video and submit an eligibility form. Once approved, they completed a digital consent agreement and received a saliva collection kit. Participants were also invited to provide information about their family history.
Helix, a clinical laboratory company headquartered in San Mateo, Calif., performed the exome sequencing.
Though Helix performed whole exome sequencing, the researchers were most interested in three specific sets of genes:
Patients received clinical results directly from Helix along with information about their ancestry. Clinical results were also transmitted to Mayo Clinic for inclusion in patients’ electronic health records (EHRs).
Among the participants, approximately 1,800 (1.9%) had what the researchers described as “actionable pathogenic or likely pathogenic variants.” About half of these were BRCA1/2.
These patients were invited to speak with a genetic counselor and encouraged to undergo additional testing to confirm the variants.
Tapestry Genomic Registry
In addition to the impact on the participants, Mayo Clinic’s now has an enormous amount of raw sequencing data stored in the Tapestry Genomic Registry, where it will be available for future research.
The database “has become a valuable resource for Mayo’s scientific community, with 118 research requests submitted,” the researchers wrote in the news release. Mayo has distribution more than a million exome datasets to other genetic researchers.
“What we’ve accomplished with the Tapestry study is a blueprint for future endeavors in medical science,” Lazaridis noted. “It demonstrates that through innovation, determination, and collaboration, we can deeply advance our understanding of DNA function and eventually other bio-molecules like RNA, proteins and metabolites, turning them into novel diagnostic tools to improve health, prevent illness, and even treat disease.”
Everything about this project is consistent with precision medicine, and the number of individuals discovered to have risk of cancers is relevant. Clinical laboratory professionals understand these ratios and the importance of early detection and early intervention.
Though the No Surprises Act was enacted to prevent such surprise billing, key aspects of the legislation are apparently not being enforced
Dani Yuengling thought she had properly prepared herself for the financial impact of a breast biopsy. After all, it’s a simple procedure, especially if done by fine needle aspiration (FNA). Then, the 35-year-old received a bill for $18,000! And that was after insurance and though she had received a much lower advanced quote, according to an NPR/Kaiser Health News (NPR/KHN) bill-of-the-month investigation.
So, what happened? And what can anatomic pathology groups and clinical laboratories do to ensure their patients don’t receive similar surprise bills?
Yuengling had lost her mother to breast cancer in 2017. Then, she found a lump in her own breast. Following a mammogram she decided to move forward with the biopsy. Her doctor referred her to Grand Strand Medical Center in Myrtle Beach, S.C.
But she needed to know how much the procedure would cost. Her health plan had a $6,000 deductible. She worried she might have to pay for the entire amount of a very expensive procedure.
However, the hospital’s online “Patient Payment Estimator” informed her that an uninsured patient typically pays about $1,400 for the procedure. Yuengling was relieved. She assumed that with insurance the amount would be even less, and thankfully, clinical laboratory test results of the biopsy found that she did not have breast cancer.
Then came the sticker shock! The bill broke down like this:
$17,979 was the total for her biopsy and everything that came with it.
Her insurer, Cigna, brought the cost down to the in-network negotiated rate of $8,424.14.
Her insurance then paid $3,254.47.
Yuengling was responsible for $5,169.67 which was the balance of her deductible.
So, why was the amount Yuengling owed higher than the bill would have been if she had been uninsured and paid cash for the procedure?
According to the NPR/KHN investigation, this is not an uncommon occurrence. The investigators reported that nearly 30% of American workers have high deductible health plans (HDHPs) and may face larger expenses than what a hospital’s cash price would have been for uninsured individuals.
Dani Yuengling (above) knew she had to take the lump in her breast seriously. Her mother had died of breast cancer. “It was the hardest experience, seeing her suffer,” Yuengling told NPR/KHN. Fortunately, following a biopsy procedure, clinical laboratory testing showed she was cancer free. But the bill for the procedure was shockingly higher than she’d expected based on the hospital’s patient payment estimator. (Photo copyright: Kaiser Health News.)
Take the Cash Price
In 2021, Bai was part of a John’s Hopkins research team that analyzed US hospital cash prices compared with commercial negotiated rates for specific healthcare services.
“The 70 CMS-specified hospital services represent 74 unique Current Procedural Terminology (CPT) diagnosis related group codes (four services were represented by two codes),” the authors wrote. “Cash prices and payer-specific negotiated prices for the 70 services were obtained from Turquoise Health, a data service company that specializes in collecting pricing information from hospitals.”
They continued, “Cash prices can affect the cost exposure of 26 million uninsured individuals and concern nearly one-third of US workers enrolled in high-deductible health plans, who are often responsible to pay for medical bills without a third-party contribution and thus are interested in having access to low cash prices. In contrast with the commercial price negotiated bilaterally between hospitals and insurers providing insurance plans, the cash price is determined unilaterally by the hospital and might be expected to be higher than negotiated prices.”
However, the team’s research found otherwise. “Across the 70 CMS-specified services … some hospitals set their cash price comparable to or lower than their commercial negotiated price,” they concluded.
Bai advises patients to ask healthcare providers about the cash price before undergoing any procedure no matter what their insurance status is. “It should be a norm,” she told NPR/KHN.
Federal No Surprises Act is not Foolproof
Yuengling was charged an extraordinarily high amount for her procedure compared to other hospitals in her area. Fair Health Consumer estimates the cost of the procedure Yuengling received cost an average of $3,500 at other local hospitals. Uninsured patients likely pay even less.
A spokesperson for Grand Street Medical Center blamed the inaccurate estimate on “a glitch” in the payment estimator system. The hospital has since removed some procedures from the tool until it can be corrected. Yuengling initially disputed the charge with the hospital but in the end decided to pay the full amount she owed.
NPR/KHN recommends that insured patients consult with their health insurance company to get an estimate before any procedure. That is the purpose of the No Surprises Act which was enacted as part of the Consolidated Appropriations Act, 2021 (CAA).
The law requires health insurance companies to provide their members with an estimate of medical costs upon their request. The Act also empowers patients to file federal complaints about their medical bills.
Patients who find themselves in a similar situation to Yuengling may want to consider paying the cash price for the procedure. Although this may not be common practice, Jacqueline Fox, JD, a healthcare attorney and professor of law at the University of South Carolina’s Joseph F. Rice School of Law, told NPR/KHN that there is not a law she is aware of that would prohibit patients from doing so.
Anatomic pathology groups and clinical laboratories should check that their online prices and estimation tools comply with the No Surprises Act to ensure that what happened to Yuengling does not happen with their patients. They also could inform patients on how to pay cash for procedures if insurance rates are too high. Medical professionals and patients can work together to achieve transparency in healthcare pricing.
What researchers call “the largest proteomic study in the world” could lead to new clinical laboratory assays for determining genetic risk for multiple cancers
Examining blood proteins may be superior to clinical information in determining an individual’s risk for developing multiple diseases. That’s according to a new study conducted by researchers from the UK, America, and Germany who determined that measuring thousands of proteins from a single drop of blood can predict the onset of several illnesses.
The findings may provide clinical laboratories and physicians with new assays to more accurately predict an individual’s risk for more than 60 diseases.
“With data on genetic, imaging, lifestyle factors and health outcomes over many years, this will be the largest proteomic study in the world to be shared as a global scientific resource,” said Naomi Allen, MSc, DPhil, chief scientist at UK Biobank and professor of epidemiology, University of Oxford, in a UK Biobank news release. “These combined data could enable researchers to make novel scientific discoveries about how circulating proteins influence our health, and to better understand the link between genetics and human disease.”
“Measuring protein levels in the blood is crucial to understanding the link between genetic factors and the development of common life-threatening diseases,” said Naomi Allen, MSc, DPhil (above), chief scientist at UK Biobank and professor of epidemiology, University of Oxford, in a news release. With further study, this research could lead to new clinical laboratory assays that help physicians predict an individual’s risk for certain diseases including many forms of cancer. (Photo copyright: UK Biobank.)
Protein Signatures Outperform PSA Testing
To conduct their research, the team collected data from the UK Biobank Pharma Proteomics Project (UKB-PPP). This initiative is “one of the world’s largest studies of blood protein concentrations” and “aims to significantly enhance the field of ‘proteomics,’ enabling better understanding of disease processes and supporting innovative drug development,” according to the Biobank’s website.
The scientists analyzed the values of approximately 3,000 plasma proteins among 41,931 participants in the UKB-PPP. They examined the 10-year potential of developing certain diseases by measuring the plasma proteome and linking those observations to incident cases noted in electronic health records (EHRs).
The team specifically looked at the pathology types for several illnesses and utilized advanced techniques to identify a signature of proteins associated with those various diseases. They found their protein-based model exceeded traditional prediction methods when comparing the models with polygenic risk scores.
“We are therefore extremely excited about the opportunities that our protein signatures may have for earlier detection and ultimately improved prognosis for many diseases, including severe conditions such as Multiple myeloma and idiopathic pulmonary fibrosis,” she added. “We identified so many promising examples; the next step is to select high priority diseases and evaluate their proteomic prediction in a clinical setting.”
Identifying Individuals at High Risk for Certain Diseases
Of the thousands of known proteins in humans, the team focused on about 20 proteins found in blood. With as few as five proteins and as many as 20, they were able to do a risk assessment on 67 diseases, including:
The model could prove to be beneficial in the development of new therapies for certain diseases.
“A key challenge in drug development is the identification of patients most likely to benefit from new medicines. This work demonstrates the promise in the use of large-scale proteomic technologies to identify individuals at high risk across a wide range of diseases, and aligns with our approach to use tech to deepen our understanding of human biology and disease,” said Robert Scott, vice president and head of human genetics and genomics, GSK, and co-lead author of the study in the UCL news release.
“Further work will extend these insights and improve our understanding of how they are best applied to support improved success rates and increased efficiency in drug discovery and development,” he added.
“We are extremely excited about the opportunity to identify new markers for screening and diagnosis from the thousands of proteins circulating and now measurable in human blood,” said Claudia Langenberg, PhD, director of the Precision Healthcare University Research Institute (PHURI) at Queen Mary University of London and professor of computational medicine at the Berlin Institute of Health, in the UCL news release. “What we urgently need are proteomic studies of different populations to validate our findings, and effective tests that can measure disease relevant proteins according to clinical standards with affordable methods.”
More research and studies are needed before the protein-based model can be used to predict disease in clinical settings. However, the model could someday provide clinical laboratories, pathologists, and physicians with new assays that more accurately forecast an individual’s risk for certain illnesses.
Compilation shows US Veterans Administration spent the most at $16B
Clinical laboratory leaders and pathologists will be interested in which hospital systems are making the largest investments in electronic health record (EHR) technologies. Especially considering laboratory information systems (LIS) must interface with these platforms and require extensive reworking when hospitals change their EHRs. For example, hospitals moving to the Epic Systems EHR often require their laboratories to implement the Epic Beaker LIS as well.
According to information sourced by Becker’s Hospital Review, the top 16 hospital systems each spent $500 million or more on EHRs, adding, however, that the information is “not an exhaustive list.”
Number three on the list is Kaiser Permanente which operates multiple hospitals within its nine healthcare networks across the United States serving 12.5 million members. For that reason, its total investment in EHR technology represents a much larger number of hospitals than the other health systems on the list.
Of the 16 providers on the list, 12 installed EHRs provided by Epic Systems of Verona, Wis. Four of the providers implemented EHRs from Oracle Health (formerly Cerner), North Kansas City, Mo., and Meditech of Westwood, Mass.
“Looking forward, there are many advantages in terms of investing in the future and how we will be aligned with technologies including digital and AI applications,” said pathologist Angelique W. Levi, MD (above), vice chair and director of pathology reference services at Yale School of Medicine, in a news release following a site visit to Geisinger Diagnostic Medicine Institute in Danville, Pa., to see Epic Beaker in operation at Geisinger’s clinical laboratory. “But what we gain immediately—having all the patient information accessible in one place in a linked and integrated fashion—is very important.” (Photo copyright: Yale School of Medicine.)
Provider, EHR, Investment
Becker’s list below shows the total amount invested by the 16 healthcare systems was approximately $38.32 billion. The average EHR implementation cost is $2.39 billion for a large healthcare provider.
Becker’s stated they assembled this list from public sources and that there may be other EHR/hospital contracts with a total cost that also would make the list. It is not common to see a list of what hospitals actually spend to acquire and deploy a new EHR.
Epic added 153 hospitals to its client base in 2023. Epic’s EHR competitors—Oracle and Meditech—both experienced declines in client retention rate, Healthcare IT News reported based on the KLAS data.
“Both current and prospective large organization customers are drawn to Epic because they see the vendor as a consistently high performer that provides strong healthcare IT [information technology], quality relationships, and the opportunity to streamline workflows and improve clinicians’ satisfaction,” Healthcare IT News said of the KLAS report’s findings.
In a blog post, authors of the KLAS report explained that in 2023 Oracle added specialty hospital clients and Meditech “saw several new sales” which included healthcare systems and independent providers.
In the next few years, the industry is “ripe for disruption. Another vendor could come in and turn everything on its head,” the KLAS blog article concluded. “Even those who choose Epic want to have more competitive options to choose from.”
Preparing for an LIS Change
Clinical laboratory leaders who may be transitioning their LIS during a new EHR installation may learn from colleagues who completed such an implementation.
Angelique Levi, MD, vice chair and director of pathology reference services at Yale School of Medicine, who was part of the pathology team, noted that one challenge for labs is addressing “information that’s from many different places when we’re talking about cancer care, prognostic testing, and diagnostics.
“It’s become much more complicated to manage all those data points,” she continued. “Without being on an integrated and aligned system, you’re getting pieces of information from different places, but not the ability to have linked and integrated reports in one spot.”
EHR implementations are among the most labor-intensive, expensive projects undertaken by hospitals. Therefore, it is crucial that clinical laboratory and pathology leaders research and learn why an EHR (and possibly LIS) change is needed, what is expected, and when results will be received.
The research also could provide new opportunities for clinical laboratories to be involved in diagnosing patients’ conditions and help guide selection of appropriate radiation therapies.
The protection comes not from D. radiodurans itself, but from a synthetic antioxidant called melatonin-derived protective (MDP) developed by Michael Daly, PhD, a professor in USU School of Medicine’s Department of Pathology who was inspired by chemistry within the microbe, according to the news release.
“It is this ternary complex that is MDP’s superb shield against the effects of radiation,” said Brian Hoffman, PhD, in the press release. Hoffman, a professor of chemistry at NWU, worked with Daly on the research.
The secret, the two scientists discovered, lies in the combination of three components: phosphate and a designed synthetic peptide known as DP1 which are bound to manganese.
“We’ve long known that manganese ions and phosphate together make a strong antioxidant, but discovering and understanding the ‘magic’ potency provided by the addition of the third component is a breakthrough,” said Brian Hoffman, PhD (above), Professor of Molecular Biosciences at Northwestern University. “This study has provided the key to understanding why this combination is such a powerful—and promising—radioprotectant.” Continuing research in this area might give clinical laboratories new opportunities to screen patients for vaccines and radiation treatments. (Photo copyright: Northwestern University.)
Surviving on Mars
The new research built on a 2022 study, also led by Daly and Hoffman, in which the scientists tried to determine how long D. radiodurans and other microorganisms could survive on Mars when dried and frozen. As noted in an earlier NWU press release, the planet “is constantly bombarded by intense galactic cosmic radiation and solar protons.”
They subjected the microbes to the same cold and arid conditions present on Mars and exposed the organisms to varying levels of radiation. The researchers determined that if deeply buried, D. radiodurans could survive for more than 280 million years and withstand 140,000 grays of radiation. “This dose is 28,000 times greater than what would kill a human,” the press release notes.
Using an advanced spectroscopy technique, the researchers measured the levels of manganese antioxidants within the microorganisms. They determined that higher amounts of the antioxidants increased resistance to radiation.
Fabricating MDP
Daly describes MDP as “a simple, cost-effective, nontoxic and highly effective radioprotector,” according to Live Science.
“Ionizing radiation—such as X-rays, gamma rays, solar protons and galactic cosmic radiation—is highly toxic to both bacteria and humans,” Daly, told Live Science, adding, “In bacteria, radiation can cause DNA damage, protein oxidation, and membrane disruption, leading to cell death. In humans, radiation exposure can result in acute radiation syndrome, increased cancer risk, and damage to tissues and organs.”
Manganese is part of a complex within the microbes that removes the free radicals, Live Science explained.
Daly’s team designed a “lab-made version” of this mechanism by combining manganese and phosphate ions with a synthetic peptide that is similar to amino acids within the microbe.
In the new study, the researchers used a technique known as advanced paramagnetic resonance spectroscopy to characterize MDP, revealing the ternary complex as the “active ingredient” that gives it protective powers.
Real-world Applications for MDP
Daly described some potential applications of their discovery.
“Astronauts on deep-space missions are exposed to chronic high-level ionizing radiation, primarily from cosmic rays and solar protons,” he told Live Science, suggesting that MDP “could be administered orally to mitigate these space radiation risks.”
He added that MDP could also be used as a form of prevention against acute radiation syndrome. “There’s also a well-recognized link between radiation resistance and aging,” he said.
The technology could also lead to new radiation-inactivated vaccines, the latest NWU press release notes.
A team of scientists at USU employed MDP to develop an experimental vaccine that could help prevent chlamydia infection, according to a USU press release. The technology enabled researchers to inactivate the bacterium with radiation while protecting the proteins needed to stimulate immune response.
“If you want an effective whole-cell chlamydia vaccine, then you should probably try not to cook, zap, or otherwise damage the surface antigens that it relies on,” said USU researcher and assistant professor in the department of microbiology and immunology George Liechti, PhD, in the press release.
In a study to gauge the vaccine’s potential, researchers vaccinated mice and then exposed them to the mouse pathogen Chlamydia muridarum, which is related to the human Chlamydia trachomatis.
The mice “showed faster infection clearance, lower bacterial levels, and less tissue damage compared to traditional vaccines,” the press release states.
This new understanding of how antioxidants work is opening avenues of research that could lead to vaccines for radiation exposure and treatments for radiation illnesses. Clinical laboratories will play a role in screening patients and helping pathologists determine the most effective treatments.
