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Next-Generation Sequencing Allows Mayo Clinic Researchers to Produce Large Dataset of Patients’ Exomes

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.

The Mayo Clinic scientists published their findings in Mayo Clinic Proceedings titled, “Mayo Clinic Tapestry Study: A Large-Scale Decentralized Whole Exome Sequencing Study for Clinical Practice, Research Discovery, and Genomic Education.”

“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.

Patients with certain medical conditions, such as dementia and hematologic cancers, were excluded.

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. 

—Stephen Beale

Related Information:

Mayo Clinic Tapestry Study: A Large-Scale Decentralized Whole Exome Sequencing Study for Clinical Practice, Research Discovery, and Genomic Education

Mayo Clinic’s Largest-Ever Exome Study Offers Blueprint for Biomedical Breakthroughs

Mayo Clinic to Study 10,000 Patients for Drug-Gene Safety

International Team of Scientists Uses Blood Proteins as Biomarkers to More Accurately Predict Risk for Diseases

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.”

The study was conducted through a collaboration between GlaxoSmithKline Research and Development (GSK), Queen Mary University of London, University College London (UCL), University of Cambridge, and the Berlin Institute of Health (BIH) in Germany.

The researchers published their findings in the journal Nature Medicine titled, “Proteomic Signatures Improve Risk Prediction for Common and Rare Diseases.”

“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.

“Several of our protein signatures performed similar or even better than proteins already trialed for their potential as screening tests, such a prostate specific antigen (PSA) for prostate cancer,” said Julia Carrasco Zanini Sanchez, PhD, postdoctoral research assistant in computational genomics and multi-omics, Queen Mary University of London, and first author of the study, in a UCL news release.

“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. 

—JP Schlingman

Related Information:

Blood Proteins Predict the Risk of Developing More than 60 Diseases

UK Biobank Launches One of the Largest Scientific Studies Measuring Circulating proteins, to Better Understand the Link Between Genetics and Human Disease

Proteomic Signatures Improve Risk Prediction for Common and Rare Diseases

Becker’s Hospital Review Ranks 16 Healthcare Systems with the Largest Investment in EHR Platforms

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. 

  • US Department of Veteran Affairs, Washington, D.C. (Oracle)    $16 billion.
  • Military Health System, Washington, D.C. (Oracle)                    $5.5 billion.
  • Kaiser Permanente, Oakland, Calif. (Epic)                                 $4.0 billion.
  • Catholic Health Initiatives (CommonSpirit Health),
    Englewood, Colo. (Oracle/Meditech)                                         $1.5 billion.
  • Mayo Clinic, Rochester, Minn. (Epic)                                        $1.5 billion.
  • Mass General Brigham, Somerville, Mass. (Epic)                       $1.2 billion.
  • Northwell Health, New Hyde Park, N.Y. (Epic)                          $1.2 billion.
  • Dignity Health, San Francisco (Oracle/Meditech)                          $1 billion.
  • NYC Health and Hospitals, New York, N.Y. (Epic)                       $1 billion.
  • Sutter Health, Sacramento, Calif. (Epic)                                        $1 billion.
  • NewYork-Presbyterian, New York, N.Y. (Epic)                       $964 million.
  • Providence, Renton, Wash. (Epic)                                            $800 million.
  • Trinity Health, Livonia, Mich. (Epic)                                       $800 million.
  • Duke University Health System, Durham, N.C. (Epic)              $700 million. 
  • AdventHealth, Altamonte Springs, Fla. (Epic)                          $660 million.
  • Memorial Hermann Health System, Houston (Epic)                  $500 million.

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.

Shifting EHR Market

According to KLAS’ 2024 US Acute Care EHR Market Share report, Epic was the only EHR vendor to increase its market share in 2023.

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. 

In September, Yale School of Medicine in New Haven, Conn., sent a department of pathology team to visit Geisinger Diagnostic Medicine Institute, Danville, Pa. Geisinger had adopted Epic Beaker and has a workflow similar to Yale’s, according to a Yale News article. 

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.

—Donna Marie Pocius

Related Information:

Most Expensive EHRs, Ranked

Broward Health Transforms Care with Epic Implementation

US Acute Care EHR Market Share 2024

Top 6 EHR Vendors Worldwide

Epic’s EHR Market Share Gains Continue, KLAS Report Shows

US Acute Care EHR Market Share in 2024

Pathology Team Encouraged about Migration to Epic Beaker Laboratory Information System

UK Researchers Use Proteomics to Identify Proteins That Indicate Presence of Cancer Years before Diagnosis

Study findings could lead to new clinical laboratory screening tests that determine risk for cancer

New disease biomarkers generally lead to new clinical laboratory tests. Such may be the case in an investigational study conducted at the University of Oxford in the United Kingdom (UK). Researchers in the university’s Cancer Epidemiology Unit (CEU) have discovered certain proteins that appear to indicate the presence of cancer years before the disease is diagnosed.

The Oxford scientists “investigated associations between 1,463 plasma proteins and 19 cancers, using observational and genetic approaches in participants of the UK Biobank. They found 618 protein-cancer associations and 317 cancer biomarkers, which included 107 cases detected over seven years before the diagnosis of cancer,” News Medical reported.

To conduct their study, the scientists turned to “new multiplex proteomics techniques”  that “allow for simultaneous assessment of proteins at a high-scale, especially those that remain unexplored in the cancer risk context,” News Medical added. 

Many of these proteins were in “blood samples of people who developed cancer more than seven years before they received a diagnosis,” an Oxford Population Health news release notes.

“To be able to prevent cancer, we need to understand the factors driving the earliest stages of its development. These studies are important because they provide many new clues about the causes and biology of multiple cancers, including insights into what’s happening years before a cancer is diagnosed,” said Ruth Travis, BA, MSc, DPhil, senior molecular epidemiologist at Oxford Population Health and senior study author, in the news release.

The Oxford researchers published their findings in the journal Nature Communications titled, “Identifying Proteomic Risk Factors for Cancer Using Prospective and Exome Analyses of 1,463 Circulating Proteins and Risk of 19 Cancers in the UK Biobank.”

“We now have technology that can look at thousands of proteins across thousands of cancer cases, identifying which proteins have a role in the development of specific cancers and which may have effects that are common to multiple cancer types,” said Ruth Travis, BA, MSc, DPhil (above), senior molecular epidemiologist, Oxford Population Health, in a news release. The study findings could lead to new clinical laboratory screening tests for cancer. (Photo copyright: University of Oxford.)

Proteomics to Address Multiple Cancers Analysis 

In their published paper, the Oxford scientists acknowledged other research that identified links between blood proteins and risk for various cancers, including breast, colorectal, and prostate cancers. They saw an opportunity to use multiplex proteomics methods for the simultaneous measurement of proteins “many of which have not previously been assessed for their associations with risk across multiple cancer sites,” the researchers noted.

The researchers described “an integrated multi-omics approach” and the use of the Olink Proximity Extension Assay (PEA) to quantify 1,463 proteins in blood samples from 44,645 participants in the UK Biobank, a large biomedical database and resource to scientists.

Olink, a part of Thermo Fisher Scientific in Waltham, Mass., explains on its website that PEA technology “uniquely combines specificity and scalability to enable high-throughput, multiplex protein biomarker analysis.”

The researchers also compared proteins of people “who did and did not go on to be diagnosed with cancer” to determine differences and identify proteins that suggest cancer risk, News Medical reported.

Proteins Could Assist in Cancer Prevention

“To save more lives from cancer, we need to better understand what happens at the earliest stages of the disease. Data from thousands of people with cancer has revealed really exciting insights into how the proteins in our blood can affect our risk of cancer. Now we need to study these proteins in depth to see which ones could be reliably used for cancer prevention,” Keren Papier, PhD, senior nutritional epidemiologist at Oxford Population Health and joint lead author of the study, told News Medical.

While further studies and regulatory clearance are needed before the Oxford researchers’ approach to identifying cancer in its early stages can be used in patient care, their study highlights scientists’ growing interest in finding biomarker combinations that can predict or diagnose cancer even when it is presymptomatic. By focusing on proteins rather than DNA and RNA, researchers are turning to a source of information other than human genes.

For anatomic pathologists and clinical laboratory leaders, the Oxford study demonstrates how scientific teams are rapidly developing new knowledge about human biology and proteins that are likely to benefit patient care and diagnostics. 

—Donna Marie Pocius

Related Information:

Blood Proteins May Be Able to Predict Risk of Cancer More than Seven Years Before It Is Diagnosed

Identifying Proteomic Risk Factors for Cancer Using Prospective and Exome Analyses of 1,463 Circulating Proteins and Risk of 19 Cancers in the UK Biobank

Proteins in the Blood Could Warn People of Cancer More than Seven Years Before It Is Diagnosed

Blood Proteins Predict Caner Risk Seven Years in Advance, Studies Find

Blood Test Could Detect Cancer Up to Seven Years Earlier

Mayo Clinic Researchers Uses Exome Sequencing to Identify Individuals at Risk of Hereditary Cancer

Half of the people tested were unaware of their genetic risk for contracting the disease

Existing clinical laboratory genetic screening guidelines may be inadequate when it comes to finding people at risk of hereditary breast-ovarian cancer syndromes and Lynch syndrome (aka, hereditary nonpolyposis colorectal cancer). That’s according to a study conducted at the Mayo Clinic in Rochester, Minn., which found that about half of the study participants were unaware of their genetic predisposition to the diseases.

Mayo found that 550 people who participated in the study (1.24%) were “carriers of the hereditary mutations.” The researchers also determined that half of those people were unaware they had a genetic risk of cancer, and 40% did not meet genetic testing guidelines, according to a Mayo Clinic news story.

The discoveries were made following exome sequencing, which the Mayo Clinic news story described as the “protein-coding regions of genes” and the sites for most disease-causing mutations.

“Early detection of genetic markers for these conditions can lead to proactive screenings and targeted therapies, potentially saving lives of people and their family members,” said lead author Niloy Jewel Samadder, MD, gastroenterologist and cancer geneticist at Mayo Clinic’s Center for Individualized Medicine and Comprehensive Cancer Center.

The Mayo researchers published their findings in the journal JCO Precision Oncology titled, “Exome Sequencing Identifies Carriers of the Autosomal Dominant Cancer Predisposition Disorders Beyond Current Practice Guideline Recommendations.”

“This study is a wake-up call, showing us that current national guidelines for genetic screenings are missing too many people at high risk of cancer,” said lead author Niloy Jewel Samadder, MD (above), gastroenterologist and cancer geneticist at Mayo Clinic’s Center for Individualized Medicine and Comprehensive Cancer Center. New screening guidelines may increase the role of clinical laboratories in helping physicians identify patients at risk of certain hereditary cancers. (Photo copyright: Mayo Clinic.)

Advancing Personalized Medicine

“The goals of this study were to determine whether germline genetic screening using exome sequencing could be used to efficiently identify carriers of HBOC (hereditary breast and ovarian cancer) and LS (Lynch syndrome),” the authors wrote in JCO Precision Oncology.

Their work was a project of the Mayo Clinic Center for Individualized Medicine Tapestry study, which aims at advancing personalized medicine and developing a dataset for genetic research.

For the current study, Helix, a San Mateo, Calif. population genomics company, collaborated with Mayo Clinic to perform exome sequencing on the following genes:

According to the Mayo Clinic:

  • BRCA1 can lead to a 50% chance of breast cancer, and a 40% chance of ovarian cancer, respectively, as well as other cancers.
  • BRCA2 mutations suggest risk of breast cancer and ovarian cancer is 50% and 20%, respectively.
  • Lynch syndrome relates to an 80% lifetime risk of developing colorectal cancer and 50% risk of uterine and endometrial cancer.

Mayo/Helix researchers performed genetic screenings on more than 44,000 study participants. According to their published study, of the 550 people who were found to have hereditary breast cancer or Lynch syndrome:

  • 387 had hereditary breast and ovarian cancer (27.2% BRCA1, 42.8% BRCA2).
  • 163 had lynch syndrome (12.3% MSH6, 8.8% PMS2, 4.5% MLH1, 3.8% MSH2, and 0.2% EPCAM).
  • 52.1% were newly diagnosed carriers.
  • 39.2% of the 550 carriers did not meet genetic evaluation criteria set by the National Comprehensive Cancer Network (NCCN).
  • Participants recruited by researchers hailed from Rochester, Minn.; Phoenix, Ariz.; and Jacksonville, Fla.
  • Minorities were less likely to meet the NCCN criteria than those who reported as White (51.5% as compared to 37.5%).

“Our results emphasize the importance of expanding genetic screening to identify people at risk for these cancer predisposition syndromes,” Samadder said.

Exome Data in EHRs  

Exomes of more than 100,000 Mayo Clinic patients have been sequenced and the results are being included in the patients’ electronic health records (EHR) as part of the Tapestry project. This gives clinicians access to patient information in the EHRs so that the right tests can be ordered at the right time, Mayo Clinic noted in its article.

“Embedding genomic data into the patient’s chart in a way that is easy to locate and access will assist doctors in making important decisions and advance the future of genomically informed medicine.” said Cherisse Marcou, PhD, co-director and vice chair of information technology and bioinformatics in Mayo’s Clinical Genomics laboratory.

While more research is needed, Mayo Clinic’s accomplishments suggest advancements in gene sequencing and technologies are making way for data-driven tools to aid physicians.

As the cost of gene sequencing continue to fall due to improvement in the technologies, more screenings for health risk factors in individuals will likely become economically feasible. This may increase the role medical laboratories play in helping doctors use exomes and whole genome sequencing to screen patients for risk of specific cancers and health conditions.

—Donna Marie Pocius

Related Information:

Exome Sequencing Identifies Carriers of the Autosomal Dominant Cancer Predisposition Disorders Beyond Current Practice Guideline Recommendation

Mayo Clinic Uncovers Genetic Cancer Risk in 550 Patients

Mayo Clinic’s Data-Driven Quest to Advance Individualized Medicine

World Economic Forum Publishes Updated List of 12 Breakthroughs in Fight against Cancer That Includes Innovative Clinical Laboratory Test (Part 2)

These advances in the battle against cancer could lead to new clinical laboratory screening tests and other diagnostics for early detection of the disease

As Dark Daily reported in part one of this story, the World Economic Forum (WEF) has identified 12 new breakthroughs in the fight against cancer that will be of interest to pathologists and clinical laboratory managers.

As we noted in part one, the WEF originally announced these breakthroughs in an article first published in May 2022 and then updated in October 2024. According to the WEF, the World Health Organization (WHO) identified cancer as a “leading cause of death globally” that “kills around 10 million people a year.”

The WEF is a non-profit organization base in Switzerland that, according to its website, “engages political, business, academic, civil society and other leaders of society to shape global, regional and industry agendas.”

Monday’s ebrief focused on four advances identified by WEF that should be of particular interest to clinical laboratory leaders. Here are the others.

Personalized Cancer Vaccines in England

The National Health Service (NHS) in England, in collaboration with the German pharmaceutical company BioNTech, has launched a program to facilitate development of personalized cancer vaccines. The NHS Cancer Vaccine Launch Pad will seek to match cancer patients with clinical trials for the vaccines. The Launch Pad will be based on messenger ribonucleic acid (mRNA) technology, which is the same technology used in many COVID-19 vaccines.

The BBC reported that these cancer vaccines are treatments, not a form of prevention. BioNTech receives a sample of a patient’s tumor and then formulates a vaccine that exposes the cancer cells to the patient’s immune system. Each vaccine is tailored for the specific mutations in the patient’s tumor.

“I think this is a new era. The science behind this makes sense,” medical oncologist Victoria Kunene, MBChB, MRCP, MSc (above), trial principal investigator from Queen Elizabeth Hospital Birmingham (QEHB) involved in an NHS program to develop personalized cancer vaccines, told the BBC. “My hope is this will become the standard of care. It makes sense that we can have something that can help patients reduce their risk of cancer recurrence.” These clinical trials could lead to new clinical laboratory screening tests for cancer vaccines. (Photo copyright: Queen Elizabeth Hospital Birmingham.)

Seven-Minute Cancer Treatment Injection

NHS England has also begun treating eligible cancer patients with under-the-skin injections of atezolizumab, an immunotherapy marketed under the brand name Tecentriq, Reuters reported. The drug is usually delivered intravenously, a procedure that can take 30 to 60 minutes. Injecting the drug takes just seven minutes, Reuters noted, saving time for patients and cancer teams.

The drug is designed to stimulate the patient’s immune system to attack cancer cells, including breast, lung, liver, and bladder cancers.

AI Advances in India

One WEF component—the Center for the Fourth Industrial Revolution (C4IR)—aims to harness emerging technologies such as artificial intelligence (AI) and virtual reality. In India, the organization says the Center is seeking to accelerate use of AI-based risk profiling to “help screen for common cancers like breast cancer, leading to early diagnosis.”

Researchers are also exploring the use of AI to “analyze X-rays to identify cancers in places where imaging experts might not be available.”

Using AI to Assess Lung Cancer Risk

Early-stage lung cancer is “notoriously hard to detect,” WEF observed. To help meet this challenge, researchers at Massachusetts Institute of Technology (MIT) developed an AI model known as Sybil that analyzes low-dose computed tomography scans to predict a patient’s risk of getting the disease within the next six years. It does so without a radiologist’s intervention, according to a press release.

The researchers tested the system on scans obtained from the National Lung Cancer Screening Trial, Mass General Hospital (MGH), and Chang Gung Memorial Hospital. Sybil achieved C-index scores ranging from 0.75 to 0.81, they reported. “Models achieving a C-index score over 0.7 are considered good and over 0.8 is considered strong,” the press release notes.

The researchers published their findings in the Journal of Clinical Oncology.

Using Genomics to Identify Cancer-Causing Mutations

In what has been described as the “largest study of whole genome sequencing data,” researchers at the University of Cambridge in the UK announced they have discovered a “treasure trove” of information about possible causes of cancer.

Using data from England’s 100,000 Genomes Project, the researchers analyzed the whole genome sequences of 12,000 NHS cancer patients.

This allowed them “to detect patterns in the DNA of cancer, known as ‘mutational signatures,’ that provide clues about whether a patient has had a past exposure to environmental causes of cancer such as smoking or UV light, or has internal, cellular malfunctions,” according to a press release.

The researchers also identified 58 new mutational signatures, “suggesting that there are additional causes of cancer that we don’t yet fully understand,” the press release states.

The study appeared in April 2022 in the journal Science.

Validation of CAR-T-Cell Therapy

CAR-T-cell therapy “involves removing and genetically altering immune cells, called T cells, from cancer patients,” WEF explained. “The altered cells then produce proteins called chimeric antigen receptors (CARs), which can recognize and destroy cancer cells.”

The therapy appeared to receive validation in 2022 when researchers at the University of Pennsylvania published an article in the journal Nature noting that two early recipients of the treatment were still in remission after 12 years.

However, the US Food and Drug Administration (FDA) announced in 2023 that it was investigating reports of T-cell malignancies, including lymphoma, in patients who had received the treatment.

WEF observed that “the jury is still out as to whether the therapy is to blame but, as a precaution, the drug packaging now carries a warning.”

Breast Cancer Drug Repurposed for Prevention

England’s NHS announced in 2023 that anastrozole, a breast cancer drug, will be available to post-menopausal women to help reduce their risk of developing the disease.

“Around 289,000 women at moderate or high risk of breast cancer could be eligible for the drug, and while not all will choose to take it, it is estimated that if 25% do, around 2,000 cases of breast cancer could potentially be prevented in England, while saving the NHS around £15 million in treatment costs,” the NHS stated.

The tablet, which is off patent, has been used for many years to treat breast cancer, the NHS added. Anastrozole blocks the body’s production of the enzyme aromatase, reducing levels of the hormone estrogen.

Big Advance in Treating Cervical Cancer

In October 2024, researchers announced results from a large clinical trial demonstrating that a new approach to treating cervical cancer—one that uses currently available therapies—can reduce the risk of death by 40% and the risk of relapsing by 36%.

Patients are commonly treated with a combination of chemotherapy and radiotherapy called chemoradiotherapy (CRT), according to Cancer Research UK. But outcomes are improved dramatically by administering six weeks of induction therapy prior to CRT, the researchers reported.

“This is the biggest improvement in outcome in this disease in over 20 years,” said Mary McCormack, PhD, clinical oncologist at the University College London and lead investigator in the trial.

The scientists published their findings in The Lancet.

Pathologists and clinical lab managers will want to keep track of these 12 breakthrough advancements in the diagnosis and treatment of cancer highlighted by the WEF. They will likely lead to new screening tests for the disease and could save many lives.

—Stephen Beale

Related Information:

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MIT Researchers Develop an AI Model That Can Detect Future Lung Cancer Risk

Largest Study of Whole Genome Sequencing Data Reveals New Clues to Causes of Cancer

Tens of Thousands of Women Set to Benefit from ‘Repurposed’ NHS Drug to Prevent Breast Cancer

Cervical Cancer Treatment Breakthrough Cuts Risk of Death By 40%

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