Recent research into transposons within DNA dark matter may produce new biomarkers for clinical laboratory testing and diagnostics
There’s been another interesting development in the study of genetic “dark matter” which may give rise to new biomarkers for clinical laboratory diagnostics and testing. This is worth noting, because biological dark matter has long been considered non-critical and immaterial to the human organism or human evolution. Researchers often refer to it as junk DNA.
However, newly-released research suggests that transposons (aka, transposable elements) contained within our genetic dark matter may play a “critical role in mammalian development,” according to a UC Berkeley news release. Transposons, the release notes, are “viral elements [that] have invaded mammalian genomes for millions of years and currently make up nearly half the DNA in the genomes of all living mammals.”
The study, led by researchers at the University of California, Berkeley, and Washington University in St. Louis, found at least one family of transposons that affected the viability of test mice. They believe the transposon could play a similar role in all mammals—including humans.
Molecular biologist Lin He, PhD (above), led the study conducted at the University of California, Berkeley, and Washington University in St. Louis, which found that bits of DNA once considered “junk” may actually perform important functions, such as ensuring fertility. These findings may one day confirm new biomarkers for clinical laboratory testing. (Photo copyright: MacArthur Foundation.)
How Removal of a Transposon Led to Death
The researchers found that the function of one type of transposon affected whether a mouse fetus could form properly and survive birth. The transposon “regulates the proliferation of cells in the early fertilized embryo and the timing of implantation in the mother’s uterus,” the news release notes.
To perform the research, the scientists removed a specific transposon that controls the proliferation of cells in the early fertilization of an embryo from the mice. After extracting that transposon, half of the mouse pups died before birth.
The researchers then looked at other mammalian species—including humans—and “found virus-derived regulatory elements linked to cell proliferation and timing of embryo implantation, suggesting that ancient viral DNA has been domesticated independently to play a crucial role in early embryonic development in all mammals,” UC Berkeley noted.
The researchers suggest that some of our dark matter DNA has an important function in our embryonic maturation and survival.
“The mouse and humans share 99% of their protein coding genes in their genomes—we are very similar with each other,” said molecular biologist and senior author of the study Lin He, PhD, Associate Professor, Department of Molecular and Cell Biology, UC Berkeley, in the news release.
“So, what constitutes the differences between mice and humans? One of the major differences is gene regulation—mice and humans have the same genes, but they can be regulated differently. Transposons have the capacity to generate a lot of gene regulatory diversity and could help us to understand species-specific differences in the world.”
“The real significance of this story is it tells us how evolution works in the most unexpected manner possible,” said geneticist and study co-author Ting Wang, PhD, Sanford and Karen Loewentheil Distinguished Professor of Medicine, Department of Genetics, Washington University School of Medicine, in the UC Berkeley news release.
“Transposons were long considered useless genetic material, but they make up such a big portion of the mammalian genome. A lot of interesting studies illustrate that transposons are a driving force of human genome evolution. Yet, this is the first example that I know of where deletion of a piece of junk DNA leads to a lethal phenotype, demonstrating that the function of specific transposons can be essential,” he added.
Their research could have implications for human fertility as many miscarriages in humans are due to undiagnosed conditions or have no apparent genetic component.
“If 50% of our genome is non-coding or repetitive—this dark matter—it is very tempting to ask the question whether or not human reproduction and the causes of human infertility can be explained by junk DNA sequences,” he said.
Thus, the UC Berkeley/Washington University study is building on prior research demonstrating that dark matter DNA may not be “junk” after all. More specifically, transposons may eventually have value as biomarkers for clinical laboratory tests and diagnostics.
Of course, additional research and studies are needed to validate these findings and provide greater knowledge about the function of specific transposons. But it’s an intriguing development that’s worth following.
Several young companies hope to expand the direct-to-consumer test market by introducing new diagnostic tests to serve the women’s health market
Providing women with at-home lab test kits is the goal of a growing class of start-up companies that are bringing to market consumer test kits for a range of health conditions common to women. These companies believe they can shift a substantial volume of such testing away from the nation’s medical laboratories.
Moreover, diagnostic startups that develop at-home direct-to-consumer (DTC) clinical laboratory genetic tests have been hot commodities among venture capitalists and other healthcare investors willing to put tens of millions of dollars into these new firms. The New York Times observed that, until recently, women’s healthcare needs have rarely been the focus of new diagnostic testing companies, but that the situation may be changing.
“Femtech” (short for female technology) products and services that address the health and wellness needs of women is the new buzz word in healthcare. It describes female-focused diagnostic startups aiming at vaginal health and other medical issues that go beyond reproductive health concerns.
This, however, is a dual-edged sword for clinical laboratory leaders. Growth in this segment could lead to new diagnostics tests that boost a medical lab’s bottom line or, conversely, it could reduce revenue as patients self-diagnose urinary tract infections (UTIs), yeast infections, and other conditions through at-home DTC testing.
“The market potential is huge,” Michelle Tempest, MD (above), a partner at the London-based healthcare consulting firm Candesic, told The New York Times. “There’s definitely an increasing appetite for anything in the world which is technology and a realization that female consumer power has arrived—and that it’s arrived in healthcare.” Tempest maintains the women’s health marketplace is ripe for growth, which could mean a boon for clinical laboratory testing and diagnostics designed specifically for women. (Photo copyright: Candesic.)
Vaginal Microbiome At-home Clinical Laboratory Tests in High Demand
One area in particular drawing the attention of several female-led startups is vaginal health. According to an article in Vogue, test developers Juno Bio and Evvy are leading the way with at-home vaginal microbiome tests that let users “know what’s up down there.”
New York City-based Evvy ($129 for a single test or $99 each for four tests per year) uses metagenomic sequencing to identify the bacteria and fungi present in the vaginal microbiome. This information helps customers to understand their levels of protective and disruptive bacteria, which can be associated with everything from reoccurring infections and transmission of sexually transmitted diseases to infertility.
London-based Juno Bio ($149 per test) does not disclose its testing method. It does, however, provide users with a “full vaginal microbiome profile.” The profile is accessed online within a “few days” of returning the vaginal swab sample to the company’s clinical laboratory.
Both companies note that their tests are intended to be used for wellness purposes and are not meant to diagnose or treat disease or substitute for a physician’s consultation.
Gynecologist Oluwatosin Goje, MD, MSCR, FACOG, a reproductive infectious disease specialist at Cleveland Clinic, believes the availability of at-home vaginal microbiome testing will provide valuable information to both women and their doctors.
“It’s a powerful tool because it enables us to look at the entire microbial community through metagenomics and decipher how the overall composition might be affecting symptoms and infections, as well as determine the best treatment pathway,” Goje, an Evvy Medical Advisor, told Vogue. “Understanding the complete vaginal microbiome allows us to be good antibiotic stewards and only administer antibiotics when needed. Patients can also retest remotely to understand how antibiotics and other treatments impacted their vaginal microbiome.”
Evvy, which offers women an at-home vaginal microbiome test (above) that can provide insights into chronic vaginal infections and proclivity to contract sexually transmitted diseases and other women’s health issues, is one of several women-led diagnostic start-ups focused on women’s health. (Photo copyright: Evvy.)
Removing the Discomfort of Shopping for Women’s Health Products
Jamie Norwood and Cynthia Plotch, co-founders of Stix, a supplier of women’s health products and education, launched their company with a product line of at-home pregnancy and ovulation tests. They have since expanded their offerings to include urinary tract infection (UTI) and yeast infection testing and treatments.
“You can test, relieve, treat, and help prevent future infections—all from the comfort of your own home,” Norwood, told Vogue. She emphasized that this is the kind of experience healthcare consumers are demanding in today’s ever-growing direct-to-consumer clinical laboratory testing landscape. “Agonizing over confusing over-the-counter products in the drugstore aisles, or bending over backwards to pick up a prescription at the pharmacy, just isn’t cutting it for Millennial and Gen Z consumers.”
According to WebMD, yeast infections are a chronic problem for many women. While 75% of women will get at least one yeast infection in their lifetime, up to 8% get more than four a year. In addition, the federal Centers for Disease Control and Prevention (CDC) points out that bacterial vaginosis is the most common vaginal condition in females ages 15-44.
Lola Priego, is CEO and founder of blood test company Base, which sells at-home saliva and finger-prick blood tests to monitor hormone levels, vitamin levels, neurotransmitters, and blood cell markers to improve everything from sleep and diet to sex drive. She predicts direct-to-consumer testing will become as common as fitness watches.
“Eventually, at-home lab testing will be another readily-used tool, similar to your health-tracking wearables, that helps us optimize for a well-rounded healthy lifestyle in a more individualized way,” Priego told Vogue.
Femtech a ‘Significantly Underdeveloped’ Market
In its latest Analyst Note, financial data firm PitchBook maintained that the market for female health products is poised for growth. TechCrunch, which reviewed PitchBook’s analysis of female-focused health products, reported that Femtech remains a “significantly underdeveloped” slice of health-tech spending.
While women spend an estimated $500 billion annually on medical expenses, only 4% of research and development money is targeted at women’s health, PitchBook noted. In its analysis, Pitchbook predicted the global market for female-focused health products will reach $3 billion by the end of 2030. By comparison, that segment of the healthcare market totaled $820.6 million last year.
“While we still view Femtech as a niche industry, we believe secular drivers could help propel new growth opportunities in the space,” PitchBook analysts wrote. “These include the increasing representation of women in the venture-backed technology community, rising awareness and acceptance of women’s health issues, and the growing prevalence of infectious diseases among women in some countries in Africa and Asia.
“Furthermore, while the majority of Femtech products have traditionally focused on reproductive health, we believe new approaches to women’s health research will help open the door to new products and services,” they noted.
Clinical laboratory leaders will be wise to carefully watch the growth of at-home DTC tests and products targeted at female healthcare consumers since fewer trips to physicians’ offices may mean fewer test orders for local labs.
At the same time, the opportunity exists for innovative pathologists and lab managers to develop digital services that allow consumers who are self-testing to store their home-test results in the lab’s app. They can then receive relevant insights from clinical pathologists to help them fully understand the implications of the test results.
Newly combined digital pathology, artificial intelligence (AI), and omics technologies are providing anatomic pathologists and medical laboratory scientists with powerful diagnostic tools
Add “spatial transcriptomics” to the growing list of “omics” that have the potential to deliver biomarkers which can be used for earlier and more accurate diagnoses of diseases and health conditions. As with other types of omics, spatial transcriptomics might be a new tool for surgical pathologists once further studies support its use in clinical care.
Among this spectrum of omics is spatial transcriptomics, or ST for short.
Spatial Transcriptomics is a groundbreaking and powerful molecular profiling method used to measure all gene activity within a tissue sample. The technology is already leading to discoveries that are helping researchers gain valuable information about neurological diseases and breast cancer.
Marriage of Genetic Imaging and Sequencing
Spatial transcriptomics is a term used to describe a variety of methods designed to assign cell types that have been isolated and identified by messenger RNA (mRNA), to their locations in a histological section. The technology can determine subcellular localization of mRNA molecules and can quantify gene expression within anatomic pathology samples.
In “Spatial: The Next Omics Frontier,” Genetic Engineering and Biotechnology News (GEN) wrote, “Spatial transcriptomics gives a rich, spatial context to gene expression. By marrying imaging and sequencing, spatial transcriptomics can map where particular transcripts exist on the tissue, indicating where particular genes are expressed.”
In an interview with Technology Networks, George Emanuel, PhD, co-founder of life-science genomics company Vizgen, said, “Spatial transcriptomic profiling provides the genomic information of single cells as they are intricately spatially organized within their native tissue environment.
“With techniques such as single-cell sequencing, researchers can learn about cell type composition; however, these techniques isolate individual cells in droplets and do not preserve the tissue structure that is a fundamental component of every biological organism,” he added.
“Direct spatial profiling the cellular composition of the tissue allows you to better understand why certain cell types are observed there and how variations in cell state might be a consequence of the unique microenvironment within the tissue,” he continued. “In this way, spatial transcriptomics allows us to measure the complexity of biological systems along the axes that are most relevant to their function.”
“Although spatial genomics is a nascent field, we are already seeing broad interest among the community and excitement across a range of questions, all the way from plant biology to improving our understanding of the complex interactions of the tumor microenvironment,” George Emanuel, PhD (above), told Technology Networks. Oncologists, anatomic pathologists, and medical laboratory scientists my soon see diagnostics that take advantage of spatial genomics technologies. (Photo copyright: Vizgen.)
According to 10x Genomics, “spatial transcriptomics utilizes spotted arrays of specialized mRNA-capturing probes on the surface of glass slides. Each spot contains capture probes with a spatial barcode unique to that spot.
“When tissue is attached to the slide, the capture probes bind RNA from the adjacent point in the tissue. A reverse transcription reaction, while the tissue is still in place, generates a cDNA [complementary DNA] library that incorporates the spatial barcodes and preserves spatial information.
“Each spot contains approximately 200 million capture probes and all of the probes in an individual spot share a barcode that is specific to that spot.”
“The highly multiplexed transcriptomic readout reveals the complexity that arises from the very large number of genes in the genome, while high spatial resolution captures the exact locations where each transcript is being expressed,” Emanuel told Technology Networks.
Spatial Transcriptomics for Breast Cancer and Neurological Diagnostics
In that paper, the authors wrote “we envision that in the coming years we will see simplification, further standardization, and reduced pricing for the ST protocol leading to extensive ST sequencing of samples of various cancer types.”
Spatial transcriptomics is also being used to research neurological conditions and neurodegenerative diseases. ST has been proven as an effective tool to hunt for marker genes for these conditions as well as help medical professionals study drug therapies for the brain.
“You can actually map out where the target is in the brain, for example, and not only the approximate location inside the organ, but also in what type of cells,” Malte Kühnemund, PhD, Director of Research and Development at 10x Genomics, told Labiotech.eu. “You actually now know what type of cells you are targeting. That’s completely new information for them and it might help them to understand side effects and so on.”
The field of spatial transcriptomics is rapidly moving and changing as it branches out into more areas of healthcare. New discoveries within ST methodologies are making it possible to combine it with other technologies, such as Artificial Intelligence (AI), which could lead to powerful new ways oncologists and anatomic pathologists diagnose disease.
“I think it’s going to be tricky for pathologists to look at that data,” Kühnemund said. “I think this will go hand in hand with the digital pathology revolution where computers are doing the analysis and they spit out an answer. That’s a lot more precise than what any doctor could possibly do.”
Spatial transcriptomics certainly is a new and innovative way to look at tissue biology. However, the technology is still in its early stages and more research is needed to validate its development and results.
Nevertheless, this is an opportunity for companies developing artificial intelligence tools for analyzing digital pathology images to investigate how their AI technologies might be used with spatial transcriptomics to give anatomic pathologists a new and useful diagnostic tool.
Speakers at this week’s Executive War College in San Antonio explained that the way records are collected and stored plays a large part in the long-term usefulness of clinical laboratory data
Data structure as a term may not flow off the lips of clinical laboratory and pathology laboratory managers, but it should be top-of-mind. Well-structured data improves reimbursements and, in aggregated form, can be an enticing avenue to partnerships with outside parties.
Data structure refers to the makeup of digital records—in other words, how data is collected, stored, and accessed. Structured information offers consistency and is easier to analyze and share.
“You have to make sense of all that messy data, and that’s a heavy lift,” she said. “Results are not standardized.”
Appeals Payments Increase with More Clinical Data
Data quality can improve claim reimbursement appeals, Goede noted. When a more complete clinical record is provided to payors, they are more likely to reimburse for services.
According to information Goede covered along with Julie Ramage, Director of Precision Medicine Quality Initiatives and Partnerships at biopharmaceutical company AstraZeneca, when appealing a denied claim for a colon cancer molecular test, for example, the average appeal payment was $318 without cross-specialist clinical records.
Meanwhile, payment for a similar claim appeal which included that added data jumped to $612!
This information is often available, but may not be structured in a way that makes it easy to share with a payer. “You really have to be thinking about what elements you need,” Goede said.
Market for Structured, Anonymized Lab Data
Clinical laboratories that want to provide or sell anonymized, aggregated data to outside parties—such as research firms or pharmaceutical companies—also need to pursue efficient data structure. The re-use of existing, high-quality lab data can create a new business revenue stream.
“But it has to be more than that vanilla, male/female, date-of-birth stuff,” Ramage noted.
For example, she said, genetic testing builds up data registries, and that’s what pharma is looking for to find patients early on.
“If you don’t have a way to structure your data, you’re not going to be able to play in the sandbox,” she added.
Co-presenters Julie Ramage (left), Director of Precision Medicine Quality Initiatives and Partnerships at AstraZeneca Pharmaceuticals, and Patricia Goede, PhD (right), Vice President of Clinical Informatics at XIFIN, Inc., answer attendee questions about data structure during their presentation at this week’s Executive War College Conference on Laboratory and Pathology Management in San Antonio. To register for EWC 2022 and receive a special early-bird rate, click here by November 6.
How Clinical Laboratories Can Improve Clinical Data Structure
Here are some tips for clinical laboratory executives to consider as they tackle data structure:
Standardize how to enter patient information and test results. A common problem with data input is that the same information is entered differently over time. For example, various patient records might refer to dates in different ways: November 1, 2021, can also be entered as 11/1/21, 11/1/2021, or 11-01-21. Structured data uses a single way to list dates in records. This lesson applies to all similar clinical data.
Use dropdown menu choices instead of free-typing, open fields. An online box to enter a test result can create a variety of entries that affect data structure. While not perfect, drop-down options create a consistent set of entries, Goede said.
Ask patient advocacy groups about common nomenclature. Clinical laboratory data should reflect how patients speak, Ramage said. For example, do patients refer to genomic and genetic testing as the same thing? Establishing more consistency improves data structure as records are updated.
Enlist your organization’s IT or research team for help. Tech workers and principal investigators can easily look at clinical laboratory data and tell what information is missing or inconsistent, said Cheryl Schleicher, Director of IT Strategy at Northwell Health Labs in Lake Success, NY. Schleicher attended this week’s Executive War College.
Look Further into Clinical Laboratory Data Structure
Data structure can help clinical laboratories and pathology laboratories grab more reimbursement dollars and potentially sell anonymized data to external partners.
It is an area many lab executives are not familiar with and need to investigate more, particularly following the accelerated move to digital lab services during the COVID-19 pandemic. Your organization’s IT department or Chief Information Officer can be a useful ally.
If you could not make it to this week’s Executive War College, then join us for our next Executive War College on April 27-28, 2022, in New Orleans. Click here to take advantage of special early-bird pricing for this critical event.
It may not be a boom trend, but more non-invasive diagnostic tests are coming to market as clinical laboratory tests that use breath as the specimen
Here’s a development that reinforces two important trends in diagnostics: non-invasive clinical laboratory assays and patient-self testing. Recently, the FDA expanded the clearance of one diagnostic test to allow patients to collect their own breath specimen at home under the supervision of the test manufacturer’s telehealth team.
Recently, however, the FDA announced it has “expanded the approval of the company’s 13C-Spirulina Gastric Emptying Breath Test (GEBT) to now include ‘at home’ administration under virtual supervision of Cairn Diagnostics.”
Self-administration of at-home tests by patients guided virtually by healthcare professionals is a major advancement in telehealth. But will this virtual-healthcare method be popular with both patients and their physicians?
Clinical Laboratory Diagnostics and Telehealth
Spurring a far greater acceptance of telehealth among patients and healthcare providers is one of the many ways the COVID-19 pandemic has impacted healthcare.
“Telehealth, particularly during the COVID-19 pandemic, has emerged as a preferred option for healthcare providers,” noted Kerry Bush, President and COO of Cairn Diagnostics, in a 2021 news release.
Cairn’s GEBT detects gastroparesis, a disease which, according to the NIH National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), affects 50 people in every 100,000. According to the CDC, it is also sometimes a complication of diabetes. Symptoms include nausea, heartburn, bloating, a feeling of fullness long after eating a meal, vomiting, belching, and pain in the upper abdomen, the NIDDK notes.
In people with gastroparesis—sometimes called “delayed gastric emptying”—muscles that normally move food from the stomach to the small intestine do not work as they should, and the food remains in the stomach for too long. The traditional diagnostic tool used to diagnose gastroparesis is scintigraphy. The patient consumes a meal that has radioactive material mixed in and the digestion process is observed using a nuclear medicine camera as the material is eliminated through the bowels.
Cairn Diagnostics’ C-Spirulina Gastric Emptying Breath Test (above) recently received an expansion to its initial 2015 FDA approval that enables patients to self-administer the test at-home while being virtually guided by the company’s telehealth team. GEBTs are interpreted by CLIA-certified clinical laboratories and the results sent to patients’ doctors within 24-48 hours after testing. (Photo copyright: Cairn Diagnostics.)
Virtual Telehealth GEBT versus Scintigraphy
The telehealth process for Cairn Diagnostic’s Gastric Emptying Breath Test (GEBT) differs significantly from traditional scintigraphy testing. Once a physician prescribes the test, Cairn’s telehealth team contacts the patient to describe the virtual process. The team then ships the at-home test kit to the patient. To complete the testing, Cairn provides the patient with a web-based link to a secure audio/video platform.
During administration of the GEBT, a Cairn technician coaches the patient and supervises via video. Once the test is complete, the patient returns the breath samples to the CLIA-certified clinical laboratory by overnight courier. The test results are sent to the prescribing physician within 24-48 hours after the lab receives the samples.
Discovering New Uses for Breath as a Specimen for Clinical Laboratory Testing
For obvious reasons, patients prefer diagnostics that use specimens obtained noninvasively. GEBT is the latest in a growing list of diagnostic tests that use breath as a specimen.
For example, at Johns Hopkins clinicians employ breath testing to diagnose several conditions, including:
Each of these tests involves the patient consuming a particular substance, technicians capturing breath samples at certain intervals, and clinical laboratory personnel analyzing the samples to look for indicators of disease or intolerance.
New Types of Breath Tests
Breath samples are commonly used to diagnose gastrointestinal issues, but researchers also are seeking methods of using them to diagnose and monitor respiratory conditions as well.
In a recent study published in Nature Nanotechnology, scientists explored how breath can be used to monitor respiratory disease, noting that although breath contains numerous volatile metabolites, it is rarely used clinically because biomarkers have not been identified.
“Here we engineered breath biomarkers for respiratory disease by local delivery of protease-sensing nanoparticles to the lungs. The nanosensors shed volatile reporters upon cleavage by neutrophil elastase, an inflammation-associated protease with elevated activity in lung diseases such as bacterial infection and alpha-1 antitrypsin deficiency,” the researchers wrote.
Indeed, the search for new ways to use breath as a biological sample is being pursued by numerous groups and organizations. Owlstone Medical in the UK, for example, is developing breathalyzer tests for the detection of cancer as well as inflammatory and infectious disease.
“Whilst we are still in this discovery stage it is time to refine our study designs so that we can make progress towards tailored clinical application,” they wrote. “Breathomics is perhaps at the ‘end of the beginning’ for asthma at least; it has a ‘sexy’ name, some promising and consistent findings, and the key questions are at least being recognized.”
Better for Patients, Clinicians, and Clinical Laboratories
Virtual telehealth tests, ordered by physicians, administered at home, and interpreted in CLIA-certified clinical laboratories, is a trend pathologists may want to watch carefully, along with the development of other tests that use human breath as the specimen.
Less invasive, more personalized diagnostic tools that can be administered at home are better for patients. When those tools also provide detailed information, clinicians can make better decisions regarding care. Clinical laboratories that approach the use of at-home tests creatively, and which can accurately and quickly process these new types of tests, may have a market advantage and an opportunity to expand and grow.
The discovery is yet another factor that must be considered when developing a liquid biopsy test clinical laboratories can use to detect cancer
How often do disruptive elements present in Liquid biopsies result in misdiagnoses and unhelpful drug therapies for cancer? Researchers at the University of Washington School of Medicine (UW Medicine) in Seattle wanted to know. And the results of their study provide another useful insight for pathologists about the elements that circulate in human blood which must be understood so that liquid biopsy tests can be developed that are not affected by that factor.
Based on their case series study of 69 men with advanced prostate cancer, the UW Medicine researchers determined that 10% of men have a clonal hematopoiesis of indeterminate potential (CHIP) that can “interfere” with liquid biopsies and cause incorrect reports and unneeded prostate cancer treatment, according to their paper published in the journal JAMA Oncology.
The UW Medicine researchers advised testing for “variants in the cell-free DNA (cfDNA)” shed in blood plasma to enable appropriate treatment for people with already diagnosed prostate cancer, noted to a UW Medicine news release.
According to pathologist Colin Pritchard, MD, PhD, Associate Professor of Laboratory Medicine and Pathology at the UW Medicine, who led the research team, “clonal hematopoiesis can interfere with liquid biopsies. For example, mutations in the genes BRCA1, BRCA2, and ATM have been closely linked to cancer development.
“The good news is that, by looking at the blood cellular compartment, you can tell with pretty good certainty whether something is cancer, or something is hematopoiesis,” he said in the news release.
What Does CHIP Interference Mean to a Clinical Laboratory Blood Test?
In their published study, the UW Medicine researchers stressed the “urgent need to understand cfDNA testing performance and sources of test interferences” in light of recent US Food and Drug Administration (FDA) clearance of two PARP inhibitors (PARPi) for prostate cancer:
“We found that a strikingly high proportion of DNA repair gene variants in the plasma of patients with advanced prostate cancer are attributable to CHIP,” the researchers wrote. “The CHIP variants were strongly correlated with increased age, and even higher than expected by age group.
“The high rate of CHIP may also be influenced by prior exposure to chemotherapy,” they added. “We are concerned that CHIP interference is causing false-positive cfDNA biomarker assessments that may result in patient harm from inappropriate treatment, and delays in delivering alternative effective treatment options.
“Without performing a whole-blood control, seven of 69 patients (10%) would have been misdiagnosed and incorrectly deemed eligible for PARP-inhibitor therapy based on CHIP interference in plasma. In fact, one patient in this series had a BRCA2 CHIP clone that had been previously reported by a commercial laboratory testing company with the recommendation to use a PARPi. To mitigate these risks, cfDNA results should be compared to results from whole-blood control or tumor tissue,” the researchers concluded.
To find the clinically relevant CHIP interference in prostate cancer cfDNA testing, researchers used the UW-OncoPlex assay (developed and clinically available at UW Medicine). The assay is a multiplexed next-generation sequencing panel aimed at detecting mutations in tumor tissues in more than 350 genes, according to the UW Medicine Laboratory and Pathology website.
“To improve cfDNA assay performance, we developed an approach that simultaneously analyzes plasma and paired whole-blood control samples. Using this paired testing approach, we sought to determine to what degree CHIP interferes with the results of prostate cancer cfDNA testing,” the researchers wrote in JAMA Oncology.
Men May Receive Unhelpful Prostate Cancer Drug Therapies
The research team studied test results from 69 men with advanced prostate cancer. They analyzed patients’ plasma cfDNA and whole-blood control samples.
Tumor sequencing enabled detection of germline (cells relating to preceding cells) variants from CHIP clones.
The UW Medicine study suggested CHIP variants “accounted for almost half of the somatic (non-germline) DNA repair mutations” detected by liquid biopsy, according to the news release.
> “About half the time when the plasma is thought to contain a mutation that would guide therapy with these drugs, it actually contains CHIP variants, not prostate cancer DNA variants. That means that in about half of those tested, a patient could be told that he should be administered a drug that is not indicated to treat to his cancer,” said Colin Pritchard, MD, PhD, pathologist and Associate Professor of Laboratory Medicine and Pathology at UW Medicine in the new release. (Photo copyright: University of Washington School of Medicine.)
Other detailed findings of the UW Medicine Study:
CHIP variants of 2% or more were detected in cfDNA from 13 of 69 men.
Seven men, or 10%, having advanced prostate cancer “had CHIP variants in DNA repair genes used to determine PARPi candidacy.
CHIP variants rose with age: 0% in those 40 to 50; 12.5% in men 51 to 60; 6.3% in those 61 to 70; 20.8% in men 71 to 80; and 71% in men 81 to 90.
Whole-blood control made it possible to distinguish prostate cancer variants from CHIP interference variants.
“Men with prostate cancer are at high risk of being misdiagnosed as being eligible for PARPi therapy using current cfDNA tests; assays should use a whole-blood control sample to distinguish CHIP variants from prostate cancer,” the researchers wrote in JAMA Oncology.
Liquid Biopsies Are ‘Here to Stay’
Surgical oncologist William Cance, MD, Chief Medical and Scientific Officer, American Cancer Society (ACS) in Atlanta, recognizes the challenge of tumor biology to liquid biopsies.
“Genetic abnormalities are only one piece of the puzzle. We need to look comprehensively at tumors for the best therapy, from their metabolic changes and protein signatures in the blood to the epigenetic modifications that may occur, as cancers take hold,” he told Oncology Times. “It’s not just shed DNA in the blood.”
The UW Medicine study demonstrates the importance of understanding how all elements in liquid biopsies interact to affect clinical laboratory test results.
“I think liquid biopsies are here to stay,” Cance told Oncology Times. “They’re all part of precision medicine, tailored to the individual.”
