In a follow-up story, investigative news team in Boston sends a reporter’s cheek swab sample to the same pet DNA testing lab: report states the reporter is part Malamute, Shar Pei, and Labrador Retriever
One pet DNA testing company returned results from human cheek swabs showing two different people were in fact part dog. The resulting local reporting calls into question the accuracy of DNA testing of our beloved furry friends and may impact the trust people have in clinical laboratory genetic testing as well.
Pet DNA analysis is nearly as popular as human DNA analysis. The market is expected to exceed $700 million by the end of the decade, according to Zion Market Research. But are customers getting their money’s worth? One CBS news station in Boston decided to find out.
Last year, the WBZ I-Team, the investigative part of a CBS News station in Boston, looked into the accuracy of pet DNA testing. They reported on a pet owner who questioned the DNA test results she received for her German Shepard. The report indicated that her dog had DNA from more than 10 breeds, besides German Shepard.
During their research, the WBZ investigative reporters learned that pet owners order these tests to reveal what one pet DNA testing company described as understanding “your dog’s unique appearance, behavior, and health.”
“So, the WBZ-TV I-Team came with more tests from different companies to compare. All came back with some German Shepherd, but the percentages ranged from 65% to just 29%. Aside from that, the three companies showed a puzzling hodgepodge of other breeds. One included Great Pyrenees, another came back with Siberian Husky, another listed Korean Jindo, and the list goes on,” WBZ News reported.
The owner of the German Shepard then sent two swab samples from her own cheeks to one of the pet DNA testing companies. The test results indicated that she was 40% Border Collie, 32% Cane Corso, and 28% Bulldog.
The company that performed that DNA testing—DNA My Dog—insisted to the WBZ I-Team that one of the pet owner’s cheek samples contained dog DNA, WBZ News reported.
“The second sample did in fact yield canine DNA. … The results provided would not be possible on a human sample,” Jessica Barnett, Director of Service Operations, DNA My Dog, told WBZ News.
This must have come as a shock to the pet owner, who is probably sure she is not part dog.
“I think that is a red flag for sure,” Lisa Moses, VMD (above), a veterinarian and bioethicist with Harvard Medical School, told WBZ News. “A company should know if they’ve in any basic way analyzed a dog’s DNA, that that is not a dog,” she said. One wonders what might happen if a dog’s DNA was secretly sent to a clinical laboratory performing human genetic testing. What might the results be? (Photo copyright: Harvard Medical School.)
Two Times is the Charm
To continue its investigation into this odd occurrence, the WBZ I-Team decided to repeat the test this year. They sent a cheek saliva sample from one of their own reporters to three different dog DNA testing companies.
According to the I-Team report, one company, Orivet, said the sample “failed to provide the data necessary to perform breed ID analysis. Another company, Wisdom Panel stated the sample “didn’t provide enough DNA to produce a reliable result.”
However, DNA My Dog once again reported that the human sample belonged to a canine. This time the company’s test reported that the DNA sample was 40% Alaskan Malamute, 35% Shar Pei, and 25% Labrador Retriever.
DNA My Dog did not respond to WBZ I-Team’s attempt to contact them for a comment, WBZ News reported.
Wild West of DNA Testing
“I personally do have concerns about the fact that, from a consumer standpoint, you don’t always know what you’re getting when you work with those companies,” said geneticist Elinor Karlsson, PhD, Director of the Vertebrate Genomics Group at the Broad Institute of MIT and Harvard, told WBZ News. “There’s not a lot of rules in this space.”
Karlsson is also founder and Chief Scientist at Darwin’s Ark, a nonprofit organization that combines dog genetics and behavior to advance the understanding of complex canine diseases. People participating in the initiative contribute data about their dogs to an open source database, which is then shared with researchers around the globe. To date, more than 44,000 dogs have been registered with the project.
She hopes that reports like the one from the WBZ I-Team will not dissuade interest in pet genetics, as the science does have significant value when performed correctly.
“We might be able to figure out which dogs are at risk of getting cancer, and screen them more often and be able to diagnose it earlier,” Karlsson said. “We might be able to develop new treatments for that cancer.”
“There isn’t necessarily a gold standard answer for what your dog is,” veterinarian and bioethicist Lisa Moses, VMD, co-director of the Capstone Program for the Master of Science in Bioethics Program at Harvard Medical School, told WBZ News. “A breed is something that we’ve decided, which is based upon essentially the way a dog looks. But that doesn’t necessarily mean that we’re going to know what their genes look like.”
DNA My Dog Awarded ‘Best Budget Dog DNA Test’
In February, US News and World Report published an article rating the best dog DNA tests of 2024. The magazine ranked the DNA My Dog Essential Breed ID Test as the “best budget dog DNA test on the market.” The test sells for $79.99. According to the company’s website, a simple cheek swab yields:
A complete breed breakdown,
Genetic health concerns,
Unique personality traits, and
Bonding tips for dogs and their owners.
“I worry about people making medical decisions … based on one of these tests,” Moses told WBZ News, which added that, “She and some of her colleagues have called on lawmakers to set standards and regulations for pet DNA labs, and to require them to share their databases with each other, for more consistent results.”
The investigation into pet DNA testing by the television news reporters in Boston is a reminder to clinical lab managers and pathologists that DNA testing can be problematic in many ways. Also, when consumers read news stories like this one about inaccurate canine DNA testing, it can cause them to question the accuracy of other types of DNA testing.
Speedy DNA sequencing and on-the-spot digital imaging may change the future of anatomic pathology procedures during surgery
Researchers at the Center for Molecular Medicine (CMM) at UMC Utrecht, a leading international university medical center in the Netherlands, have paired artificial intelligence (AI) and machine learning with DNA sequencing to develop a diagnostic tool cancer surgeons can use during surgeries to determine in minutes—while the patient is still on the operating table—whether they have fully removed all the cancerous tissue.
The method, “involves a computer scanning segments of a tumor’s DNA and alighting on certain chemical modifications that can yield a detailed diagnosis of the type and even subtype of the brain tumor,” according to The New York Times, which added, “That diagnosis, generated during the early stages of an hours-long surgery, can help surgeons decide how aggressively to operate, … In the future, the method may also help steer doctors toward treatments tailored for a specific subtype of tumor.”
This technology has the potential to reduce the need for frozen sections, should additional development and studies confirm that it accurately and reliably shows surgeons that all cancerous cells were fully removed. Many anatomic pathologists would welcome such a development because of the time pressure and stress associated with this procedure. Pathologists know that the patient is still in surgery and the surgeons are waiting for the results of the frozen section. Most pathologists would consider fewer frozen sections—with better patient outcomes—to be an improvement in patient care.
“It’s imperative that the tumor subtype is known at the time of surgery,” Jeroen de Ridder, PhD (above), associate professor in the Center for Molecular Medicine at UMC Utrecht and one of the study leaders, told The New York Times. “What we have now uniquely enabled is to allow this very fine-grained, robust, detailed diagnosis to be performed already during the surgery. It can figure out itself what it’s looking at and make a robust classification,” he added. How this discovery affects the role of anatomic pathologists and pathology laboratories during cancer surgeries remains to be seen. (Photo copyright: UMC Utrecht.)
Rapid DNA Sequencing Impacts Brain Tumor Surgeries
The UMC Utrecht scientists employed Oxford Nanopore’s “real-time DNA sequencing technology to address the challenges posed by central nervous system (CNS) tumors, one of the most lethal type of tumor, especially among children,” according to an Oxford Nanopore news release.
The researchers called their new machine learning AI application the “Sturgeon.”
According to The New York Times, “The new method uses a faster genetic sequencing technique and applies it only to a small slice of the cellular genome, allowing it to return results before a surgeon has started operating on the edges of a tumor.”
Jeroen de Ridder, PhD, an associate professor in the Center for Molecular Medicine at UMC Utrecht, told The New York Times that Sturgeon is “powerful enough to deliver a diagnosis with sparse genetic data, akin to someone recognizing an image based on only 1% of its pixels, and from an unknown portion of the image.” Ridder is also a principal investigator at the Oncode Institute, an independent research center in the Netherlands.
The researchers tested Sturgeon during 25 live brain surgeries and compared the results to an anatomic pathologist’s standard method of microscope tissue examination. “The new approach delivered 18 correct diagnoses and failed to reach the needed confidence threshold in the other seven cases. It turned around its diagnoses in less than 90 minutes, the study reported—short enough for it to inform decisions during an operation,” The New York Times reported.
But there were issues. Where the minute samples contain healthy brain tissue, identifying an adequate number of tumor markers could become problematic. Under those conditions, surgeons can ask an anatomic pathologist to “flag the [tissue samples] with the most tumor for sequencing, said PhD candidate Marc Pagès-Gallego, a bioinformatician at UMC Utrecht and a co-author of the study,” The New York Times noted.
“Implementation itself is less straightforward than often suggested,” Sebastian Brandner, MD, a professor of neuropathology at University College London, told The Times. “Sequencing and classifying tumor cells often still required significant expertise in bioinformatics as well as workers who are able to run, troubleshoot, and repair the technology,” he added.
“Brain tumors are also the most well-suited to being classified by the chemical modifications that the new method analyzes; not all cancers can be diagnosed that way,” The Times pointed out.
Thus, the research continues. The new method is being applied to other surgical samples as well. The study authors said other facilities are utilizing the method on their own surgical tissue samples, “suggesting that it can work in other people’s hands.” But more work is needed, The Times reported.
UMC Utrecht Researchers Receive Hanarth Grant
To expand their research into the Sturgeon’s capabilities, the UMC Utrecht research team recently received funds from the Hanarth Fonds, which was founded in 2018 to “promote and enhance the use of artificial intelligence and machine learning to improve the diagnosis, treatment, and outcome of patients with cancer,” according to the organization’s website.
The researchers will investigate ways the Sturgeon AI algorithm can be used to identify tumors of the central nervous system during surgery, a UMC Utrecht news release states. These type of tumors, according to the researchers, are difficult to examine without surgery.
“This poses a challenge for neurosurgeons. They have to operate on a tumor without knowing what type of tumor it is. As a result, there is a chance that the patient will need another operation,” said de Ridder in the news release.
The Sturgeon application solves this problem. It identifies the “exact type of tumor during surgery. This allows the appropriate surgical strategy to be applied immediately,” the news release notes.
The Hanarth funds will enable Jeroen and his team to develop a variant of the Sturgeon that uses “cerebrospinal fluid instead of (part of) the tumor. This will allow the type of tumor to be determined already before surgery. The main challenge is that cerebrospinal fluid contains a mixture of tumor and normal DNA. AI models will be trained to take this into account.”
The UMC Utrecht scientists’ breakthrough is another example of how organizations and research groups are working to shorten time to answer, compared to standard anatomic pathology methods. They are combining developing technologies in ways that achieve these goals.
New technology could enable genetic scientists to identify antibiotic resistant genes and help physicians choose better treatments for genetic diseases
Genomic scientists at the Icahn School of Medicine at Mount Sinai Medical Center in New York City have developed what they call a “smart tweezer” that enables researchers to isolate a single bacterium from a patient’s microbiome in preparation for genetic sequencing. Though primarily intended for research purposes, the new technology could someday be used by clinical laboratories and microbiologists to help physicians diagnose chronic disease and choose appropriate genetic therapies.
The researchers designed their new technology—called mEnrich-seq—to improve the effectiveness of research into the complex communities of microorganisms that reside in the microbiomes within the human body. The discovery “ushers in a new era of precision in microbiome research,” according to a Mount Sinai Hospital press release.
“Imagine you’re a scientist who needs to study one particular type of bacteria in a complex environment. It’s like trying to find a needle in a large haystack,” said the study’s senior author Gang Fang, PhD (above), Professor of Genetics and Genomic Sciences at Icahn School of Medicine at Mount Sinai Medical Center, in a press release. “mEnrich-seq essentially gives researchers a ‘smart tweezer’ to pick up the needle they’re interested in,” he added. Might smart tweezers one day be used to help physicians and clinical laboratories diagnose and treat genetic diseases? (Photo copyright: Icahn School of Medicine.)
Addressing a Technology Gap in Genetic Research
Any imbalance or decrease in the variety of the body’s microorganisms can lead to an increased risk of illness and disease.
In researching the microbiome, many scientists “focus on studying specific types of bacteria within a sample, rather than looking at each type of bacteria present,” the press release states. The limitation of this method is that a specific bacterium is just one part of a complicated environment that includes other bacteria, viruses, fungi and host cells, each with their own unique DNA.
“mEnrich-seq effectively distinguishes bacteria of interest from the vast background by exploiting the ‘secret codes’ written on bacterial DNA that bacteria use naturally to differentiate among each other as part of their native immune systems,” the press release notes. “This new strategy addresses a critical technology gap, as previously researchers would need to isolate specific bacterial strains from a given sample using culture media that selectively grow the specific bacterium—a time-consuming process that works for some bacteria, but not others. mEnrich-seq, in contrast, can directly recover the genome(s) of bacteria of interest from the microbiome sample without culturing.”
Isolating Hard to Culture Bacteria
To conduct their study, the Icahn researchers used mEnrich-seq to analyze urine samples taken from three patients with urinary tract infections (UTIs) to reconstruct Escherichia coli (E. Coli) genomes. They discovered their “smart tweezer” covered more than 99.97% of the genomes across all samples. This facilitated a comprehensive examination of antibiotic-resistant genes in each genome. They found mEnrich-seq had better sensitivity than standard study methods of the urine microbiome.
They also used mEnrich-seq to selectively examine the genomes of Akkermansia muciniphila (A. muciniphila), a bacterium that colonizes the intestinal tract and has been shown to have benefits for obesity and Type 2 diabetes as well as a response to cancer immunotherapies.
“Akkermansia is very hard to culture,” Fang told GenomeWeb. “It would take weeks for you to culture it, and you need special equipment, special expertise. It’s very tedious.”
mEnrich-seq was able to quickly segregate it from more than 99.7% of A. muciniphila genomes in the samples.
Combatting Antibiotic Resistance Worldwide
According to the press release, mEnrich-seq could potentially be beneficial to future microbiome research due to:
Cost-Effectiveness: It offers a more economical approach to microbiome research, particularly beneficial in large-scale studies where resources may be limited.
Broad Applicability: The method can focus on a wide range of bacteria, making it a versatile tool for both research and clinical applications.
Medical Breakthroughs: By enabling more targeted research, mEnrich-seq could accelerate the development of new diagnostic tools and treatments.
“One of the most exciting aspects of mEnrich-seq is its potential to uncover previously missed details, like antibiotic resistance genes that traditional sequencing methods couldn’t detect due to a lack of sensitivity,” Fang said in the news release. “This could be a significant step forward in combating the global issue of antibiotic resistance.”
More research and clinical trials are needed before mEnrich-seq can be used in the medical field. The Icahn researchers plan to refine their novel genetic tool to improve its efficiency and broaden its range of applications. They also intend to collaborate with physicians and other healthcare professionals to validate how it could be used in clinical environments.
Should all this come to pass, hospital infection control teams, clinical laboratories, and microbiology labs would welcome a technology that would improve their ability to detect details—such as antibiotic resistant genes—that enable a faster and more accurate diagnosis of a patient’s infection. In turn, that could contribute to better patient outcomes.
Research could lead to similar treatments for other diseases, as well as creating a demand for a new line of oncology tests for clinical labs and pathology groups
Cancer treatment has come a long way in the past decades, and it seems poised to take another leap forward thanks to research being conducted at Rice University in Houston. Molecular scientists there have developed what they call a “molecular jackhammer” that uses special molecules and near-infrared light to attack and kill cancer cells.
The technique has been effective in research settings. Should it be cleared for use in patient care, it could change the way doctors treat cancer patients while giving clinical laboratories a new diagnostic tool that could guide treatment decisions.
The researchers “found that the atoms of a small dye molecule used for medical imaging can vibrate in unison—forming what is known as a plasmon [a quantum of plasma oscillation]—when stimulated by near-infrared light, causing the cell membrane of cancerous cells to rupture,” a Rice University news release noted.
The small dye molecule is called aminocyanine, a type of fluorescent synthetic dye that is already in use in medical imaging.
“These molecules are simple dyes that people have been using for a long time,” said physical chemistry scientist Ciceron Ayala-Orozco, PhD, the researcher who led the study, in the news release. “They’re biocompatible, stable in water, and very good at attaching themselves to the fatty outer lining of cells. But even though they were being used for imaging, people did not know how to activate these as plasmons.”
“The method had a 99% efficiency against lab cultures of human melanoma cells, and half of the mice with melanoma tumors became cancer-free after treatment,” according to the Rice University news release.
“I spent approximately four years working with these ideas on using molecular forces and what is called blue-light activated molecular motors,” Ciceron Ayala-Orozco, PhD (above), told Oncology Times. “At some point, I connected the dots that what I wanted to do is use a simple molecule, not necessarily a motor, that absorbs NIR light in similar ways as plasmonic nanoparticles do and go deeper into the tissue. When activated, we found that the molecules vibrate even faster than our minds can imagine and serve as a force to break the cancer cells apart.” Once approved for use treating cancer patients, clinical laboratories working with oncologists may play a key role in diagnosing candidates for the new treatment. (Photo copyright: Rice University.)
How the Technique Works
Nuclei of the aminocyanine molecules oscillate in sync when exposed to near-infrared radiation and pummel the surface of the cancer cell. These blows are so powerful they rupture the cell’s membrane sufficiently enough to destroy it.
“The speed of this type of therapy can completely kill the cancer much faster than, say, photodynamic therapy,” Ayala-Orozco noted. “The mechanical action through the molecular jackhammer is immediate, within a few minutes.”
One advantage to near-infrared light is that it can infiltrate deeper into the body than visible light and access organs and bones without damaging tissue.
“Near-infrared light can go as deep as 10 centimeters (four inches) into the human body as opposed to only half a centimeter (0.2 inches), the depth of penetration for visible light, which we used to activate the nanodrills,” said James Tour, PhD, T. T. and W. F. Chao Professor of Chemistry, Professor of Materials Science and NanoEngineering at Rice University, in the news release. “It is a huge advance.”
The molecular plasmons identified by the team had a near-symmetrical structure. The plasmons have an arm on one side that does not contribute to the motion, but rather anchors the molecule to the lipid bilayer of the cell membrane. The scientists had to prove that the motion could not be categorized as a form of either photodynamic or photothermal therapy.
“What needs to be highlighted is that we’ve discovered another explanation for how these molecules can work,” Ayala-Orozco said in the Rice news release. “This is the first time a molecular plasmon is utilized in this way to excite the whole molecule and to actually produce mechanical action used to achieve a particular goal—in this case, tearing apart cancer cells’ membrane.
“This study is about a different way to treat cancer using mechanical forces at the molecular scale,” he added.
New Ways to Treat Cancer
The likelihood of cancer cells developing a resistance to these molecular jackhammers is extremely low, which renders them a safer and more cost effective method for inducing cancer cell death.
“The whole difference about this is because it’s a mechanical action, it’s not relying on some chemical effect,” Tour told KOMO News. “It’s highly unlikely that the cell will be able to battle against this. Once it’s cell-associated, the cell is toast once it gets hit by light. Only if a cell could prevent a scalpel from being able to cut it in half, could it prevent this.
“It will kill all sorts of cell types. With our other mechanical action molecules, we’ve demonstrated that they kill bacteria; we’ve demonstrated that they kill fungi. If a person has lost the ability to move a limb, if you can stimulate the muscle with light, that would be quite advantageous. Cancer is just the beginning,” he added.
“From the medical point of view, when this technique is available, it will be beneficial and less expensive than methods such as photothermal therapy, photodynamics, radio-radiation, and chemotherapy,” said Jorge Seminario, PhD, Professor in the Artie McFerrin Department of Chemical Engineering at Texas A&M University in a news release.
“This is one of the very few theoretical-experimental approaches of this nature. Usually, research in the fields related to medicine does not use first principles quantum-chemistry techniques like those used in the present work, despite the strong benefit of knowing what the electrons and nuclei of all atoms are doing in molecules or materials of interest,” Seminario noted.
“It’s really a tremendous advance. What this is going to do is open up a whole new mode of treatment for medicine,” Tour said. “It’s just like when radiation came in [and] when immunotherapy came in. This is a whole new modality. And when a new modality comes in, so much begins to open up.
“Hopefully, this is going to change medicine in a big way,” he added.
More research and clinical studies are needed before this new technology is ready for patient care. Clinical laboratories and anatomic pathology groups will likely be involved identifying patients who would be good candidates for the new treatment. These molecular jackhammers could be a useful tool in the future fight against cancer, which is ranked second (after heart disease) as the most common cause of death in the US.
The ASBMB story notes that nanopore technology depends on differences in charges on either side of the membrane to force DNA or RNA through the hole. This is one reason why proteins pose such a challenge.
“Think of a cell as a miniature city, with proteins as its inhabitants. Each protein-resident has a unique identity, its own characteristics, and function. If there was a database cataloging the fingerprints, job profiles, and talents of the city’s inhabitants, such a database would undoubtedly be invaluable!” said Behzad Mehrafrooz, PhD (above), Graduate Research Assistant at University of Illinois at Urbana-Champaign in an article he penned for the university website. This research should be of interest to the many clinical laboratories that do protein testing. (Photo copyright: University of Illinois.)
How the Maglia Process Works
In a Groningen University news story, Maglia said protein is “like cooked spaghetti. These long strands want to be disorganized. They do not want to be pushed through this tiny hole.”
His technique, developed in collaboration with researchers at the University of Rome Tor Vergata, uses electrically charged ions to drag the protein through the hole.
“We didn’t know whether the flow would be strong enough,” Maglia stated in the news story. “Furthermore, these ions want to move both ways, but by attaching a lot of charge on the nanopore itself, we were able to make it directional.”
The researchers tested the technology on what Maglia described as a “difficult protein” with many negative charges that would tend to make it resistant to flow.
“Previously, only easy-to-thread proteins were analyzed,” he said in the news story. “But we gave ourselves one of the most difficult proteins as a test. And it worked!”
Maglia now says that he intends to commercialize the technology through a new startup called Portal Biotech.
Detecting Post-Translational Modifications in the UK
In another recent study, researchers at the University of Oxford reported that they have adapted nanopore technology to detect post-translational modifications (PTMs) in protein chains. The term refers to changes made to proteins after they have been transcribed from DNA, explained an Oxford news story.
“The ability to pinpoint and identify post-translational modifications and other protein variations at the single-molecule level holds immense promise for advancing our understanding of cellular functions and molecular interactions,” said contributing author Hagan Bayley, PhD, Professor of Chemical Biology at University of Oxford, in the news story. “It may also open new avenues for personalized medicine, diagnostics, and therapeutic interventions.”
Bayley is the founder of Oxford Nanopore Technologies, a genetic sequencing company in the UK that develops and markets nanopore sequencing products.
The news story notes that the new technique could be integrated into existing nanopore sequencing devices. “This could facilitate point-of-care diagnostics, enabling the personalized detection of specific protein variants associated with diseases including cancer and neurodegenerative disorders,” the story states.
In another recent study, researchers at the University of Washington reported that they have developed their own method for protein sequencing with nanopore technology.
“This opens up the possibility for barcode sequencing at the protein level for highly multiplexed assays, PTM monitoring, and protein identification!” Motone wrote.
Single-cell proteomics, enabled by nanopore protein sequencing technology, “could provide higher sensitivity and wider throughput, digital quantification, and novel data modalities compared to the current gold standard of protein MS [mass spectrometry],” they wrote. “The accessibility of these tools to a broader range of researchers and clinicians is also expected to increase with simpler instrumentation, less expertise needed, and lower costs.”
There are approximately 20,000 human genes. However, there are many more proteins. Thus, there is strong interest in understanding the human proteome and the role it plays in health and disease.
Technology that makes protein testing faster, more accurate, and less costly—especially with a handheld analyzer—would be a boon to the study of proteomics. And it would give clinical laboratories new diagnostic tools and bring some of that testing to point-of-care settings like doctor’s offices.
Pathologists and clinical laboratories have an opportunity to help create newborn rWGS programs in their parent hospitals and health systems
Diagnosing disease in infants is particularly difficult using typical clinical laboratory testing and modalities. Thus, the use of rapid Whole Genome Sequencing (rWGS) is gaining acceptance when such a procedure is deemed “medically appropriate” based on the child’s symptoms.
In “Whole Genome Sequencing for Newborns Gains Favor,” Robert Michel, Editor-in-Chief of Dark Daily’s sister publication The Dark Report wrote, “Evidence is swiftly accumulating that use of rapid Whole Genome Sequencing for certain children in NICUs can enable diagnostic insights that guide effective interventions. Further, these pilot rWGS programs in children’s hospitals are showing a solid return on investment because of improved care. It is predicted that more hospitals may soon offer rWGS.”
Conducted at Tufts Medical Center in Boston, the researchers found that “Whole genome tests are nearly twice as good as narrower tests at unearthing genetic abnormalities that can cause disease in infants—the study found 49% of abnormalities, compared to 27% with more commonly used tests targeting particular types of genetic diseases,” the Associate Press reported.
The AP story follows the medical journey of a now 4-year-old who was diagnosed with a rare bleeding disorder. The nearly fatal condition was only caught because broad genetic testing found she suffered from factor XIII deficiency, a blood disorder characterized by the inability to clot properly.
“I’ve been doing clinical trials of babies for over 40 years,” neonatologist Jonathan Davis, MD (above), Chief, Division of Newborn Medicine at Tufts Children’s Hospital at Tufts Medical Center and Professor of Pediatrics, Tufts University School of Medicine, told the AP. “It’s not often that you can do something that you feel is going to really change the world and change clinical practice for everyone.” Clinical laboratories that work with oncologists to treat children suffering from cancer will understand Davis’ enthusiasm. (Photo copyright: Tufts Medicine.)
Incorporating Rapid Whole Genome Sequencing into Infant Care
Genetic diseases are responsible for 41% of infant deaths, according to a Rady Children’s Institute press release, which goes on to say the usage of rWGS may significantly improve the odds for infants born with genetic disorders.
“Broad use of genomic sequencing during the first year of life could have a much greater impact on infant mortality than was recognized hitherto,” said Stephen Kingsmore MD, President/CEO, Rady Children’s Institute for Genomic Medicine, which was one of the additional study sites for the Tufts Medicine researchers.
Genetic testing is already used to predict infant health outcomes, but the Tufts study highlights further developments that could improve the process. Prenatal genetic testing can be utilized both through carrier testing to determine any potential genetic red flags in the parents, and during prenatal screening and diagnostic testing of the fetus.
When an infant presents symptoms after birth, rWGS can then be implemented to cast a broad net to determine the best course of treatment.
According to ScienceDaily, the Tufts study found rWGS “to be nearly twice as effective as a targeted gene sequencing test at identifying abnormalities responsible for genetic disorders in newborns and infants.”
However, the rWGS tests took an average of six days to come back, whereas the targeted tests took only four days, ScienceDaily reported. Also, there is not full consensus on whether a certain gene abnormality is actually the cause of a specific genetic disorder.
“Many neonatologists and geneticists use genome sequencing panels, but it’s clear there are a variety of different approaches and a lack of consensus among geneticists on the causes of a specific patient’s medical disorder,” Jill Maron, MD, Vice Chair of Pediatric Research, Tufts Medical Center, and a co-principal investigator of the Tufts study, told Science Daily.
rWGS Costs versus Return on Investment
Some also question the upfront cost of genetic testing. It can be high, but it’s coming down and Maron stresses the importance of the tests.
“Genome sequencing can be costly, but in this targeted, at-risk population, it proves to be highly informative. We are supportive of ongoing efforts to see these tests covered by insurance,” she told ScienceDaily.
Each of the doctors associated with the Tufts study emphasized the importance of this testing and the good that can be done for this vulnerable group. The potential value to the children, they say, far outweighs the drawbacks of the testing.
“This study provides further evidence that genetic disorders are common among newborns and infants,” Kingsmore told ScienceDaily, “The findings strengthen support for early diagnosis by rapid genomic sequencing, allowing for the use of precision medicine to better care for this vulnerable patient population.”
For clinical laboratories, there is also good news about reimbursement for rWGS. In a story published last fall KFF Health News wrote, “Since 2021, eight state Medicaid programs have added rapid whole-genome sequencing to their coverage or will soon cover it, according to GeneDX, a provider of the test. That includes Florida … The test is also under consideration for coverage in Georgia, Massachusetts, New York, and North Carolina, according to the nonprofit Rady Children’s Institute for Genomic Medicine, another major provider of the test.”
“Collectively, these developments are encouraging children’s hospitals, academic centers, and tertiary care centers to look at establishing their own rWGS programs,” wrote Michel in The Dark Report. “In settings where this is appropriate, hospital and health system-based clinical laboratories have an opportunity to take an active role in helping jump start a newborn rWGS program in their institutions.”
Pathologists should continue to monitor rWGS, as well as prenatal and carrier testing, to have a full awareness of its growing use in infant and young child cancer screening.
