Technology enables sampling of an individual’s microbiome over time to observe changes associated with different illnesses or different diets
There is now a pill-sized device that can non-invasively collect and deliver a sample of gut bacteria taken directly from specific areas of a person’s gastrointestinal (GI) tract. One benefit of this new technology is that it can collect samples from the upper digestive system. Although not ready for clinical use, this is the kind of technology that would enable microbiologists and clinical laboratory scientists to add more microbiome assays to their test menu.
Researchers at Stanford University, Envivo Bio, and the University of California, Davis (UC Davis) have developed a vitamin capsule-sized device—dubbed CapScan—that can measure the microbial, viral, and bile acid profiles contained in the human intestines as it passes through on its way to being expelled.
Currently, scientists rely on stool samples to collect similar data as they are easy to gather and readily available. However, stool samples may not provide the most accurate analysis of the various microorganisms that reside in the human gut.
“Measuring gut metabolites in stool is like studying an elephant by examining its tail,” said Dari Shalon, PhD, Founder and CEO at Envivo Bio, one of the authors of the study, in a UC Davis news release. “Most metabolites are made, transformed, and utilized higher up in the intestines and don’t even make it into the stool. CapScan gives us a fuller picture of the gut metabolome and its interactions with the gut microbiome for the first time.” Shalon is the inventor of the CapScan device.
This demonstrates how technological advancements are giving scientists new diagnostic tools to guide selection of therapies and to monitor a patient’s progress.
Microbiologists will take a special interest in this published study because, once confirmed by further studies, it would provide microbiology laboratories and clinical labs with a new way to collect samples. In clinical laboratories throughout the country, handling fecal specimens is considered an unpleasant task. Once cleared for clinical use, devices like CapScan would be welcomed because the actual specimen would be contained within the capsule, making it a cleaner, less smelly specimen to handle than conventional fecal samples.
“This capsule and reports are the first of their kind,” said Oliver Fiehn, PhD, Professor of Molecular and Cell Biology at UC Davis, in a news release. “All other studies on human gut microbiota focused on stool as a surrogate for colon metabolism. However, of course, the fact is that 90% of human digestion happens in the upper intestine, not the colon.” Clinical laboratories have long worked with stool samples to perform certain tests. If CapScan proves clinically viable, labs may soon have a new diagnostic tool. (Photo copyright: UC Davis.)
Collecting Small Intestine Microbiota
Human digestion occurs mostly in the small intestine where enzymes break down food particles so they can later be absorbed through the gut wall and processed in the body. Stool samples, however, only sample the lower colon and not the small intestine. This leaves out vital information about a patient.
“The small intestine has so far only been accessible in sedated people who have fasted, and that’s not very helpful,” Oliver Fiehn, PhD, Professor of Molecular and Cell Biology at UC Davis and one of the study authors, said in the news release.
According to their Nature paper, to perform their research the team recruited 15 healthy adults to participate in the study. Each participant swallowed four CapScan “pills,” either twice daily or on two consecutive days. The pills were designed to respond to different pH (potential of hydrogen) levels.
Each pill’s pH-sensitive outer coating enables scientists to select which area of the intestinal tract to sample. The outer coating dissolves at a certain point as it travels from the upper intestine to the colon. When this happens, a one-way valve gathers miniscule amounts of biofluids into a tiny, inflatable bladder. Once full, the bladder seals shut and the CapScan continues its journey until it is recovered in the stool. The researchers then genetically sequenced the RNA from the collected samples.
The scientists discovered that the microbiome varied substantially at distinctive sections of the GI tract. When compared to collected stool samples, the researchers determined that traditional stool sampling could not capture that variability.
“There’s enormous potential as you think about how the environment is changing as you go down the intestinal tract,” Kerwyn Huang, PhD, Professor of Bioengineering and of Microbiology and Immunology at Stanford, one of the authors of the study, told Drug Discovery News. “Identifying how something like diet or disease affects the variation in the individual microbiome may even provide the potential to start discovering these important health associations.”
The genetic sequencing also revealed which participants had taken antibiotics within one to five months before the study because their data was so incongruous with the other participants. Those individuals had distinctive differences in their microbiome and bile acid composition, which illustrates that antibiotics can potentially affect gut bacteria even months after being taken.
Researchers Use Multiple ‘Omics’ Approach
The researchers used “multiomics” to analyze the samples. They identified the presence of 2,000 metabolites and found associations between metabolites and diet.
According to the Envivo Bio website, the CapScan allows for the regional measurement of:
“Overall, this device can help elucidate the roles of the gut microbiome and metabolome in human physiology and disease,” Fiehn said in the press release.
Future of Collecting Gut Bacteria
Using CapScan is a non-invasive procedure that makes it possible to sample an individual’s microbiome once, or to monitor it over time to observe changes associated with different illnesses or diets. Since it takes time for the device to pass through the digestive system, it is not a rapid test, but initial studies show it could be more accurate than traditional clinical laboratory testing.
“This technology makes it natural to think about sampling from many places and many times from one person, and it makes that straightforward and inexpensive,” Huang said.
Advancements in technology continue to provide microbiology and clinical laboratories with new, innovative tools for diagnosing and monitoring diseases, as well as guiding therapy selection by medical professionals. Though more research and clinical studies are needed before a device like the CapScan can be commonly used by medical professionals, it may someday provide a cutting-edge method for collecting microbiome samples.
Advances in genome sequencing give virologists and microbiologists new tools for tracking SARS-CoV-2 variants to their sources
Wastewater surveillance has emerged as an essential tool in the detection and tracking of the SARS-CoV-2 coronavirus within communities. Though COVID-19 infections are decreasing in the United States—and clinical laboratories are performing fewer diagnostic tests for the disease—researchers continue to monitor populations for the presence of the coronavirus and its variants to be prepared for the next outbreak.
Genetic sequencing of samples extracted from sewer systems throughout the country have revealed dozens of strains of the coronavirus containing multiple mutations in unusual combinations called cryptic genetic variants (CVG), also known as cryptic lineages. A recent study has indicated that wastewater may also provide answers to questions about long COVID as these mutations can be traced back to individuals who are living with chronic COVID-19 infections.
“Because increases in wastewater [viruses] generally occur before corresponding increases in clinical cases, wastewater surveillance serves as an early warning system for the emergence of COVID-19 in a community,” said Amy Kirby, PhD (above), CDC program lead for the National Wastewater Surveillance System, during a media telebriefing. Wastewater testing for viruses and bacteria may eventually lead to the implementation of systems to alert clinical laboratories in a region whenever infectious agents are detected in wastewater. (Photo copyright: Center for Global Safe Water, Sanitation, and Hygiene.)
Humans Found to Be Primary Source of Cryptic Lineages
To conduct their study, scientist at the University of Wisconsin-Madison and the University of Missouri School of Medicine examined the evolution of a SARS-CoV-2 Omicron subvariant found in wastewater coming from a single facility in Wisconsin that employed about 30 people. The researchers discovered the mutation had been present in the wastewater for more than a year.
Dark Daily originally covered their findings in “New, Cryptic COVID-19 Lineage Found in Ohio Wastewater by Molecular Virologist Tracking Spread of SARS-CoV-2 Variants.” We reported how scientists had tracked the lineage of the cryptic strain to Ohio, where it appeared to have originated from one individual who travels regularly between the cities of Columbus and Washington Court House. They believed the person had a form of long COVID and was unaware that he or she was infected with the coronavirus.
According to Marc Johnson, PhD, Professor of Microbiology and Immunology at the University of Missouri and one of the authors of the study, the individual who shed the mutations had been shedding at least a thousand times more COVID-19 virus than an average infected person sheds. The scientists examined other wastewater monitoring data and identified 37 related cases in the US. They concluded that humans are the main source of the cryptic lineages.
“The fact that someone can have this kind of infection—and there’s every indication that they are still an active member of society and not just lying in the hospital—it’s just amazing,” Johnson told CNN.
Wastewater Surveillance Not an Exact Science, CDC Says
Although not directly involved in this study, through its National Wastewater Surveillance System (NWSS) the US Centers for Disease Control and Prevention (CDC) has been tracking wastewater surveillance programs. The federal agency believes cryptic lineages do not pose a threat to public health.
“The signal we really look for is specific variants increasing in frequency in a community, because that’s what happens at the beginning of a variant surge,” Amy Kirby, PhD, Health Scientist, National Wastewater Surveillance System Lead for the CDC, told CNN. “And it’s not what we’re seeing with these cryptic lineages.”
Kirby also noted that wastewater surveillance is not an exact science and that many factors can impede the interpretation of the data. The mutations observed for this study could be from people with long COVID or even from an infected animal. To be certain of the results, she said, researchers would have to directly link the genetic sequence from a clinical test to a specific wastewater sample.
“Best-case scenario is you find the person, they have long COVID but had no idea they had this infection, and you get them with a doctor who can get them on medicines that will actually give their immune system a bit of an upper hand, and they get better,” Johnson told CNN. “But we only know about the ones we can find, and we don’t know what the implications are, because we still don’t know who those people are.”
Public health messaging in local communities is needed to raise awareness. But though tracking down specific infected individuals could help them receive medical attention, it may not be the most desirable course of action.
“Part of the power of wastewater surveillance is that it is inherently anonymous. It’s a community-level surveillance method,” Kirby said. “And so, tracking back through the wastewater system to identify a person is not what the system is intended for.”
Clinical Laboratories Play Key Role in Public Health
The cryptic lineage that Johnson and his team identified was a mutation that appeared in two watersheds in Ohio—one located in southern Columbus and one in the town of Washington Court House, which is about 40 miles south of Columbus. The researchers hypothesized that an individual living in that area had COVID for more than two years and did not know it, was most likely asymptomatic, and lives in one area and spends a lot of time (perhaps working) in the other area.
“There is almost zero chance the patient in Ohio knew about their infection. There is almost zero chance their doctor would figure it out. It is very likely the infection is causing long term damage,” Johnson wrote in a Twitter tweet. “I’m glad that there is a chance now that they might get appropriate care.”
Wastewater surveillance has materialized as a common method of identifying and monitoring strains of COVID-19 and other infectious diseases. And clinical laboratories play a key role in that process. With genetic sequencing technologies becoming more advanced, lower in cost, faster and more accurate, it’s feasible that those technologies will be utilized more to direct public health initiatives.
Genetic scientists show how rapid WGS is helping doctors determine best treatments for patients with life-threatening conditions
Clinical laboratory scientists will recall that last year, Dark Daily covered how researchers at Stanford University School of Medicine had developed a method for performing rapid whole genomic sequencing (WGS) in as little as five hours. We predicted that their new ultra-rapid genome sequencing approach could lead to significantly faster diagnostics and improved clinical laboratory treatments for cancer and other diseases. And it has.
The research scientist responsible for that breakthrough is cardiologist and Associate Dean of Stanford University School of Medicine, Euan Ashley, MD, PhD. Ashley is also a professor of genomics and precision health, cardiovascular medicine, genetics, and biomedical data science and pathology.
Ashley’s success demonstrates that the drive to reduce the diagnostic time to answer is a market dynamic encouraging research companies to continue finding ways to make WGS faster to accomplish, cheaper to perform, and the DNA sequences generated more accurate.
It is precisely these developments that will provide clinical laboratories and anatomic pathology groups with new means for improving diagnosis and the identification of the most appropriate therapies for individual patients—a core element of precision medicine.
Ashley’s team is now looking at how faster genetic sequencing results could help physicians make life-and-death treatment decisions, STAT reported.
“There’s just never been a better time to be doing genomics,” cardiologist Euan Ashley, MD, PhD, Associate Dean of the Stanford University School of Medicine, told STAT. “Now there are lots of choices. If you’re a genome center and you need to do half a million genomes, you’re going to be extremely price-sensitive. If you’re a clinical lab, where you get a few exomes and a few genomes every day, and what really matters to you is the highest possible accuracy for diagnosis, then you’re definitely going to make a different choice,” he added. (Photo copyright: euanangusashley.com.)
Getting Crucial Genetic Information Faster
Ashley believes that if doctors who work with rare and deadly diseases get crucial genetic information faster, they can more precisely determine which surgical procedures are best for their patients during life-or-death situations.
Already, his work is proving highly successful. In a letter his team published in the New England Journal of Medicine (NEJM), the researchers reported 12 cases of sequencing seriously ill patients, five of whom were diagnosed in seven hours and 18 minutes. Every single case resulted in tangible changes in treatments given to the patients.
“We continue to be interested in sequencing genomes faster and more accurately, for a broader range of clinical applications. We’re recruiting from intensive care units similar kinds of patients to the ones we did before, but with every aspect of the pipeline upgraded, which helps both from a speed but also from an accuracy perspective,” he told STAT.
Ashley and his team continue to delve into the patient care aspects, striving to continue to make a big impact. In addition, the group is being sought out by cancer doctors who need faster diagnoses.
“We also have a lot of interest from cancer doctors saying it’s really important to make a cancer diagnosis quickly. And of course, there is no person who’s ever had the specter of cancer hanging over them for a moment that didn’t want some kind of an answer faster. If you can have it in the next minute, you would take it rather than waiting several weeks,” he noted.
As a result, the group has initiated pilot studies “to look at returning results faster in the same way that we were speeding up the intensive care unit with whole genome sequencing,” Ashley told STAT.
Though the work is in the early stages, the team has a few scenarios where access to genetic data changes medical decision making. For instance, when genetic test results showing a positive BRCA variant alter a doctor’s surgical plan.
“We don’t wait for a cardiac enzyme [test] if somebody’s having a heart attack. That comes back within 10 minutes to a few hours from the lab. I don’t see why you should have to wait for a test to tell you if you’re positive for BRCA variant,” he told STAT.
“Another very obvious place is acute leukemia. And there’s a number of actionable conditions where if they can be detected rapidly, then treatment can be started faster,” he added.
Improving Genetic Sequencing Accuracy while Lowering Costs
STAT asked Ashley about a claim that his team could cut their Guinness World Record sequencing time in half.
“It’s easy to throw that number around, harder to deliver on it. But I think we’re definitely on track to knock hours, not minutes, off that record,” he said.
Additionally, the team continues to work on decreasing cost per genome. In just the time since the record was set, there has already been great strides in this area. The market is filled with new companies and the competition has lowered costs.
“It has definitely come down,” Ashely noted. “In fact, by the time we ended up publishing the [NEJM] paper—as opposed to when we first did this calculation—the cost was already lower. And that was actually before the entry of these new companies to the market, which added downward pressure on costs of sequencing,” he added.
Getting Payers to Reimburse for Genetic Sequencing
Even though costs for WGS is dropping, getting health plans to reimburse for genetic testing remains difficult.
“The challenge now is persuading payers to the very obvious fact that this technology makes patients’ lives better and saves them money,” Ashley told STAT. “And that’s the amazing part. There are so many cost-effectiveness studies now for this technology and yet we are still paying people to sit on the phone all day long and debate with insurance companies.
“And in a world where we pay a very large amount of money for therapeutics, these diagnostics can be cost-saving and lifesaving. At some level, it’s hard to understand why it hasn’t been deployed much more readily,” he concluded.
Clinical laboratory leaders, pathologists, and research scientists should continue to monitor the development of rapid genetic sequencing for diagnostic purposes.
In partnership with the CDC, the collected samples will be sent to approved clinical laboratories for testing as a way to monitor for traces of the SARS-CoV-2 virus
Microbiologists and virologists engaged in tracing sources of viral infections will be interested to learn that the San Francisco International Airport (SFO), in partnership with the Centers for Disease Control and Prevention (CDC), has launched a clinical laboratory testing program where wastewater from airplanes will be screened to search for traces of emerging SARS-CoV-2 coronavirus variants, the virus responsible for COVID-19 infections.
SFO announced in a press release that it is “The first airport in the United States to launch a CDC program to continuously monitor airplane wastewater samples from the onsite [airline waste] triturator for variants of SARS-CoV-2,” adding, “Concentric by Ginkgo, the biosecurity and public health unit of Boston-based synthetic biology company Ginkgo Bioworks, has installed an automatic sampling device that regularly collects combined wastewater flows from international arriving flights at SFO. These samples are then sent to an approved clinical laboratory for testing.”
This is another example of how the COVID-19 pandemic triggered advances in technologies that detect infectious diseases earlier using various samples—and access to different sources of samples—that have been historically used in the field of public health.
“This program is critical for early detection and filling in many blind spots in global surveillance,” Cindy Friedman, MD, Chief of the Travelers’ Health Branch at the CDC, told Time. Clinical laboratories approved for the SFO/CDC screening program will receive the samples for testing. (Photo copyright: NAFSA.)
CDC Program That Monitors International Travelers for Disease
When SFO wastewater samples test positive for the SARS-CoV-2 virus, scientists will perform genome sequencing on the samples to identify which variant of the pathogen is present. This process takes five to seven days. The results are then reported to the CDC.
“As we know from the COVID-19 pandemic, pathogens can spread quickly across the globe, impacting travel and trade,” said Cindy Friedman, MD, Chief of the Travelers’ Health Branch of the CDC’s Division of Global Migration and Quarantine in an SFO press release. “Testing of airplane wastewater can provide early detection of new COVID-19 variants and other pathogens that can cause outbreaks and pandemics. CDC appreciates the collaboration with SFO to further enhance these efforts.”
Concentric by Ginkgo has installed an automatic device that will collect wastewater samples from various international flights upon arrival at SFO. Those samples will then be sent to a diagnostic laboratory where they will be examined for traces of known and unknown viruses, including new variants of SARS-CoV-2.
“It’s a little gross when you start thinking about it,” epidemiologist Katelyn Jetelina, PhD, a scientific consultant for the CDC, told CNN. “But these are really long flights, and we would expect the majority of people would go to the bathroom.”
Other Airports Conducting CDC Screening
The CDC’s Traveler-based Genomic Surveillance (TGS) program was introduced in 2021 to monitor international travelers entering the US for variants of the SARS-CoV-2 coronavirus. Volunteers participate by providing nasal swabs that get batched into pools at the airport. The pooled samples are then sent to Ginkgo’s lab network where they undergo polymerase chain reaction (PCR) testing. All positive samples then receive genomic sequencing.
According to the CDC website, 110,000 volunteers participated in TGS nasal swab testing between November 2021 and February of this year. During that same period, 2,700 positive pools were sequenced and the samples shared with the CDC for viral characterization.
There are currently seven airports in the US participating in the voluntary TGS initiative. In addition to SFO, the other airports in the CDC program are:
John F. Kennedy International Airport
Newark Liberty International Airport
Hartsfield-Jackson Atlanta International Airport
Los Angeles International Airport
Seattle-Tacoma International Airport
Washington Dulles International Airport
However, at this time, SFO is the only airport where wastewater from aircrafts is being tested for coronavirus variants.
Wastewater Best Way to Assess Infections in Community
“Biology doesn’t respect borders, and airports and other ports of entry are critical nodes for monitoring the spread of pathogens,” said Matthew McKnight, General Manager, Biosecurity, at Ginkgo Bioworks, in the SFO press release. “We are proud to partner with SFO on developing cutting-edge biosecurity technology to support public health.”
Because traces of the virus that causes COVID-19 can be detected in human fecal matter, even if symptoms are not present, wastewater sampling will continue to be an important tool in the fight against the coronavirus.
“Wastewater surveillance is really the best way to assess infections in the community because people just aren’t testing as much due to the relaxing of testing requirements and a rise in testing fatigue, among other factors,” Ashish Jha, MD, a general internist physician and White House Coronavirus Response Coordinator, told CNN.
“So, when I look at data every day on trying to assess where we are with infections, I look at wastewater data,” he added.
And so, since clinical laboratories will continue to be relied upon for sample testing and population health screenings, we will continue to monitor and report on advances in wastewater testing for SARS-CoV-2, as well as other infectious agents that might be added to these sampling programs.
Microbiology team has tracked 37 unique strains of the coronavirus since they began researching lineages two years ago
Microbiologists and clinical laboratory scientists will be interested to learn about the discovery of a new strain of SARS-CoV-2, the coronavirus that caused the COVID-19 pandemic, in wastewater sampled in Ohio.
According to an article published in Nature Reviews Genetics, a CVG is “a genetic variation that normally has little or no effect on phenotype but that—under atypical conditions that were rare in the history of a population—generates heritable phenotypic variation.”
Johnson tracked the lineage of the cryptic strain to Ohio, where it appears to have originated from one individual who travels regularly between the cities of Columbus and Washington Court House. He believes this person may have a form of long COVID and is unaware that he or she is infected with the coronavirus.
“This person was shedding thousands of times more material than a normal person ever would,” Johnson told The Columbus Dispatch. “I think this person isn’t well. … I’m guessing they have GI issues.”
“If someone has this infection, the chances are nil that they’re going to figure out what it is,” Marc Johnson, PhD, Professor of Molecular Microbiology and Immunology at the University of Missouri School of Medicine, told Insider. Microbiologists and clinical laboratory scientists in the Columbus, Ohio, area may be able to help locate this person. (Photo Copyright: University of Missouri.)
Other Cryptic COVID-19 Lineages
This isn’t the only “Cryptic COVID” case identified by Johnson and his team. In Wisconsin, another unique strain was discovered and narrowed down to a single facility and about 30 individuals. Two thirds of the employees were tested but, unfortunately, all tests came back negative. The cryptic strain seemed to have disappeared.
“We don’t know why,” Johnson told The Hill. “Either [the infected person] left the job, or got better, or is in remission—we don’t know. But we’re still monitoring it. And we’ve actually now gotten started collecting stool samples from the company.”
“We systematically sampled [sewer] maintenance holes to trace the Wisconsin lineage’s origin. We sequenced spike RBD [receptor-binding domain] domains, and where possible, whole viral genomes, to characterize the evolution of this lineage over the 13 consecutive months that it was detectable.
“The high number of unusual mutations found in these wastewater-specific cryptic sequences raises the possibility that they originate from individual prolonged shedders or even non-human sources. The Wisconsin lineage’s persistence in wastewater, single-facility origin, and heavily mutated Omicron-like genotype support the hypothesis that cryptic wastewater lineages arise from persistently infected humans.”
Johnson and his team have tracked 37 unique strains of the COVID-19 virus, including one in New York City, The New York Times reported.
In a statement to The Columbus Dispatch regarding the Columbus strain, the federal Centers for Disease Control and Prevention (CDC) noted that, “The virus lineage in question is not currently spreading or a public health threat.
“Unusual or ‘cryptic’ sequences identified in wastewater may represent viruses that can replicate in particular individuals, but not in the general population,” the CDC noted. “This can be because of a compromised immune system. CDC and other institutions conduct studies in immunocompromised individuals to understand persistent infection and virus evolution.”
In identifying these lineages, and the individuals who shed them, scientists can learn more about how COVID-19 mutates and spreads.
Mitigating Consequences of COVID-19 Variants
Although the CDC says that particular strain is not a threat to the public it could pose a long-term health risk for the individual suffering. And this individual may hold clues for the future of how the COVID-19 virus mutates and grows. Therefore, locating these people is a priority.
“The coronavirus will continue to spread and evolve, which makes it imperative for public health that we detect new variants early enough to mitigate consequences,” Rob Knight, PhD, Founding Director of the Center for Microbiome Innovation and Professor of Pediatrics, Computer Science and Engineering at the University of California San Diego (UCSD).
“Before wastewater sequencing, the only way to do this was through clinical testing, which is not feasible at large scale, especially in areas with limited resources, public participation, or the capacity to do sufficient testing and sequencing,” said Knight in a UCSD press release. “We’ve shown that wastewater sequencing can successfully track regional infection dynamics with fewer limitations and biases than clinical testing to the benefit of almost any community.”
Although tracing the individuals shedding cryptic COVID-19 lineages may not have an immediate effect on public health, it could lead to future discoveries about the SARS-CoV-2 coronavirus that can help shape public health goals in fighting future pandemics.
At the very least, one individual in Columbus may learn how to treat long COVID’s adverse symptoms. Microbiologists and clinical laboratory scientists involved in COVID-19 wastewater research can learn much from following these research investigations.
Both programs seek to achieve early diagnosis by detecting a range of disorders where an existing treatment can be given as early as possible
Two separate genetic sequencing projects—one in the United Kingdom and one in New York City—aim to perform whole-genome sequencing for clinical laboratory diagnostic purposes on 100,000 newborns each to identify up to 200 rare genetic disease that are treatable with early diagnosis and intervention.
Genomics England announced its Newborn Genomes Program in 2022 and plans to start signing up expectant parents for the genetic sequencing project later this year, an article in Science reported. Parents will be invited to participate in the $129 million pilot program through the UK’s National Health Service (NHS) with the goal of enrolling 100,000 newborns over the next two years.
In the US, the Guardian Study (Genomic Uniform-screening Against Rare Diseases In All Newborns) was launched last year in New York City. The program will run for four years and sequence the DNA of 100,000 newborns looking for 160 rare genetic diseases. “Parents can opt to add 100 neurodevelopmental disorders that can’t be cured, but for which speech and physical therapy could help,” Science noted.
More than 200 babies have already been enrolled in the Guardian study, and about 70% of those invited to participate have agreed to do so, according to GenomeWeb.
“I think expanding the number of diseases we look for could make a radical improvement in the way we diagnose and treat children with rare diseases,” said molecular geneticist Wendy Chung, MD, PhD, Director of the Clinical Genetics Program at New York Presbyterian Hospital/Columbia University Medical Center, in a press release. Clinical laboratories that perform newborn screenings may soon have new genomic screening tools for a larger number of rare genetic disorders. (Photo copyright: Columbia University.)
Giving Parents the Ability to Make Informed Decisions
In many countries, newborns are screened for several dozen genetic illnesses via biochemical tests using a drop of blood collected from the baby’s heel. Whole-genome sequencing could potentially detect more disorders and allow for earlier care and treatments to avoid permanent disability or death.
Parents enrolled in the US/UK genomics sequencing programs will receive results for as many as 200 genetic diseases that are known to be caused by genetic variants and which typically display symptoms before the age of five. All the illnesses are treatable with remedies ranging from a simple vitamin supplement to a bone marrow transplant.
“For the parents who may be offered whole genome sequencing for their babies as part of our pilot, they need to know which of these many conditions will be looked for, so that they can make an informed decision about whether or not to take part in the study,” said pediatrician and geneticist David Bick, MD, Principal Clinician for the Newborn Genomes Program, in a Genomics England press release.
Parents will not receive data regarding gene variants with unknown risks or variants that only cause disease in adulthood.
Detecting a Range of Genetic Disorders in Newborns
The UK’s Newborn Genomes Program expects to identify genetic disease in at least 500 newborns. Researchers involved in the project estimate that utilizing genetic sequencing in newborns could detect those diseases in up to 3,000 babies if used across the country.
“The primary goal of the program is to detect a range of disorders where we already have an intervention that could be given at the earliest possible point in life to reduce disability or potentially to avoid harm,” said Sir Mark Caulfield, MD, Director of the William Harvey Research Institute at Queen Mary University of London and Chief Scientist for Genomics England, in a Queen Mary University press release.
“It turns out that approximately one in 190 births (circa 10 babies born every day in the UK) has one of these problems, and if the intervention is employed, this could be life changing. The majority of these interventions are dietary shifts or vitamin supplements, and only 8% are expensive treatments, for example, gene therapies or transplantation,” Caulfield noted. “The children may not be cured, but the interventions may reduce disability or even allow a normal life, so getting these life-changing opportunities to children at the earliest point is so important.”
The US initiative is using genomic sequencing to screen for 250 medical conditions that are not currently detectable in newborn screenings in New York. Like the UK program, these disorders are treatable and symptomatic before the age of five. The goal is to diagnose these illnesses earlier to allow for early treatment and better health outcomes.
“I think expanding the number of diseases we look for could make a radical improvement in the way we diagnose and treat children with rare diseases”, said Chung in a Columbia University press release. “Families and pediatricians don’t need to go through those diagnostic odysseys anymore with the genomic technology we now have. We can make the diagnosis at birth.
“I think genomic screening will also make sure we leave no baby behind. It will provide equitable access to a diagnosis,” Chung added. “We want to address health disparities, which we’ve seen happen after screening for SCID (severe combined immunodeficiency disorders) was added to state newborn screening panels. When every newborn is screened, the family’s socioeconomic status is irrelevant.”
Saving Children from Lifelong Disease
The US and UK genomics sequencing programs may have considerable influence on encouraging more newborn screening all over the world. Technological advancements in recent years have dramatically reduced genomic sequencing costs.
Additionally, sequences can be done faster and more accurately, and the technology is enabling complex analysis of data in ways that expands the information contained in the genome. This could lead to life-saving breakthroughs in treatment for many rare genetic disorders.
These developments may also encourage more clinical laboratories within the United States to consider offering a genome sequencing service for newborn screening. With hundreds of diseases now detectable through genetic technology, screening a newborn’s genome for mutations could provide more accurate and faster diagnosis of illnesses and potentially help more children avoid serious diseases.
