Researchers find genome sequencing identified conditions missed by standard newborn screening programs that use common clinical laboratory tests
Interim results from a large ongoing pilot study suggest that genome sequencing of newborn children may be more effective than traditional clinical laboratory screening for detection of early-onset genetic conditions. The researchers also found that parents were highly receptive to the idea of performing the sequencing on their newborns.
“The results show us that genome sequencing can radically improve children’s medical care,” said study co-author Joshua Milner, MD, chief of allergy, immunology, and rheumatology services at NewYork-Presbyterian/Columbia University Irving Medical Center, in a Columbia University press release.
“Genome sequencing allows us to detect things that cause serious illness and take action to prevent those illnesses in a significant number of children, not just a few rare cases. It should be instituted as the next standard for newborn screening because it can detect so much more than current methods,” said study co-author Joshua Milner, MD (above), chief of allergy, immunology, and rheumatology services at NewYork-Presbyterian/Columbia University Irving Medical Center, in a press release. Study finding suggest genetic sequencing can be more effective than clinical laboratory screening tests for early detection of genetic disorders. (Photo copyright: Columbia University.)
GUARDIAN Study Details
For the pilot study, the researchers sought consent from 5,555 families, with 4,000 (72%) agreeing to participate. The babies studied were born between September 2022 and July 2023. At that time, the researchers screened for 156 treatable conditions. Parents could also choose to add a panel of 99 neurodevelopmental disorders that do not have treatments, but where “affected children may benefit from early intervention,” the press release notes.
The total—255 genetic tests—included the 50 conditions in the standard Newborn Screening Program as a quality control, principal investigator Wendy Chung, MD, PhD, told Healio.
Among the 4,000 participants, 147 children (3.7%) screened positive for one of the conditions. Further testing confirmed diagnoses in 120 children. “Only 10 of these children were detected through standard screening,” the Columbia press release states.
The vast majority—92 of 120 children—were diagnosed with glucose-6-phosphate dehydrogenase (G6PD) deficiency. “G6PD is not included in traditional screening but individuals with G6PD deficiency can have moderate to life-threatening reactions to certain foods and medications which can easily be prevented by avoiding them,” the press release notes.
Screening for Previously Unscreened Treatable Disorders
The New York State Department of Health mandates free Newborn Screening (NBS) in which a blood sample is collected for testing, generally 24 to 36 hours after birth. The test screens for 50 disorders.
Genome sequencing, however, “offers an additional method to improve screening for conditions already included in NBS and to add those that cannot be readily screened because there is no biomarker currently detectable in dried blood spots,” the GUARDIAN researchers wrote in JAMA.
In the GUARDIAN study, families planning to give birth at an NYP hospital can authorize the researchers to perform genome sequencing of the same dried blood spots to screen for additional pre-selected genetic conditions. At present, the study screens for more than 450 conditions, according to the study website.
“It would be prohibitive to screen for all these diseases with standard testing, but with genomic screening, there’s minimal extra cost when adding a condition,” said study co-author Jordan Orange MD, PhD, chair of pediatrics at Columbia University’s Vagelos College of Physicians and Surgeons and physician-in-chief of NewYork-Presbyterian’s Morgan Stanley Children’s Hospital, in the Columbia press release. “We can screen for treatable disorders that we never thought of screening for before.”
GeneDX, which performs the genomic sequencing for GUARDIAN, issued a press release in which it listed other conditions that are not part of the standard screening. These include Long QT syndrome, which the company described as “a rare heart condition that may cause Sudden Infant Death Syndrome (SIDS) and can be treated with beta-blockers.”
GUARDIAN also detected conditions that came up as false negatives in the standard screening, Chung told Healio. One baby had a genetic variant that causes severe combined immunodeficiency disorder (SCID), a rare and often-fatal condition. Chung said that the genomic sequencing identified the condition while the standard newborn screening missed it.
“We know that a bone marrow transplant is a cure for these children, but safety and success are the highest when the transplant occurs in the first few months of life, before the child starts developing infections or other symptoms,” Milner said in the Columbia press release. “Only because of the genomic screening were we able to identify this child in time.”
Excluding the G6PD cases, the positive screening rate was 0.6%, twice the rate of standard screening. As of last November, more than 12,000 babies had been enrolled in the study. The researchers hope to enroll 100,000.
Advances in Genomic Sequencing Bring Benefits to NBS
“In my practice, I’ve seen many patients who’ve spent years going from doctor to doctor with symptoms that no one can explain. But by the time they receive a diagnosis, the window to best manage the disease has usually passed,” said Chung in the Columbia University press release.
Looking ahead, Chung told Healio that she’d like to expand outside of New York, “in part for generalizability to demonstrate that this is something that could be done with our national public health newborn screening system.”
She’d also like to cut the turnaround time from the current three weeks to one week, she said. And she’d like to drive down the cost.
“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,” she said.
The GUARDIAN study shows how advances in genetic testing are moving fast enough that the point has been reached where the classic clinical laboratory methodologies for newborn screening used for decades are becoming outmoded because of the superior performance/cost of genome sequencing.
Goal is to demonstrate how whole human genome sequencing of newborns can deliver important diagnostic findings associated with 250 genetic conditions
Clinical laboratory testing and genetics are moving closer to the delivery room than ever before. In the largest study of its kind in North America, genomic scientists plan to supplement traditional screening for inherited diseases—traditionally performed on a blood sample taken shortly after birth—with whole genome sequencing (WGS) on 100,000 newborns in New York City during their first five years of life, LifeSciencesIntelligence reported.
Conducted by genetic scientists at NewYork-Presbyterian (NYP) and Columbia University, in collaboration with genetic company GeneDx, a wholly-owned subsidiary of health intelligence company Sema4 (NASDAQ:SMFR), the genetic research study, called GUARDIAN (Genomic Uniform-screening Against Rare Diseases In All Newborns), will screen newborn babies for 250 rare diseases that are generally not tested for.
The GUARDIAN program will “drive earlier diagnosis and treatment to improve the health of the babies who participate, generate evidence to support the expansion of newborn screening through genomic sequencing, and characterize the prevalence and natural history of rare genetic conditions,” according to a Sema4 news release.
“The appetite for this is growing. The awareness of this is growing. We all see it as inevitable,” medical geneticist Robert Green, MD, at Brigham and Women’s Hospital and Harvard Medical School told USA Today. “We are grossly underutilizing the life-saving benefits of genetics and we have to get past that.” Clinical laboratory leaders understand the value of early detection of disease and subsequent early treatment. (Photo copyright: Harvard Medical School.)
Improving Health of Babies Through Early Detection of Disease
GUARDIAN aims to use WGS to identify conditions at birth that can affect long-term health and subsequently enhance treatment options and possibly prevent disability or death.
The 250 different diseases GUARDIAN will be screening for typically strike young children. They are mostly rare conditions that:
have an onset before five years of age,
have a greater than 90% probability of the condition developing based on the genetic result,
have effective approaches and treatments that are already available, and/or
have a well-established natural history of the condition.
“We’re entering the therapeutic era and leaving the diagnostic era,” Paul Kruszka, MD, Chief Medical Officer at GeneDx told USA Today. “This potentially has the opportunity to change the way we practice medicine, especially in rare disease.”
Some Parents Reluctant to Agree to Genetic Testing
Green and his research team first began analyzing the genetic sequences of newborns back in 2013. They believe the costs of performing infant WGS is worthwhile because it can improve lives. However, Green also recognizes that some parents are reluctant to agree to this type of genetic testing due to concerns regarding privacy and the fear of discovering their baby may have an illness.
“You’ve gone through all this pregnancy and you’re sitting there with a healthy baby (and I’m) offering you the opportunity to find out something that’s devastating and terrifying,” he told USA Today. “How fun is that?”
Green continued. “We can respect people who don’t want to know, but also respect people who do want to know. Some families will say ‘I treasure the precious ignorance.’ Others will say ‘If I could have known, I would have poured my heart and soul into clinical trials or spent more time with the child when she was healthy.’”
WGS Screening Identifies Undiagnosed Illnesses in Newborn’s Family
The scientists also found that performing WGS in newborns can detect diseases in the infants as well as unknown illnesses in the families of those babies. According to Kruszka, many parents often seek a diagnosis for a rare disease present in their children for several years. Since many common diseases develop as a result of certain combinations of genes, if illnesses are diagnosed at birth, it could extradite the treatment process, prevent complications, and provide better health outcomes for patients.
“We are relentlessly focused on accelerating the adoption and use of genomic information to impact the lives of as many people as possible, particularly newborns and children,” said Katherine Stueland, President and CEO, Sema4, in the Sema4 news release. “As the first commercial laboratory to launch a rapid whole genome sequencing offering, to address broad unmet needs for early diagnosis, participation in this study is an important step forward for healthcare and in delivering on our goal to sequence once, analyze forever.”
The study is open to all babies in New York City who are born in a health system that participates in the GUARDIAN program, regardless of their race, income, or health insurance coverage.
“The results from this study will help us understand the true impact sequencing at birth can have on newborns and their families in comparison to the current standard of care, particularly as we’ll evaluate clinical outcomes in addition to the psychosocial effect on families,” said Kruszka in the Sema4 news release.
Anything that improves the health of newborn babies is a good thing. Regardless of the cost, if DNA analysis can give newborns and their families a better chance at detecting inherited diseases early while clinical laboratory treatment could make a difference, it is worth pursuing.
Biomarkers used by clinical laboratories and anatomic pathologists are usually biological substances or states that can be measured during testing either in vivo or in vitro. However, clinical laboratories may soon be working with biomarkers based on measurable aspects of external human anatomy. One such biomarker employs facial analysis and facial recognition technology to produced phenotypic data that could help pathologists diagnose rare genetic disorders. A human phenotype is data comprised of a person’s “observable characteristics or traits.”
Phenotypic Data from Photographs
Three genomics companies: FDNA, GeneDx, and Blueprint Genetics, are collaborating on a unique project, dubbed Face2Gene Labs. They are using a facial recognition application called Face2Gene developed by FDNA. The application uses artificial intelligence (AI) and phenotyping technology to extract data from facial photographs of patients. The data is then examined and compared to a database of hundreds of thousands of patterns that were generated from photos of patients with known rare genetic disorders. The algorithm then compiles a list of possible diagnoses. The goal is to produce phenotypic data that clinicians can transmit in real-time directly to medical laboratories for analysis.
“Trying to diagnose patients with genetic sequencing is like searching for a pin in a 22,000-needle haystack,” stated Dekel Gelbman, CEO, FDNA, in a news release. “By providing accurate phenotypic and clinical data to the lab directly at the point of genetic interpretation, we are truly realizing the promise of precision medicine. And, with the power of artificial intelligence behind it, clinicians will be pointed toward potential diagnoses that they may have never otherwise considered.”
The Face2Gene application developed by FDNA uses artificial intelligence to compare digital photographs of patients’ faces against hundreds of thousands of stored patterns to help clinicians identify genetic disorders in children. (Photo copyright: FDNA.)
Solomon goes on to praise GeneDx and Blueprint Genetics as examples of innovative and renowned labs adopting technology that will lead the way in pinpointing rare disease and promote further medical advancements.
“This is an important collaboration for several reasons,” states Ben Solomon, MD, a Clinical Geneticist and Managing Director of GeneDx, in the news release. “It’s a great way to leverage clinical and genetic information and machine learning approaches to find answers for the clinicians, patients, and families GeneDx serves. Aside from providing answers, this integration will make the diagnostic testing process easier, smoother, and more enjoyable for clinicians.”
85% Increase in Diagnostic Yield with Addition of Phenotypic Data
A recent multi-center study called PEDIA (short for Prioritization of Exome Data by Image Analysis) looked into the accuracy of genetic testing when using FDNA’s Face2Gene tool. The study, conducted by researchers at the Berlin Institute of Health and Charité University of Medicine in Berlin, showed promising results of the collaboration.
“We estimate that the addition of phenotypic features [encoded in HPO terms] increases the diagnostic yield to about 60% [from 25% without],” stated Peter Krawitz, MD, PhD, and Principal Investigator for PEDIA. “When adding facial analysis, FDNA’s technology, to that process, the diagnostic yield increases to more than 85%,” he explained in the FDNA news release.
The Rarity Paradox and Diagnosing Genetic Disorders in Children
According to Global Genes, a rare disease patient advocacy non-profit organization, one in 10 Americans (approximately 30 million people) suffer from a rare genetic disorder. These disorders also affect the same percentage of people worldwide, or about 350 million people. There are more than 7,000 distinct rare diseases known to exist and approximately 80% of those illnesses are caused by faulty genes. In addition, about half of the people affected by rare genetic illnesses are children.
“We call it the rarity paradox,” stated Gelbman in an article published in Wired. “Each rare disease in itself affects very few people, but on aggregate the effect is pretty staggering.”
The three companies hope their collaboration will help clinicians determine faster, more accurate diagnoses, while diminishing anxiety among patients and their families regarding the unknowns of rare genetic disorders.
“Since 2012, Blueprint Genetics has been developing technological innovations in sequencing and clinical interpretation to improve the quality and performance of rare disease diagnostics,” noted Tero-Pekka Alastalo, MD, PhD, President, Chief Medical Officer of Blueprint Genetics, in the FDNA news release. “It’s great to see how these innovations are now helping the genetics community and patients suffering from inherited disorders. Combining these technological innovations with our transparent approach to diagnostics and next generation phenotyping tools like Face2Gene represents the next steps forward in molecular genetic diagnostics.”
Pathology groups and clinical laboratories are advised to monitor this exciting development in genomic research. It illustrates how unrelated technologies, such as facial analysis software, could soon be used for diagnostic purposes to detect the presence of genetic disorders, and to determine the best therapies for patients. Labs will want to be prepared to engage with clinicians who adopt this technology and to answer patients’ questions about it.
The National Institute of Health’s ClinVar public database of genetic variation is demonstrating good accuracy, and a handful of clinical labs are learning to share and review this relatively small genetic database
Accessible databases like ClinVar, which was launched by the National Institute of Health (NIH) in 2013, have emerged to aggregate genetic sequencing with acceptable results. ClinVar exists to meet the needs of the medical genetics community. It collaborates with organizations to make pertinent genetic information available.
ClinVar is an archive of compiled data relating to genotype and phenotype variations among humans. Through this database, individuals can present and peruse submissions regarding variants found in patient samples.
ClinVar is averaging about 6,000 submissions per month by both commercial laboratory companies and reference labs. Major contributors to the database include: (more…)
When completed, this acquisition means that the third largest public lab company in the United States will be owned by a multinational biopharmaceutical and diagnostics firm
It’s a big medical laboratory acquisition that has some experts on Wall Street shaking their heads. Last Thursday, it was announced that OPKO Health Inc. of Miami, Florida, would pay $1.47 billion to acquire Bio-Reference Laboratories Inc. (NASDAQ: BRLI), the nation’s third largest full-service clinical laboratory. OPKO (NYSE: OPK) is a multinational biopharmaceutical and diagnostics company in Miami, Florida.
No cash is involved in this purchase. OPKO will pay for the acquisition by exchanging 2.75 shares of OPKO common stock for each share of BRLI common stock. The deal puts a value of BRLI’s common stock of $52.58 per share, the companies announced.
The boards of directors of both companies have already approved the deal, which should close in the second half of the year. (more…)
