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.
The results come from the GUARDIAN (Genomic Uniform-screening Against Rare Disease in All Newborns) study conducted by Columbia University Irving Medical Center, NewYork-Presbyterian (NYP) Health System, and the New York State Department of Health. Collaborators also included Illumina, a maker of next-generation sequencing (NGS) equipment, and GeneDx, a genetic testing company.
Study participants consist of families giving birth at six NYP hospitals in New York City.
The researchers published their findings so far in the Journal of the American Medical Association (JAMA), titled, “Expanded Newborn Screening Using Genome Sequencing for Early Actionable Conditions.”
“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.
—Stephen Beale
Related Information:
In Pioneering Study, Gene Technology Outperforms Standard Newborn Screening Tests
Expanded Newborn Screening Using Genome Sequencing for Early Actionable Conditions