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In Healthy Newborn Study, Genome Sequencing IDs More Potential Early-Onset Diagnoses Than Panel Test

This article has been updated with more information about ViaCord and its offerings.

NEW YORK — Researchers at Revvity (formerly PerkinElmer) have found that screening seemingly healthy babies with genome sequencing is better at identifying their risk for pediatric-onset disorders than more limited gene panel sequencing.

For a study published in JAMA Network Open on Monday, the researchers analyzed data, collected between 2018 and 2022, from a genetic newborn screening service offered to parents of apparently healthy babies by ViaCord, a unit of Revvity, and paid for out of pocket. 

Parents could opt for genome sequencing or, at less than a third of the cost, for a panel of 268 genes associated with actionable pediatric conditions. Genome sequencing analyzed 6,000 disease-associated genes — including SNPs, indels, and copy number variants — but only reported results for childhood-onset conditions. It included both nuclear and mitochondrial DNA.

Both tests used whole blood, saliva, or dried-blood spot samples to extract DNA, and all assays were conducted at Revvity's laboratory, with turnaround times of 56 days for genome sequencing and 37 days for panel testing.

"We wanted to compare two conceptually different newborn screening approaches for proactive screening of pediatric population-onset genetic risks," corresponding author Jorune Balciuniene, associate director of clinical genomics at Revvity Omics, said in an email.

Genome sequencing identified potential diagnoses in 8.2 percent of the children, while only 2.1 percent of babies screened with the gene panel were found to be at risk for a childhood-onset disease.

Of note, close to 50 percent of the genome sequencing findings were associated with high-penetrance conditions, compared to 18.2 percent in the gene panel group.

"A significant proportion of apparently healthy children screened by [genome sequencing] were found to be at risk for a wide range of pediatric-onset conditions likely to be missed on limited gene panels," the authors wrote.

Most potential diagnoses from genome sequencing involved two main disease categories — metabolic and neurodevelopmental disorders involving syndromes with intellectual disability and autism. The authors noted that not all potential metabolic disorders identified with genome sequencing could have been detected by Recommended Universal Screening Panel (RUSP) newborn screening.

Newborn screening approaches in the US are currently limited to the RUSP, with 37 core conditions. Different states in the US offer limited, full, or enhanced screening for additional RUSP disorders depending on their program. "While these are well-established actionable conditions, less than 1 percent of newborns are found to be at risk for these [newborn screening] disorders," said Balciuniene. Even if screening expanded to include the 268 actionable conditions of the gene panel, she added, three-fourths of children with genetic risk would be missed compared to a genome-open approach.

According to the authors, the results of genome sequencing-based screening would help in better health management of children, such as early intervention, disease surveillance, and avoidance of aggravating factors and medicines, all of which could subsequently improve clinical outcomes. Moreover, they said that genome sequencing provides high coverage of mitochondrial genomes, enabling simultaneous detection of low-heteroplasmy variants.

Despite those benefits, affordability could be a significant barrier. "[Genome sequencing] has entered mainstream medicine; however, cost considerations and reimbursement have hindered widespread acceptance," the authors wrote.

According a brochure available on ViaCord's website, the panel test, called Genetic Insights Panel, costs $750 and the whole-genome sequencing test has a price of $2,500.

Balciuniene said, though, that sequencing technologies are evolving so fast that in the near future, costs may not be the limiting factor any longer.

A major limitation of the study was that the researchers did not include any clinical follow-up information. It also did not consider the ethical, legal, and societal considerations of genome sequencing-based newborn screening, which was beyond the scope of the work. "We look forward to publications from experts in this area," Balciuniene said.