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Whole-Genome Sequencing Can Yield Diagnoses for NICU Cases

NEW YORK (GenomeWeb) – Whole-genome sequencing can quickly and cost-effectively provide diagnoses for some babies in neonatal intensive care units.

Researchers at Rady Children's Institute for Genomic Medicine conducted whole-genome sequencing and interpretation for 42 infants in the NICU. As Rady's Shimul Chowdhury reported today at the American Society of Human Genetics annual meeting in Orlando, Florida, he and his colleagues were able to obtain genetic diagnoses for slightly more than a third of the infants within a week. For many, that diagnosis led to a change in treatment.

"Newborns often don't fit traditional methods of diagnosis, as they may present with non-specific symptoms or display different signs from older children," Chowdhury said in a statement.

In addition, he and his colleagues estimated that such a sequencing approach is cheaper than traditional testing.

Chowdhury and his colleagues obtained blood samples for sequencing from 42 sick infants and, when available, from their parents. They tried to obtain samples within the first 48 hours to 72 hours of admission. They also matched patients' symptoms to Human Phenotype Ontology terms and mapped them to potential genetic causes.

They performed PCR-free rapid whole-genome sequencing to obtain between 40X and 45X coverage. They aligned the sequences and identified variants using commercially available tools, and then curated and prioritized the variants.

For 43 percent of the patients, the researchers were able to make a genetic diagnosis. On average, diagnoses were obtained within a week, though the fastest one was within 37 hours. The researchers also made personalized medicine recommendations to clinicians based on the results. The conditions that they uncovered were known genetic disorders.

Those diagnoses led to changes in medical care for 13 patients. The changes ranged from taking medications targeting the disease to changes in surgical interventions as well as guiding palliative care. This indicated to the researchers that early diagnoses could change patient care. 

Chowdhury and his colleagues also calculated that taking a whole-genome sequencing approach from the start saves money. They calculated the cost savings by modeling six cases in depth for which they either had similar cases in the past at Rady or for which there were published costs in the literature and also by relying on DELPHI, which surveys outside physicians about whether the assumptions in that modeling are reasonable.

For the 42 infants in their study, they estimated that sequencing saved more than $1.8 million, as compared to what the standard care would have cost.

"The cost savings were especially striking, given that sequencing costs are still high — even with those costs, we found that rapid WGS was not just clinically useful, but economically prudent," Chowdhury added. "Given these benefits, we'd eventually like to see rapid WGS as a reimbursable first-tier test for a proportion of infants in the NICU."

Chowdhury added in an interview that he hopes that this and additional data on increased numbers of patients will show insurers that whole-genome sequencing is cost-effective. He and his colleagues plan to expand and scale up their study, and have partnered with children's hospitals in California and Minnesota to do so.