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50-Hour Whole Genome Test Could Reduce Deaths In Critically Ill Babies

Many babies requiring critical care have genetic diseases that can progress rapidly, and the sooner doctors can diagnose them, the sooner the infants get the treatment they need, which can often be life-saving. Currently it takes weeks to test just one gene, but US researchers reporting in Science Translational Medicine this week describe how they have developed a prototype whole genome sequencing test that only takes 50 hours from blood sample in the neonatal intensive care unit (NICU) to doctors seeing the results.

Corresponding author Stephen Kingsmore, Director of the Center for Pediatric Genomic Medicine at Children's Mercy Hospital in Kansas City in the US, says in a press statement:

"Up to one third of babies admitted to a NICU in the US have genetic diseases."

There are at least 3,500 known genetic diseases caused by mutations in DNA, and treatments are available for more than 500 of them. In about 70 of these, such as infantile Pompe disease and Krabbe disease, starting treatment as early as possible in newborns can help prevent disabilities and life-threatening illnesses.

In their paper, Kingsmore and colleagues report how they used a whole genome sequencing (WGS) program they developed themselves called STAT-Seq, in conjunction with Illumina's HiSeq 2500 sequencing machine, to cast a broad net over the 3,500 or so known genetic diseases and achieve results in time for doctors to make clinical decisions.

"By obtaining an interpreted genome in about two days, physicians can make practical use of diagnostic results to tailor treatments to individual infants and children," says Kingsmore.

Currently it takes about a month to get these kinds of results.

Kingsmore and colleagues have cut down the time by developing statistical software that matches up doctors' unique descriptions of the patient's condition and symptoms, against a comprehensive set of relevant diseases while looking at the genome test results.

By allowing the individual features to be entered, the software substantially automates identification of the DNA variations that can explain the child's condition.

"We describe 50-hour differential diagnosis of genetic disorders by whole-genome sequencing (WGS) that features automated bioinformatic analysis and is intended to be a prototype for use in neonatal intensive care units," they write.

Kingsmore and colleagues tested their prototype by doing retrospective 50-hour WGS on two children whose molecular diagnoses had already been done the conventional way.

Then they did tests on children not tested before, and confirmed the results by sequencing genomes of parents and siblings. These tests revealed, in one newborn a "severe GJB2-related skin disease", in another they uncovered "BRAT1-related lethal neonatal rigidity and multifocal seizure syndrome", and also found other gene defects in other children, including a new disease-causing mutation, BCL9L.

"Thus, rapid WGS can potentially broaden and foreshorten differential diagnosis, resulting in fewer empirical treatments and faster progression to genetic and prognostic counseling," write the researchers.

Although further research is needed, they believe STAT-Seq also has the potential to bring down costs of genetic testing in the NICU.

"By shortening the time-to-diagnosis, we may markedly reduce the number of other tests performed and reduce delays to a diagnosis," says Kingsmore.

"Reaching an accurate diagnosis quickly can help to shorten hospitalization and reduce costs and stress for families," he adds.

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