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STAT-Seq Proof-of-Principle Study Shows Way Forward for Neonatal WGS

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As a first step toward implementing clinical whole-genome sequencing in a neonatal intensive care unit, researchers from Children's Mercy Hospital have published a proof-of-principle study demonstrating that their protocol can diagnose genetic disease in newborns.

Moving forward, the team plans to begin offering the so-called STAT-Seq test, which runs on Illumina's HiSeq 2500, on a research basis from its hospital until it receives CLIA certification.

Additionally, the hospital plans to launch a CLIA-validated test on the MiSeq by the end of October that sequences more than 500 genes associated with around 600 inherited diseases. The team had originally developed the test on the HiSeq 2000, but is launching it as a clinical test on the MiSeq through a collaboration with Illumina on the company's TruSight Inherited Disease panel. The test will have an out-of-pocket cost of $1,250.

The STAT-Seq proof-of-principle study, which was published in Science Translational Medicine, demonstrated that sequencing on the HiSeq 2500 machine, which can sequence a whole genome in around 26 hours, combined with the hospital's internally developed automated analysis pipeline could provide an answer in around 50 hours for an estimated cost of $13,500.

"We can now consider whole-genome sequencing to be relevant for hospital medicine," Stephen Kingsmore, director of Children's Mercy Hospital's Center for Pediatric Genomic Medicine, said in a conference call discussing the study.

In the study, the actual time to result was around one week because the sequencing was done at Illumina's UK facility, so data had to be shipped between the Kansas City, Mo.-based hospital and the UK. But turnaround time will be 50 hours when the hospital is able to run the test from its own facilities. Furthermore, Kingsmore said that by the end of the year the team will be able to reduce turnaround time to less than 36 hours through improvements to alignment and variant calling.

In an interview, Kingsmore adds that STAT-Seq would initially be offered to patients in the NICU at Children's Mercy Hospital because for those patients there is an "intense urgency." Additionally, while an economic analysis has not yet been done on the protocol, beds in the NICU can cost upwards of $8,000 a day, and a series of single-gene tests will quickly add up to several thousands of dollars.

While $13,500 is not cheap, "a few days saved or more effective treatments" could lead to a greater financial gain.

Other newborns or pediatric patients with suspected genetic disease for whom urgency is not as critical could be offered the hospital's inherited disease panel test, Kingsmore adds.

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