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Faster Whole Genome Sequencing Developed for Infants

Baby laughing (D Sharon Pruitt/Flickr)A team led by researchers at Children’s Mercy Hospital in Kansas City, Missouri reported on the first use of a two-day whole-genome sequencing technique for diagnosing genetic diseases in infants. The team that included researchers from University of Missouri-Kansas City, University of Kansas, and Illumnia Inc. in the U.K. described the process in this week’s issue of the journal Science Translational Medicine (paid subscription required).

Genetic diseases, say the authors, affect about three percent of children and account for 15 percent of childhood hospitalizations. While treatments may be available for some 500 genetic diseases, in about 70 of these disorders, such as infantile Pompe disease and Krabbe disease, starting therapy in newborns can help prevent disabilities and life-threatening illnesses.

Thus speed of diagnosis is critical in acute care situations involving infants. The technique, called STAT-Seq, sequences the whole genome of infants in neonatal intensive care units, from blood sample to returning results to a physician, in about 50 hours. Current testing methods of even a single gene, say the authors, can take six weeks or more.

STAT-Seq uses software developed at Children’s Mercy Hospital that translates clinical features of patients into a comprehensive set of relevant diseases. After taking a drop of blood and extracting the baby’s DNA, doctors interact with the system to describe the disease features they are seeing in a patient.

The software then automates much of the identification process of the DNA variations that can explain the child’s condition. That process involves mapping the disease features to the entire set of some 7,500 genes and genetic diseases, and then looks for changes in the DNA code that explain the baby’s illness. The software runs on Illumina’s HiSeq 2500 system, which sequences an entire genome at high coverage in about 25 hours.

The journal article describes the system’s use with four children in the hospital’s neonatal intensive care unit. With this technology, the researchers were able to make a definitive diagnosis in three out of the four babies they tested.

“By shortening the time-to-diagnosis, we may markedly reduce the number of other tests performed and reduce delays to a diagnosis,” says Stephen Kingsmore, Director of the Center for Pediatric Genomic Medicine at Children’s Mercy Hospital. “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.”

The research team next plans to test 100 or more babies with this system to more precisely gauge its benefits and costs and uncover any further problems. They also believe the testing time can be reduced to about 36 hours by the end of the year.

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Photo: D. Sharon Pruitt/Flickr

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