US scientists have sequenced the entire genetic code of four gravely ill newborns and identified genetic diseases in three of them in two days, quick enough to help doctors make treatment decisions.
Doctors behind the preliminary study released on Wednesday say it demonstrates a practical use for whole genome sequencing, in which researchers analyze all 3.2 billion chemical “bases” or “letters” that make up the human genetic code.
“It is now feasible to decode an entire genome and provide interim results back to the physician in two days,” said Stephen Kingsmore, director of the Center for Pediatric Genomic Medicine at Children’s Mercy medical center in Kansas City, Missouri, whose study was published in the journal Science Translational Medicine.
The study tested two software programs developed at Children’s Mercy that were used in conjunction with a high-speed gene sequencer from Illumina called HiSeq 2500, which can sequence an entire genome in about 25 hours.
The company helped pay for the study and company researchers took part in it.
Next-generation gene sequencing machines have driven down the cost of whole genome sequencing, but making practical use of the data has been more challenging, largely because of the time it takes to analyze.
As many as a third of babies admitted to a neonatal intensive care unit in the US have some form of genetic disease. Treatments are currently available for more than 500 diseases, but identifying them quickly has been a problem.
Typically, genetic testing on newborns using conventional methods takes four to six weeks, long enough that the infant has either died or been sent home.
Neil Miller, director of informatics at Children’s Mercy, said the software helps doctors identify which genes to test, and analyze the data quickly.
One of these programs, called SSAGA, allows doctors to order this test based on the child’s symptoms, without having to know in advance which genes to test for.
The software only maps genes associated with the child’s symptoms. SSAGA does this for nearly 600 diseases, but the team is expanding this to include all 3,500 known disease genes, Miller told the briefing.
The team developed a second software program called Runes that helps determine which of the suspected genes was most likely to be the cause of the child’s illness.
Even though the study did not provide cures for the babies, she said, it could give parents more information about the cause of their child’s illness.
The test is projected to cost US$13,500, but the team believes that may be worth it given the high cost of care in a neonatal intensive care unit, which runs roughly US$8,000 per night.
The next move is to broaden the test to include 100 or more babies to determine the benefits, costs and potential problems linked with the testing.
Because the Illumina machine was not available in the US, the team had to discount the time it took to ship the blood samples to Britain, where the actual sequencing was done.
However, Kingsmore said the hospital expects to receive its own HiSeq 2500 machine next month.