CHICAGO, (Reuters) – U.S. 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 yesterday 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 Dr. 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 all of the data.
As many as a third of babies admitted to a neonatal intensive care unit in the United States 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.
“Up until now, they have really had to practice medicine blindfolded,” Kingsmore said in a telephone briefing with reporters.
Dr. Neil Miller, director of informatics at Children’s Mercy, said the software programs help 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.
