For the first time, researchers have used next-gen DNA sequencing to make an actionable diagnosis on a patient. A report of the case was published in an article in the New England Journal of Medicine this Wednesday, June 4.
14-year old Joshua Osborne, of Madison Wisconsin, had been placed in a medically induced coma last July due to severe swelling in his brain. When testing for multiple diseases turned up nothing, his doctor, James Gern, of the University of Wisconsin School of Medicine, reached out to two of his fellow research collaborators: Dr. Joseph DeRisi, and his colleague, pathologist Dr. Charles Chiu. Both researchers are based at the University of California, San Francisco.
DeRisi, a biochemist by training, first used a microarray for DNA sequencing in 2003 to identify the cause of the SARS virus. He and his team now employ a process called unbiased next-generation sequencing, in which they extract all DNA from a patient’s blood, spinal fluid or stool sample and then separate the fragments belonging to pathogens.
Dr. Chiu and his team have developed computer software that matches these fragments with DNA sequences available in online databases. Drs. DeRisi and Chiu combined the new sequencing method and software to identify the elusive cause of Joshua’s encephalitis: the bacteria Leptospira, which can be effectively treated with penicillin.
The entire process of sequencing, analysis, and diagnosis took 48 hours; Joshua was given high doses of penicillin and the swelling in his brain began to go down immediately after receiving treatment. He was on his feet two weeks later.
Next-gen sequencing shows great promise for diagnosing a wide variety of conditions. According to an overview of the case published in the New York Times, 60% of the time encephalitis isn’t even diagnosed.
There are still many hurdles to overcome, however. The human body is teeming with microbes, and even though many of them may turn up during sequencing, their sheer numbers can make it difficult to tell which one of them is causing the problem.
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