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A Dramatic Case of Clinical Pathogen Detection through Gene Sequencing



June 5, 2014 | At the New York Times, Carl Zimmer describes the first case in which unbiased DNA sequencing was used to find an unknown pathogen causing a serious illness, leading to immediate treatment. The case concerns 14-year-old Joshua Osborn, who was placed in a medically induced coma during a dangerous bout of encephalitis. Osborn was quickly enrolled in a study to test a new next-generation sequencing bioinformatics pipeline developed at UC San Francisco, called SURPI (Sequence-based Ultra Rapid Pathogen Identification). Samples of Osborn's blood and cerebrospinal fluid were sent to UCSF to be sequenced. After raw sequencing of the samples, SURPI was performed in just over an hour and a half, first discarding any sequence fragments that aligned to the human genome, then matching the remaining fragments with a huge library of reference genomes kept in NCBI databases. SURPI successfully aligned a small fraction of the reads from Osborn's cerebrospinal fluid to the genome of Leptospira borgpetersenii, a rare pathogenic bacterium. The information led to an immediate course of penicillin G, which allowed Osborn to recover and be discharged within 14 days. The full case report can be read in the New England Journal of Medicine, and a more detailed description of SURPI appeared yesterday in Genome Research. As Zimmer notes, this is a significant development in DNA diagnostics because the rapid turnaround allowed real clinical action to follow the sequencing analysis. New York Times
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