Faster DNA sleuthing saves critically ill boy

PUBLIC RELEASE DATE:

4-Jun-2014

Contact: Jeffrey Norris jeffrey.norris@ucsf.edu 415-502-6397 University of California - San Francisco

A 14-year-old boy's turnaround and quick recovery after mysteriously being stricken by brain-inflaming encephalitis -- which led to him being hospitalized for six weeks and put into a medically induced coma after falling critically ill -- shows that the newest generation of DNA analysis tools can be harnessed to reveal the cause of a life-threatening infection even when physicians have no suspects.

The quick diagnosis and successful treatment of the adolescent just 48 hours after cerebrospinal spinal fluid and blood were received for analysis portends the broader application of powerful, "next-generation sequencing" (NGS) techniques in solving infectious disease mysteries, not only in cutting-edge research labs, but also in clinical laboratories accessible to hospital physicians everywhere, according to Charles Chiu, MD, PhD, a professor of laboratory medicine at UC San Francisco (UCSF). Chiu is senior author of the case study, published online in the New England Journal of Medicine (NEJM) on June 4, 2014.

The workflow pipeline developed in Chiu's UCSF laboratory to streamline genetic sleuthing of disease pathogens with NGS dramatically cut the time between sample collection and actionable diagnosis and helped a medical team at the University of Wisconsin save the young patient's life.

The NEJM study reflects the convergence of faster DNA sequencing, ever-growing genome databases for identifying pathogens and other organisms, and more sophisticated computational analysis tools to quickly analyze millions of data points. The protocol enabled rapid sequencing and simultaneous identification of all DNA in the patient samples without culturing or targeting for specific infectious disease agents.

"From the perspective of cost and turnaround time, this is a very powerful technology that has become practical to implement routinely in clinical laboratories," Chiu said. Some clinical labs now offer NGS testing to identify cancer mutations in clinical trials and to identify mutations underlying birth defects, but until now NGS has been regarded as too slow and laborious to be useful for routine infectious disease diagnosis.

Study co-author Joseph DeRisi, PhD, chair of biochemistry and biophysics at UCSF, a Howard Hughes Medical Institute (HHMI) investigator, and a leader in using new genomics techniques to identify previously unknown pathogens, such as the SARS coronavirus, said that at a cost of a few thousand dollars, essentially any pathogen now can be detected with a single test.

"This is one test to rule them all," DeRisi said.

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Faster DNA sleuthing saves critically ill boy