Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

A 14-year-old boy with severe combined immunodeficiency presented 3 times to a medical facility over 4 months with fever and headache that progressed to hydrocephalus and status epilepticus necessitating a medically-induced coma after starting empiric steroids for a suspected autoimmune condition. An exhaustive diagnostic workup including brain biopsy was unrevealing. In collaboration with Dr. Charles Chiuís lab (UCSF Department of Laboratory Medicine), unbiased next-generation sequencing of the patientís cerebrospinal fluid and computational analysis of the results using an ultra-rapid bioinformatics pipeline for comprehensive pathogen detection identified 475 sequence reads out of 3,063,784 (0.016%) corresponding to Leptospira spp. This result was obtained within 48 hours of sample receipt. The patient responded dramatically when treated with appropriate antimicrobials and discontinuation of steroids, and was discharged home 24 days later near his premorbid baseline.

[ Read the Article in the New York Times ] ē [ Press Release ]


Oct 29th, 2013. UCSF, Cold Spring Harbor Laboratory, MIT, and Davidson College receive $400,000 from Dr. David Botstein to further advanced technology courses for graduate education. Dr. Botstein is the recent recipient of the Breakthrough Prize in Life Science, and has pledged a portion of that prize to these four institutions in recognition of their efforts to further advanced teaching, especially at the graduate school level. At UCSF, the award recognizes the recently built Teaching Lab at Mission Bay together with the Integrated Program in Complex Biological Systems, an NIBIB T32 supported program that promotes a project-based curriculum for students in biophysics and bioinformatics. The Teaching Lab was opened in 2011 and was funded by QB3.
Read the CSHL Press Release here


We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of pre-assembled contigs. It was designed to address the challenge of assembling viral genomes that constituted a small minority of the reads within ultra-deep, short-read, metagenomic, shotgun datasets. PRICE has already enabled the discovery of several novel virus genomes from such complex datasets.
The early online edition of the PRICE paper, published in G3, is here.
Download PRICE