 Metagenomic next-generation sequencing reveals Miamiensis avidus (Ciliophora: Scuticociliatida) in the 2017 epizootic of leopard sharks (Triakis semifasciata) in San Francisco Bay, California BioRxiv, 2018
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 Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing JAMA Network, 2018
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 Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients American Journal of Respiratory and Critical Care Medicine, 2018
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 Complete Genome Sequence of a Divergent Human Rhinovirus C Isolate from an Infant with Severe Community- Acquired Pneumonia in Colorado, USA ASM, 2017
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 Topical silver diamine fluoride for dental caries arrest in preschool children: A randomized controlled trial and microbiological analysis of caries associated microbes and resistance gene expression Journal of Dentistry, 2017
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 IFN-stimulated Gene Expression, Type 2 Inflammation, and Endoplasmic Reticulum Stress in Asthma ATS Journals, 2017
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 Metagenomic deep sequencing of aqueous fluid detects intraocular lymphomas Innovations, 2017
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 Depletion of Abundant Sequences by Hybridization (DASH): Using Cas9 to remove unwanted highabundance species in sequencing libraries and molecular counting applications
With widespread adoption of next-generation sequencing (NGS) technologies, the need has arisen for a broadly applicable method to remove unwanted high-abundance species prior to sequencing. We introduce DASH (Depletion of Abundant Sequences by Hybridization), a facile technique for targeted depletion of undesired sequences. Sequencing libraries are DASHed with recombinant Cas9 protein complexed with a library of single guide RNAs (sgRNAs) programmed to target unwanted species for cleavage, thus preventing them from consuming sequencing space. We demonstrate up to 99% reduction of mitochondrial ribosomal RNA (rRNA) in HeLa cells, and enrichment of pathogen sequences up to 4-fold in metagenomic samples from patients with infectious diseases. Similarly, we demonstrate the utility of DASH in the context of cancer diagnostics by significantly increasing the detectable fraction of KRAS mutant sequences over the predominant wild-type allele. This simple single-tube method is reprogrammable for virtually any sample type to increase sequencing yield without additional cost. Read full publication here |
 Balamuthia mandrillaris is a rare, but almost always fatal cause of meningoencephalitis. The DeRisi Lab seeks contributions to support research and small molecule screening to identify possible therapeutic compounds. See our recent publication, Diagnosing Balamuthia mandrillaris Encephalitis with Metagenomic Deep Sequencing for more information about Balamuthia.
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