title: Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications.
abstract: Next-generation sequencing has generated a need for a broadly applicable method to remove unwanted high-abundance species prior to sequencing. We introduce DASH (Depletion of Abundant Sequences by Hybridization). Sequencing libraries are 'DASHed' with recombinant Cas9 protein complexed with a library of guide RNAs targeting unwanted species for cleavage, thus preventing them from consuming sequencing space. We demonstrate a more than 99 % reduction of mitochondrial rRNA in HeLa cells, and enrichment of pathogen sequences in patient samples. We also demonstrate an application of DASH in cancer. This simple method can be adapted for any sample type and increases sequencing yield without additional cost.
authors.affiliation: Departments of Pathology and Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. microfluidics@gmail.com.
authors.forename: W
authors.initials: W
authors.lastname: Gu
authors.affiliation: Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA. Emily.Crawford@ucsf.edu.|Howard Hughes Medical Institute, Chevy Chase, MD, USA. Emily.Crawford@ucsf.edu.
authors.forename: E D
authors.initials: ED
authors.lastname: Crawford
authors.affiliation: Integrative Program in Quantitative Biology, Bioinformatics, University of California San Francisco, San Francisco, CA, USA. Brian.Odonovan@ucsf.edu.
authors.forename: B D
authors.initials: BD
authors.lastname: O'Donovan
authors.affiliation: Department of Neurology, University of California San Francisco, San Francisco, CA, USA. Michael.Wilson@ucsf.edu.
authors.forename: M R
authors.initials: MR
authors.lastname: Wilson
authors.affiliation: Center for Advanced Technology, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA. Eric.Chow@ucsf.edu.
authors.forename: E D
authors.initials: ED
authors.lastname: Chow
authors.affiliation: Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA. Hanna.Retallack@ucsf.edu.
authors.forename: H
authors.initials: H
authors.lastname: Retallack
authors.affiliation: Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA. Joe@derisilab.ucsf.edu.|Howard Hughes Medical Institute, Chevy Chase, MD, USA. Joe@derisilab.ucsf.edu.
authors.forename: J L
authors.initials: JL
authors.lastname: DeRisi
mesh_terms: D064113:CRISPR-Cas Systems / Q000235:genetics; D003141:Communicable Diseases / Q000235:genetics; D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D009693:Nucleic Acid Hybridization / Q000379:methods*; D012313:RNA / Q000235:genetics; D017393:RNA Editing / Q000235:genetics; D000077278:RNA, Mitochondrial; D012335:RNA, Ribosomal / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D000077278:RNA, Mitochondrial; D012335:RNA, Ribosomal; D012313:RNA