Abstract
* Wei Gu and Emily Crawford contributed equally to this work
Background: 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.
Results: 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.
Conclusion: This simple single-tube method is reprogrammable for virtually any sample type to increase sequencing yield without additional cost.
Footnotes
Email addresses:
WG: microfluidics{at}gmail.com
EDC1 (Crawford): Emily.Crawford{at}ucsf.edu
BDO: Brian.Odonovan{at}ucsf.edu
MRW: Michael.Wilson{at}ucsf.edu
EDC2 (Chow): Eric.Chow{at}ucsf.edu
HR: Hanna.Retallack{at}ucsf.edu
JLD: Joe{at}derisilab.ucsf.edu