myNGS Guides – sgRNA Pools for CRISPR-powered NGS

The powerful CRISPR/Cas system enables new dimensions of targeted sequencing.

Like probe-based hybridization capture technology (e.g., myBaits®), the CRISPR/Cas system can be used for targeted high-throughput sequencing. In addition to standard targeted resequencing and rare variant detection, CRISPR/Cas-driven targeted sequencing is especially useful for resolving genomic regions too complex for short-molecule sequence capture. The several reported techniques are extremely versatile, and have been coupled with both short-read Illumina and long-read PacBio and Oxford Nanopore platforms.

Guide RNA Libraries

CRISPR/Cas-driven targeted sequencing generally follows two basic procedural paradigms, enrichment or depletion. Enrichment techniques enable site-specific adapter ligation after sequestration from background molecules. Depletion techniques use the system’s site-specific nuclease activity to sever unwanted genomic sequences and render them non-sequenceable.

Whichever the application, the key component of all CRISPR/Cas-driven techniques is a collection (library) of sequence-targeting guide RNAs (gRNAs). When combined with Cas enzymes, these gRNA libraries drive complex sequence-specific effects in a simple, single reaction.

Thanks to our ultra-efficient parallelized nucleic acid synthesis technology, Arbor is uniquely equipped to provide robust, affordable, expert-designed gRNA libraries of up to thousands of unique sequences, perfect for CRISPR/Cas-driven targeted sequencing. As with all of our genomics and synthetic biology products, we offer complimentary expert design consultation to help you achieve your goals.

For your next CRISPR/Cas-driven targeted sequencing project, contact us for a custom guide RNA library powered by Arbor’s myNGS Guides


  • Depletion of mitochondrial DNA (mtDNA) from ATAC-Seq libraries

(e.g., CARM)

  • Removal of abundant unwanted sequences from RNA-seq libraries

(e.g., DASH, MAD-DASH)

  • Isolation of long genomic fragments for downstream use


  • Ultra-sensitive and accurate short fragment targeted sequencing

(e.g., CRISPR-DS)

  • Accurate targeted sequencing of repeat-rich regions

(e.g., STR-Seq, Amp-free for SMRT sequencing)

  • Capture of gDNA and its associated proteins using the dCas9 mutant

(e.g., in vitro enChip, RGEN-D)



As each application is unique, please contact us to discuss the specifics of myNGS Guides™  for your project.

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Hardigan, A.A. et al. (2018). CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries. bioRxiv.

Nachmanson, D. et a. (2018). Targeted genome fragmentation with CRISPR/Cas9 enables fast and efficient enrichment of small genomic regions and ultra-accurate sequencing with low DNA input (CRISPR-DS). Genome Research.

Gabrieli, T. et al. (2018). Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH). Nucleic Acid Research.

Slesarev, A. et al. (2018). CRISPR/Cas9 Targeted Capture Of Mammalian Genomic Regions For Characterization By NGS. bioRxiv.

Montefiori, L. et al. (2017). Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9. Scientific Reports.

Bennett-Baker, P.E. & Mueller, JL. (2017). CRISPR-mediated isolation of specific megabase segments of genomic DNA. Nucleic Acid Research.

Shin, GW. et al. (2017). CRISPR–Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis. Nature Communications.

Tsai, YC. et al. (2017). Amplification-free, CRISPR-Cas9 Targeted Enrichment and SMRT Sequencing of Repeat-Expansion Disease Causative Genomic Regions. bioRxiv.

Fujita, T. et al. (2016). Efficient sequence‐specific isolation of DNA fragments and chromatin by in vitro enChIP technology using recombinant CRISPR ribonucleoproteins. Genes to Cells

Gu, W. et al. (2016). Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biology.

Wu, J. et al. (2016). The landscape of accessible chromatin in mammalian preimplantation embryos. Nature.

Jiang, W. et al. (2015). Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters. Nature Communications.

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