Oxford Nanopore enters into a non-exclusive agreement with Caribou Biosciences for CRISPR-Cas9 enrichment for nanopore sequencing

Oxford Nanopore and Caribou Biosciences, Inc. have entered into a non-exclusive license agreement under which Caribou has granted Oxford Nanopore a worldwide, non-exclusive license under foundational CRISPR-Cas9 intellectual property controlled by Caribou for nanopore sequencing.

“The Cas9 technique will enable users to select and isolate the regions of the genome they are most interested in, including those not available to existing methods, ready for rapid analysis using our long-read, real-time sequencing technology”, said Dr Gordon Sanghera, CEO of Oxford Nanopore.

“The entire library preparation process takes less than two hours so if combined with our portable sequencer MinION, this has the potential to open up fast-turnaround, near-sample testing in new ways.”

A fast, flexible and targeted approach

CRISPR-Cas9-mediated enrichment for nanopore sequencing enables fast, simple, flexible and targeted sequencing of long regions of interest, without the need for amplification – read lengths of over 100Kb have been observed to date. The technique opens up regions of the genome previously only accessible with long read whole genome sequencing, significantly reducing the cost, data output and turnaround time.

The method is suitable for characterising repeat expansions, SNVs and SVs, whilst retaining the methylation status of the native molecule, information about which is provided as standard with the latest basecalling software. It can also be used to sequence many targets simultaneously, allowing users to build their own panels or look across larger regions.

Many teams have already been successful using this approach and Oxford Nanopore plan to release a Cas9 Sequencing Kit later in the year. For now, researchers can access a protocol and bioinformatics tutorial.

Rapid characterisation of challenging regions

Timothy Gilpatrick and team demonstrated the capacity of Cas9 enrichment and long-read nanopore sequencing to thoroughly characterise cancer driver genes. Several hundred-fold enrichment of target loci enabled identification of known large structural variants, SNPs, and differential methylation patterns in genes with prognostic implications in breast cancer.

Using a Cas9 enrichment strategy, in combination with long-read single-molecule nanopore sequencing, Chris Watson and team resolved two challenging clinical cases in which duplications had been identified by array CGH, but the precise breakpoints at nucleotide resolution had remained elusive.

Cas9 enrichment with Oxford Nanopore sequencing enables scientists to cost-effectively sequence targeted regions previously not accessible; including repeat expansion, methylation, low complexity sequence and large regions of structural variation. The potential impact of this is substantial, particularly across clinical research and in validating genome edits.