Targeted sequencing with Oxford Nanopore: Fast, flexible, PCR-free Cas9 Sequencing Kit now available in store
Wed 16th September 2020
New Cas9 Sequencing Kit provides reagents for one-stop targeted sequencing, enabling scientists to cost-effectively sequence previously inaccessible target regions.
Cas9 targeted sequencing with nanopore enables fast, simple, flexible target enrichment of long regions of interest – read lengths of over 100 kb have been observed to date. The approach is amplification-free, opening 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 enables the enrichment and characterisation of structural variants (SVs), repeat expansions, and SNVs. By avoiding PCR, the approach preserves methylation in the native DNA, which can be detected without any additional library preparation steps. 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 Cas9 targeted sequencing to date and we’re now delighted to offer a kit providing all the reagents required for this approach in one place, alongside a protocol and bioinformatics tutorial.
Rapid characterisation of challenging regions
Cas9 enrichment with Oxford Nanopore sequencing enables scientists to cost-effectively sequence targeted regions that were previously not accessible, including low-complexity or GC-rich regions and large structural variants. The potential impact of this is substantial, particularly across clinical research and in validating genome edits.
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.
As Christina Stangl explained in her NCM 2019 talk, she used Cas9 enrichment and nanopore sequencing to perform targeted and directional fusion gene detection, which was partner and breakpoint-location independent, fast, and spanned large regions of interest.
Using a Cas9 enrichment strategy, in combination with long-read single-molecule nanopore sequencing, Chris Watson and team resolved two challenging clinical research cases in which duplications had been identified by array CGH, but the precise breakpoints at nucleotide resolution had remained elusive.
Oxford Nanopore has a non-exclusive license agreement with Caribou Biosciences Inc., under which they have granted Oxford Nanopore a worldwide, non-exclusive license under foundational CRISPR-Cas9 intellectual property controlled by Caribou for nanopore sequencing.
Oxford Nanopore has a non-exclusive license agreement with the Broad Institute of MIT and Harvard, under which they have granted Oxford Nanopore a worldwide, non-exclusive license under foundational CRISPR-Cas9 intellectual property controlled by Broad for nanopore-based sensing and sample preparation.