Rapid characterization of complex killer cell immunoglobulin-like receptor regions using Cas9 enrichment and nanopore sequencing
About Jesse Bruijnesteijn
Jesse Bruijnesteijn obtained his Ph.D. in immunogenetics at the Biomedical Primate Research Centre (Rijswijk, Netherlands). He is specialized in the characterization of complex gene clusters that encode for components of the immune system, such as the MHC and KIR receptors, in humans and other primate species.
Long-read sequencing approaches bear the potential to resolve even extremely complex genome regions. Deep sequencing coverage, however, is required to overcome low nucleotide accuracy, especially in regions with high homopolymer density, copy number variation, and sequence similarity, such as the MHC and KIR gene clusters of the immune system. We have adapted a targeted Cas9 enrichment protocol in combination with long-read sequencing on an Oxford Nanopore Technologies MinION platform, which allowed phasing of highly complex KIR haplotypes. This strategy facilitates rapid characterization of multigenic regions, including its epigenetic footprint, and is applicable in multiple species, even in the absence of a reference genome.