NCM 2021: Rapid characterisation of complex killer cell immunoglobulin-like receptor regions using Cas9 enrichment and nanopore sequencing

Jesse presented his work on characterising the human killer cell immunoglobulin-like receptor (KIR) locus. KIR receptors are involved in modulating the activity of natural killer (NK) cells of the immune system. The KIR genes are highly polymorphic and have very high sequence similarity, so are hard to resolve. Jesse aimed to sequence complete KIR haplotypes (~150–350 kbp in length), using Cas9-based enrichment of the haplotype and nanopore sequencing on a MinION Flow Cell. With long nanopore reads and ‘very high accuracy’, Jesse’s team characterised KIR haplotypes at allele-level resolution — even when this involved a difference of only a single nucleotide. As the method was ‘free of any form of amplification’, they also obtained methylation profiles for the KIR regions. Jesse explained that the regulation of KIR gene expression is expected to be via promoter methylation; methylation profiles suggested as such. To summarise, Jesse stated that they had achieved high-resolution characterisation of the complex KIR region. They had defined KIR haplotypes at allele-level resolution and their amplification-free approach enabled epigenetic profiling from the same dataset. Such high-resolution characterisation of KIR haplotypes ‘helps us to understand the rapid evolution of the immune regions’, and along with understanding the methylation profiles and therefore gene expression patterns, Jesse hoped that the data could eventually be used in improving clinical applications.