Haplotype-resolved assembly of MHC and KIR with ONT Adaptive Sampling
Recently long-read sequencing technologies and bioinformatics have enabled the construction of haplotype-resolved genome assemblies. Here, we present the complete and accurate de novo characterization of two challenging genomic regions, the major histocompatibility complex (MHC) and Killer-cell immunoglobulin-like receptors (KIR), in phased haplotypic form, using Oxford Nanopore Technology Adaptive Sampling sequencing, and a newly developed bioinformatics pipeline. These critical regions for our immune response have been notoriously difficult to characterize due to their sequence variability and structural complexity. The key features of our approach are 1, focused sequencing on specific regions, instead of the whole genome, 2, the usage of only ONT as opposed to a combination of sequencing technologies, and 3, the unique phasing methodology of our pipeline, combining reads, methylation and a reference sequence panel. Ten samples with known haplotypic information for the MHC and KIR were sequenced and assembled to demonstrate the potential of our approach. We achieved efficient target enrichment resulting in 100% coverage and accuracy ranging from 99.96% to 99.99% across the MHC and KIR. Its simplicity, reproducibility, and affordability distinguish this method as a unique and effective approach for the targeted haplotypic characterization of the MHC and KIR and possibly other specific genomic regions. These efforts will in turn facilitate future studies that further advance the functional deconvolution of our genome.