Haplotypic resolution of the challenging genomic regions of MHC and KIR using a combination of targeted sequencing and a novel assembly pipeline

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 (ONT) 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 of specific regions rather than the entire genome, 2) exclusive use of ONT instead of combining multiple sequencing technologies, and 3) a unique phasing methodology that integrates sequencing reads, methylation signals, and a reference panel. Ten samples with known MHC and KIR haplotypes were sequenced and assembled, demonstrating 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. This project contains the resouce files required to run the nextflow assembly pipelines and the final assemblies presented in the manuscript.