Revealing Complete Complex KIR Haplotypes Phased By Long-Read Sequencing Technology

Abstract

The killer cell immunoglobulin-like receptor (KIR) region of human chromosome 19 contains up to sixteen genes for natural killer (NK) cell receptors that recognize human leukocyte antigen (HLA)/peptide complexes and other ligands. The KIR proteins fulfill functional roles in infections, pregnancy, autoimmune diseases, and transplantation. However, their characterization remains a constant challenge. Not only are the genes highly homologous due to their recent evolution by tandem duplications, but the region is structurally dynamic due to frequent transposon-mediated recombination. A sequencing approach that precisely captures the complexity of KIR haplotypes for functional annotation is desirable.\n\nWe present a unique approach to haplotype the KIR loci using Single Molecule, Real-Time (SMRT(R)) Sequencing. Using this method, we have - for the first time - comprehensively sequenced and phased sixteen KIR haplotypes from eight individuals without imputation. The information revealed four novel haplotype structures, a novel gene-fusion allele, novel and confirmed insertion/deletion events, a homozygous individual, and overall diversity for the structural haplotypes and their alleles.\n\nThese KIR haplotypes augment our existing knowledge by providing high-quality references, evolutionary informers, and source material for imputation. The haplotype sequences and gene annotations provide alternative loci for the KIR region in the human genome reference GrCh38.p8.\n\nAuthor contributionsDR, CVG, SS, SR, DEG, MM designed the project. CWP, KE, RH performed the preparation and sequencing experiments. DR, CVG, RK, SR, DWG wrote the majority of the manuscript.