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Revealing complete complex KIR haplotypes phased by long-read sequencing technology.

D Roe1,2, C Vierra-Green3, C-W Pyo4

  • 1Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN USA.

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Single-molecule sequencing precisely characterized killer cell immunoglobulin-like receptor (KIR) haplotypes, revealing novel structures and alleles. This advances understanding of KIR gene diversity and function in immunity and disease.

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Area of Science:

  • Genomics and Immunogenetics
  • Human Molecular Genetics
  • Natural Killer Cell Biology

Background:

  • The killer cell immunoglobulin-like receptor (KIR) region on human chromosome 19 encodes receptors crucial for natural killer (NK) cell function.
  • KIR genes are highly homologous and the region is structurally dynamic, posing challenges for accurate characterization and haplotype analysis.
  • Understanding KIR diversity is vital for roles in infections, pregnancy, autoimmune diseases, and transplantation.

Purpose of the Study:

  • To develop and apply a sequencing approach for precise characterization of KIR haplotypes.
  • To comprehensively sequence and phase KIR haplotypes without imputation for functional annotation.
  • To identify novel structural variations and alleles within the KIR region.

Main Methods:

  • Utilized single-molecule, real-time (SMRT) sequencing to analyze the complex KIR loci.
  • Sequenced and phased sixteen KIR haplotypes from eight individuals.
  • Performed comprehensive analysis of gene structures, alleles, and structural variations.

Main Results:

  • Successfully sequenced and phased sixteen KIR haplotypes, providing the first comprehensive dataset without imputation.
  • Discovered four novel haplotype structures, a novel gene-fusion allele, and novel/confirmed insertion/deletion events.
  • Identified a homozygous individual and revealed significant diversity in structural haplotypes and alleles.

Conclusions:

  • SMRT sequencing offers a robust method for resolving complex KIR haplotype structures.
  • The findings significantly augment knowledge of KIR diversity, providing high-quality references and evolutionary insights.
  • Generated haplotype sequences and annotations offer alternative loci for the KIR region in the human genome reference.