Tsung-Kai Hung1, Wan-Chi Liu2, Sheng-Kai Lai3,4, Hui-Wen Chuang1, Yi-Che Lee2, Hong-Ye Lin5, Chia-Lang Hsu1,6, Chien-Yu Chen5, Ya-Chien Yang2,7, Jacob Shujui Hsu1 and Pei-Lung Chen1,3,4,8,9 1Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei 100233, Taiwan; 2Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100229, Taiwan; 3Department of Medical Genetics, National Taiwan University Hospital, Taipei 100229, Taiwan; 4Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan; 5Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan; 6Department of Medical Research, National Taiwan University Hospital, Taipei 100229, Taiwan; 7Department of Laboratory Medicine, National Taiwan University Hospital, Taipei 100229, Taiwan; 8Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 100229, Taiwan; 9Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei 100229, Taiwan Corresponding authors: ycyangntuntu.edu.tw, jacobhsuntu.edu.tw, paylongntu.edu.tw Abstract

The killer-cell immunoglobulin-like receptor (KIR) gene complex, a highly polymorphic region of the human genome that encodes proteins involved in immune responses, poses strong challenges in genotyping owing to its remarkable genetic diversity and structural intricacy. Accurate analysis of KIR alleles, including their structural variations, is crucial for understanding their roles in various immune responses. Leveraging the high-quality genome assemblies from the Human Pangenome Reference Consortium (HPRC), we present a novel bioinformatic tool, the structural KIR annoTator (SKIRT), to investigate gene diversity and facilitate precise KIR allele analysis. In 47 HPRC-phased assemblies, SKIRT identifies a recurrent novel KIR2DS4/3DL1 fusion gene in the paternal haplotype of HG02630 and maternal haplotype of NA19240. Additionally, SKIRT accurately identifies eight structural variants and 15 novel nonsynonymous alleles, all of which are independently validated using short-read data or quantitative polymerase chain reaction. Our study has discovered a total of 570 novel alleles, among which eight haplotypes harbor at least one KIR gene duplication, six haplotypes have lost at least one framework gene, and 75 out of 94 haplotypes (79.8%) carry at least five novel alleles, thus confirming KIR genetic diversity. These findings are pivotal in providing insights into KIR gene diversity and serve as a solid foundation for understanding the functional consequences of KIR structural variations. High-resolution genome assemblies offer unprecedented opportunities to explore polymorphic regions that are challenging to investigate using short-read sequencing methods. The SKIRT pipeline emerges as a highly efficient tool, enabling the comprehensive detection of the complete spectrum of KIR alleles within human genome assemblies.

Footnotes

[Supplemental material is available for this article.]

Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.278358.123.

Freely available online through the Genome Research Open Access option.

Received November 12, 2023. Accepted August 14, 2024.