A novel framework for human leukocyte antigen (HLA) genotyping using probe capture-based targeted next-generation sequencing and computational analysis

Sheng-Kai Lai; Allen Chilun Luo; I-Hsuan Chiu; Hui-Wen Chuang; Ting-Hsuan Chou; Tsung-Kai Hung; Jacob Shujui Hsu; Chien-Yu Chen; Wei-Shiung Yang; Ya-Chien Yang; Pei-Lung Chen

doi:10.1016/j.csbj.2024.03.030

A novel framework for human leukocyte antigen (HLA) genotyping using probe capture-based targeted next-generation sequencing and computational analysis

Comput Struct Biotechnol J. 2024 Apr 2:23:1562-1571. doi: 10.1016/j.csbj.2024.03.030. eCollection 2024 Dec.

Authors

Sheng-Kai Lai^{1

2}, Allen Chilun Luo², I-Hsuan Chiu², Hui-Wen Chuang³, Ting-Hsuan Chou³, Tsung-Kai Hung³, Jacob Shujui Hsu³, Chien-Yu Chen⁴, Wei-Shiung Yang^{3

5

6}, Ya-Chien Yang^{7

8}, Pei-Lung Chen^{1

2

3

5

6}

Affiliations

¹ Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan.
² Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
³ Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan.
⁴ Department of Biomechatronics Engineering, National Taiwan University, Taipei, Taiwan.
⁵ Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
⁶ Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
⁷ Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.
⁸ Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.

Abstract

Human leukocyte antigen (HLA) genes play pivotal roles in numerous immunological applications. Given the immense number of polymorphisms, achieving accurate high-throughput HLA typing remains challenging. This study aimed to harness the human pan-genome reference consortium (HPRC) resources as a potential benchmark for HLA reference materials. We meticulously annotated specific four field-resolution alleles for 11 HLA genes (HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4 and -DRB5) from 44 high-quality HPRC personal genome assemblies. For sequencing, we crafted HLA-specific probes and conducted capture-based targeted sequencing of the genomic DNA of the HPRC cohort, ensuring focused and comprehensive coverage of the HLA region of interest. We used publicly available short-read whole-genome sequencing (WGS) data from identical samples to offer a comparative perspective. To decipher the vast amount of sequencing data, we employed seven distinct software tools: OptiType, HLA-VBseq, HISAT genotype, SpecHLA, T1K, QzType, and DRAGEN. Each tool offers unique capabilities and algorithms for HLA genotyping, allowing comprehensive analysis and validation of the results. We then compared these results with benchmarks derived from personal genome assemblies. Our findings present a comprehensive four-field-resolution HLA allele annotation for 44 HPRC samples. Significantly, our innovative targeted next-generation sequencing (NGS) approach for HLA genes showed superior accuracy compared with conventional short-read WGS. An integrated analysis involving QzType, T1K, and DRAGEN was developed, achieving 100% accuracy for all 11 HLA genes. In conclusion, our study highlighted the combination of targeted short-read sequencing and astute computational analysis as a robust approach for HLA genotyping. Furthermore, the HPRC cohort has emerged as a valuable assembly-based reference in this realm.

Keywords: DRAGEN; HISAT-genotype; HLA-VBseq; Human Pangenome Reference Consortium (HPRC); Human leukocyte antigen (HLA); IPD-IMGT/HLA; Next-generation sequencing (NGS); Probe capture; QzType; SpecHLA; T1K; Targeted sequencing.