1
|
Lai SK, Luo AC, Chiu IH, Chuang HW, Chou TH, Hung TK, Hsu JS, Chen CY, Yang WS, Yang YC, Chen PL. 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; 23:1562-1571. [PMID: 38650588 PMCID: PMC11035020 DOI: 10.1016/j.csbj.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
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.
Collapse
Affiliation(s)
- Sheng-Kai Lai
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Allen Chilun Luo
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - I-Hsuan Chiu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Hui-Wen Chuang
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ting-Hsuan Chou
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tsung-Kai Hung
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jacob Shujui Hsu
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chien-Yu Chen
- Department of Biomechatronics Engineering, National Taiwan University, Taipei, Taiwan
| | - Wei-Shiung Yang
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ya-Chien Yang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Lung Chen
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| |
Collapse
|
2
|
Huang YH, Yu KY, Huang SP, Chuang HW, Lin WZ, Cherng JH, Hung YW, Yeh MK, Hong PD, Liu CC. Development of a Nucleic Acid Lateral Flow Immunoassay for the Detection of Human Polyomavirus BK. Diagnostics (Basel) 2020; 10:E403. [PMID: 32545649 PMCID: PMC7345645 DOI: 10.3390/diagnostics10060403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 01/20/2023] Open
Abstract
The BK virus (BKV) is an emerging pathogen in immunocompromised individuals and widespread in the human population. Polymerase chain reaction is a simple and highly sensitive method for detecting BKV, but it is time consuming and requires expensive instruments and expert judgment. The lateral flow assay, a rapid, low-cost, minimal-labor, and easy-to-use diagnostic method, was successfully applied for pathogen detection. In this study, we used oligonucleotide probes to develop a simple and rapid sandwich-type lateral flow immunoassay for detecting BKV DNA within 45 minutes. The detection limit for the synthetic single-stranded DNA was 5 nM. The specificity study showed no cross-reactivity with other polyomaviruses, such as JC virus and simian virus 40. For the Escherichia coli containing BKV plasmid cultured samples, the sensitivity was determined to be 107 copies/mL. The approach offers great potential for BKV detection of various target analytes in point-of-care settings.
Collapse
Affiliation(s)
- Yi-Huei Huang
- Biomedical Engineering Program, Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan;
| | - Kuan-Yi Yu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11490, Taiwan; (K.-Y.Y.); (H.-W.C.); (M.-K.Y.)
| | - Shou-Ping Huang
- Department of Physiology and Biophysics, Graduate Institute of Physiology, National Defense Medical Center, Taipei 11490, Taiwan;
| | - Hui-Wen Chuang
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11490, Taiwan; (K.-Y.Y.); (H.-W.C.); (M.-K.Y.)
| | - Wen-Zhi Lin
- Institute of Preventive Medicine, National Defense Medical Center, Taipei 11490, Taiwan; (W.-Z.L.); (Y.-W.H.)
| | - Juin-Hong Cherng
- Department and Graduate Institute of Biology and Anatomy, National Defense Medical Center, Taipei 11490, Taiwan;
- Department of Gerontological Health Care, National Taipei University of Nursing and Health Sciences, Taipei 11219, Taiwan
| | - Yao-Wen Hung
- Institute of Preventive Medicine, National Defense Medical Center, Taipei 11490, Taiwan; (W.-Z.L.); (Y.-W.H.)
| | - Ming-Kung Yeh
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11490, Taiwan; (K.-Y.Y.); (H.-W.C.); (M.-K.Y.)
| | - Po-Da Hong
- Biomedical Engineering Program, Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan;
| | - Cheng-Che Liu
- Department of Physiology and Biophysics, Graduate Institute of Physiology, National Defense Medical Center, Taipei 11490, Taiwan;
- Institute of Preventive Medicine, National Defense Medical Center, Taipei 11490, Taiwan; (W.-Z.L.); (Y.-W.H.)
| |
Collapse
|
3
|
Chen IS, Chuang HW, Tai CM. Gastrointestinal: Ileal Dieulafoy's lesion presenting as a bleeding submucosal tumor. J Gastroenterol Hepatol 2016; 31:1914. [PMID: 27163182 DOI: 10.1111/jgh.13441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/05/2016] [Indexed: 12/09/2022]
Affiliation(s)
- I S Chen
- Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - H W Chuang
- Department of Pathology, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - C M Tai
- Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| |
Collapse
|
5
|
Mao L, Begum D, Chuang HW, Budiman MA, Szymkowiak EJ, Irish EE, Wing RA. JOINTLESS is a MADS-box gene controlling tomato flower abscission zone development. Nature 2000; 406:910-3. [PMID: 10972295 DOI: 10.1038/35022611] [Citation(s) in RCA: 245] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Abscission is a universal and dynamic process in plants whereby organs such as leaves, flowers and fruit are shed, both during normal development, and in response to tissue damage and stress. Shedding occurs by separation of cells in anatomically distinct regions of the plant, called abscission zones (AZs). During abscission, the plant hormone ethylene stimulates cells to produce enzymes that degrade the middle lamella between cells in the AZ. The physiology and regulation of abscission at fully developed AZs is well known, but the molecular biology underlying their development is not. Here we report the first isolation of a gene directly involved in the development of a functional plant AZ. Tomato plants with the jointless mutation fail to develop AZs on their pedicels and so abscission of flowers or fruit does not occur normally. We identify JOINTLESS as a new MADS-box gene in a distinct phylogenetic clade separate from those functioning in floral organs. We propose that a deletion in JOINTLESS accounts for the failure of activation of pedicel AZ development in jointless tomato plants.
Collapse
Affiliation(s)
- L Mao
- Clemson University Genomics Institute, South Carolina 29634, USA
| | | | | | | | | | | | | |
Collapse
|