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Kazan HH, Karaca M, Akan G, Özgen Ö, Tuncel G, Özketen AÇ, Balcı MC, Körbeyli HK, Atalar F, Gökçay GF. Oxford nanopore sequencing-based assay for BTD gene screening: Design, clinical validation, and variant frequency assessment in the Turkish population. Gene 2024; 928:148782. [PMID: 39033936 DOI: 10.1016/j.gene.2024.148782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/28/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
Biotinidase deficiency (BTD) is an autosomal recessive disorder characterized by impaired recycling of the water-soluble vitamin biotin which leads to a spectrum of clinical manifestations ranging from mild to severe, including mainly neurological and cutaneous symptoms. Biotin supplementation is a cornerstone of treatment, but diagnosis often relies on measuring serum enzyme activity, which needs to be confirmed by genetic analysis. Thus, molecular methods become necessary in the differential diagnosis of BTD. Accordingly, countries with a high-incidence have implemented next-generation sequencing (NGS) techniques to newborn screening programs for BT. Nevertheless, NGS platforms, while well-established, present challenges in cost, labor, accessibility, and duration for newborn screening programs targeting BTD, therefore these limitations necessitate the exploration of alternative systems to ensure efficient and widespread screening. Here, third-generation sequencing platforms, notably Oxford Nanopore Technology (ONT), present promising solutions to the associated challenges. Hence, in the present study, we aimed to develop an ONT-based assay for the screening of BTD gene. After designing and optimizing primers for long-PCR using reference DNA, we assessed the performance of the ONT assay in BTD patients previously diagnosed by enzyme assay and confirmed using Illumina-based sequencing. The results demonstrate a strong correlation between the two methods, indicating the reliability of the ONT-based assay. Moreover, this first in-house single gene testing specifically tailored for BTD successfully detected previously known genetic variants with high sequencing depths, affirming the effectiveness of ONT-based sequencing in human genetics.
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Affiliation(s)
- Hasan Hüseyin Kazan
- Department of Medical Biology, Gulhane Faculty of Medicine, University of Health Sciences, Ankara, Turkey
| | - Meryem Karaca
- Division of Pediatric Nutrition and Metabolism, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Gökçe Akan
- DESAM Institute, Near East University, Mersin 10, Turkey
| | - Özge Özgen
- Rare Diseases Research Laboratory, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Gülten Tuncel
- DESAM Institute, Near East University, Mersin 10, Turkey
| | | | - Mehmet Cihan Balcı
- Division of Pediatric Nutrition and Metabolism, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Hüseyin Kutay Körbeyli
- Division of Pediatric Nutrition and Metabolism, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Fatmahan Atalar
- Rare Diseases Research Laboratory, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey; Department of Rare Diseases, Child Health Institute, Istanbul University, Istanbul, Turkey.
| | - Gülden Fatma Gökçay
- Division of Pediatric Nutrition and Metabolism, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
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Lang J, Qin L. NanoHLA: A Method for Human Leukocyte Antigen Class I Genes Typing Without Error Correction Based on Nanopore Sequencing Data. Methods Mol Biol 2024; 2809:115-126. [PMID: 38907894 DOI: 10.1007/978-1-0716-3874-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Human leukocyte antigen (HLA) typing is of great importance in clinical applications such as organ transplantation, blood transfusion, disease diagnosis and treatment, and forensic analysis. In recent years, nanopore sequencing technology has emerged as a rapid and cost-effective option for HLA typing. However, due to the principles and data characteristics of nanopore sequencing, there was a scarcity of robust and generalizable bioinformatics tools for its downstream analysis, posing a significant challenge in deciphering the thousands of HLA alleles present in the human population. To address this challenge, we developed NanoHLA as a tool for high-resolution typing of HLA class I genes without error correction based on nanopore sequencing. The method integrated the concepts of HLA type coverage analysis and the data conversion techniques employed in Nano2NGS, which was characterized by applying nanopore sequencing data to NGS-liked data analysis pipelines. In validation with public nanopore sequencing datasets, NanoHLA showed an overall concordance rate of 84.34% for HLA-A, HLA-B, and HLA-C, and demonstrated superior performance in comparison to existing tools such as HLA-LA. NanoHLA provides tools and solutions for use in HLA typing related fields, and look forward to further expanding the application of nanopore sequencing technology in both research and clinical settings. The code is available at https://github.com/langjidong/NanoHLA .
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Affiliation(s)
- Jidong Lang
- Department of Bioinformatics, Qitan Technology (Beijing) Co., Ltd, Beijing, China
| | - Liu Qin
- Department of Bioinformatics, Qitan Technology (Beijing) Co., Ltd, Beijing, China
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3
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Hughes AEO, Montgomery MC, Liu C, Weimer ET. Allele-specific quantification of human leukocyte antigen transcript isoforms by nanopore sequencing. Front Immunol 2023; 14:1199618. [PMID: 37662944 PMCID: PMC10471969 DOI: 10.3389/fimmu.2023.1199618] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/05/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction While tens of thousands of HLA alleles have been identified by DNA sequencing, the contribution of alternative splicing to HLA diversity is not well characterized. In this study, we sought to determine if long-read sequencing could be used to accurately quantify allele-specific HLA transcripts in primary human lymphocytes. Methods cDNA libraries were prepared from peripheral blood lymphocytes from 12 donors and sequenced by nanopore long-read sequencing. HLA reads were aligned to donor-specific reference sequences based on the known type of each donor. Allele-specific exon utilization was calculated as the proportion of reads aligning to each allele containing known exons, and transcript isoforms were quantified based on patterns of exon utilization within individual reads. Results Splice variants were rare among class I HLA genes (median exon retention rate 99%-100%), except for several HLA-C alleles with exon 5 spliced out of up to 15% of reads. Splice variants were also rare among class II HLA genes (median exon retention rate 98%-100%), except for HLA-DQB1. Consistent with previous work, exon 5 of HLA-DQB1 was spliced out in alleles with a mutated splice acceptor site at rs28688207. Surprisingly, a 28% loss of exon 5 was also observed in HLA-DQB1 alleles with an intact splice acceptor site at rs28688207. Discussion We describe a simple bioinformatic workflow to quantify allele-specific expression of HLA transcript isoforms. Further studies are warranted to characterize the repertoire of HLA transcripts expressed in different cell types and tissues across diverse populations.
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Affiliation(s)
- Andrew E. O. Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Maureen C. Montgomery
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, University of North Carolina Hospitals, Chapel Hill, NC, United States
| | - Chang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Eric T. Weimer
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, University of North Carolina Hospitals, Chapel Hill, NC, United States
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
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4
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Bruijnesteijn J. HLA/MHC and KIR characterization in humans and non-human primates using Oxford Nanopore Technologies and Pacific Biosciences sequencing platforms. HLA 2023; 101:205-221. [PMID: 36583332 DOI: 10.1111/tan.14957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/12/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
The gene products of the HLA/MHC and KIR multigene families are important modulators of the immune system and are associated with health and disease. Characterization of the genes encoding these receptors has been integrated into different biomedical applications, including transplantation and reproduction biology, immune therapies and in fundamental research into disease susceptibility or resistance. Conventional short-read sequencing strategies have shown their value in high throughput typing, but are insufficient to uncover the entire complexity of the highly polymorphic HLA/MHC and KIR gene systems. The implementation of single-molecule and real-time sequencing platforms, offered by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), revolutionized the fields of genomics and transcriptomics. Using fundamentally distinct principles, these platforms generate long-read data that can unwire the plasticity of the HLA/MHC and KIR genes, including high-resolution characterization of genes, alleles, phased haplotypes, transcription levels and epigenetics modification patterns. These insights might have profound clinical relevance, such as improved matching of donors and patients in clinical transplantation, but could also lift disease association studies to a higher level. Even more, a comprehensive characterization may refine animal models in preclinical studies. In this review, the different HLA/MHC and KIR characterization approaches using PacBio and ONT platforms are described and discussed.
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Affiliation(s)
- Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
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5
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Liu Y, Fan F, Drmanac R, Peters BA, Wang O. Large-Scale Complete Sequencing and Haplotyping of 1-10 kb DNA Molecules Using Short Massively Parallel Reads. Methods Mol Biol 2023; 2590:59-70. [PMID: 36335492 DOI: 10.1007/978-1-0716-2819-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In this chapter, we describe a simple, low-cost method for making many copies of a single DNA molecule (1-10 kb in length) as a concatemer on a long DNA strand. This can enable applications requiring high-quality contiguous sequence and haplotype data from long single DNA molecules at large scale.
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Affiliation(s)
- Youtao Liu
- MGI, Shenzhen, Guangdong Province, PR China
| | - Fei Fan
- BGI-Shenzhen, Shenzhen, Guangdong Province, PR China
| | - Radoje Drmanac
- Advanced Genomics Technology Laboratory, Complete Genomics/MGI, San Jose, CA, USA
| | - Brock A Peters
- Advanced Genomics Technology Laboratory, Complete Genomics/MGI, San Jose, CA, USA
| | - Ou Wang
- BGI-Shenzhen, Shenzhen, Guangdong Province, PR China.
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Enhancing Molecular Testing for Effective Delivery of Actionable Gene Diagnostics. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9120745. [PMID: 36550951 PMCID: PMC9774983 DOI: 10.3390/bioengineering9120745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022]
Abstract
There is a deep need to navigate within our genomic data to find, understand and pave the way for disease-specific treatments, as the clinical diagnostic journey provides only limited guidance. The human genome is enclosed in every nucleated cell, and yet at the single-cell resolution many unanswered questions remain, as most of the sequencing techniques use a bulk approach. Therefore, heterogeneity, mosaicism and many complex structural variants remain partially uncovered. As a conceptual approach, nanopore-based sequencing holds the promise of being a single-molecule-based, long-read and high-resolution technique, with the ability of uncovering the nucleic acid sequence and methylation almost in real time. A key limiting factor of current clinical genetics is the deciphering of key disease-causing genomic sequences. As the technological revolution is expanding regarding genetic data, the interpretation of genotype-phenotype correlations should be made with fine caution, as more and more evidence points toward the presence of more than one pathogenic variant acting together as a result of intergenic interplay in the background of a certain phenotype observed in a patient. This is in conjunction with the observation that many inheritable disorders manifest in a phenotypic spectrum, even in an intra-familial way. In the present review, we summarized the relevant data on nanopore sequencing regarding clinical genomics as well as highlighted the importance and content of pre-test and post-test genetic counselling, yielding a complex approach to phenotype-driven molecular diagnosis. This should significantly lower the time-to-right diagnosis as well lower the time required to complete a currently incomplete genotype-phenotype axis, which will boost the chance of establishing a new actionable diagnosis followed by therapeutical approach.
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7
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Cornaby C, Montgomery MC, Liu C, Weimer ET. Unique Molecular Identifier-Based High-Resolution HLA Typing and Transcript Quantitation Using Long-Read Sequencing. Front Genet 2022; 13:901377. [PMID: 35879986 PMCID: PMC9308011 DOI: 10.3389/fgene.2022.901377] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/05/2022] [Indexed: 01/03/2023] Open
Abstract
HLA typing provides essential results for stem cell and solid organ transplants, as well as providing diagnostic benefits for various rheumatology, gastroenterology, neurology, and infectious diseases. It is becoming increasingly clear that understanding the expression of patient HLA transcripts can provide additional benefits for many of these same patient groups. Our study cohort was evaluated using a long-read RNA sequencing methodology to provide rapid HLA genotyping results and normalized HLA transcript expression. Our assay used NGSEngine to determine the HLA genotyping result and normalized mRNA transcript expression using Athlon2. The assay demonstrated an excellent concordance rate of 99.7%. Similar to previous studies, for the class I loci, patients demonstrated significantly lower expression of HLA-C than HLA-A and -B (Mann-Whitney U, p value = 0.0065 and p value = 0.0154, respectively). In general, the expression of class II transcripts was lower than that of class I transcripts. This study demonstrates a rapid high-resolution HLA typing assay using RNA-Seq that can provide accurate HLA genotyping and HLA allele-specific transcript expression in 7-8 h, a timeline short enough to perform the assay for deceased donors.
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Affiliation(s)
- Caleb Cornaby
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, United States
| | - Maureen C Montgomery
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, United States
| | - Chang Liu
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Eric T Weimer
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, United States.,Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
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8
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Yang J, Liu H, Pan W, Song M, Lu Y, Wang-Ngai Chow F, Hang-Mei Leung P, Deng Y, Hori M, He N, Li S. Recent Advances of Human Leukocyte Antigen (HLA) Typing Technology Based on High-Throughput Sequencing. J Biomed Nanotechnol 2022; 18:617-639. [PMID: 35715925 DOI: 10.1166/jbn.2022.3280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The major histocompatibility complex (MHC) in humans is a genetic region consisting of cell surface proteins located on the short arm of chromosome 6. This is also known as the human leukocyte antigen (HLA) region. The HLA region consists of genes that exhibit complex genetic polymorphisms, and are extensively involved in immune responses. Each individual has a unique set of HLAs. Donor-recipient HLA allele matching is an important factor for organ transplantation. Therefore, an established rapid and accurate HLA typing technology is instrumental to preventing graft-verses-host disease (GVHD) in organ recipients. As of recent, high-throughput sequencing has allowed for an increase read length and higher accuracy and throughput, thus achieving complete and high-resolution full-length typing. With more advanced nanotechnology used in high-throughput sequencing, HLA typing is more widely used in third-generation single-molecule sequencing. This review article summarizes some of the most widely used sequencing typing platforms and evaluates the latest developments in HLA typing kits and their clinical applications.
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Affiliation(s)
- Jin Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Mengru Song
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Yutong Lu
- School of Electrical and Information Engineering, Hunan University, Changsha 410012, Hunan, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Masahi Hori
- 2-16-5 Edagawa, Koto-Ku, Tokyo, 135-0051, Japan
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
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9
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Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 2021; 39:1348-1365. [PMID: 34750572 PMCID: PMC8988251 DOI: 10.1038/s41587-021-01108-x] [Citation(s) in RCA: 537] [Impact Index Per Article: 179.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/22/2021] [Indexed: 12/13/2022]
Abstract
Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.
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Affiliation(s)
- Yunhao Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yue Zhao
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA
| | - Audrey Bollas
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yuru Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA.
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10
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Johansson T, Koskela S, Yohannes DA, Partanen J, Saavalainen P. Targeted RNA-Based Oxford Nanopore Sequencing for Typing 12 Classical HLA Genes. Front Genet 2021; 12:635601. [PMID: 33763116 PMCID: PMC7982845 DOI: 10.3389/fgene.2021.635601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/11/2021] [Indexed: 01/29/2023] Open
Abstract
Identification of human leukocyte antigen (HLA) alleles from next-generation sequencing (NGS) data is challenging because of the high polymorphism and mosaic nature of HLA genes. Owing to the complex nature of HLA genes and consequent challenges in allele assignment, Oxford Nanopore Technologies' (ONT) single-molecule sequencing technology has been of great interest due to its fitness for sequencing long reads. In addition to the read length, ONT's advantages are its portability and possibility for a rapid real-time sequencing, which enables a simultaneous data analysis. Here, we describe a targeted RNA-based method for HLA typing using ONT sequencing and SeqNext-HLA SeqPilot software (JSI Medical Systems GmbH). Twelve classical HLA genes were enriched from cDNA of 50 individuals, barcoded, pooled, and sequenced in 10 MinION R9.4 SpotON flow cell runs producing over 30,000 reads per sample. Using barcoded 2D reads, SeqPilot assigned HLA alleles to two-field typing resolution or higher with the average read depth of 1750x. Sequence analysis resulted in 99-100% accuracy at low-resolution level (one-field) and in 74-100% accuracy at high-resolution level (two-field) with the expected alleles. There are still some limitations with ONT RNA sequencing, such as noisy reads, homopolymer errors, and the lack of robust algorithms, which interfere with confident allele assignment. These issues need to be inspected carefully in the future to improve the allele call rates. Nevertheless, here we show that sequencing of multiplexed cDNA amplicon libraries on ONT MinION can produce accurate high-resolution typing results of 12 classical HLA loci. For HLA research, ONT RNA sequencing is a promising method due to its capability to sequence full-length HLA transcripts. In addition to HLA genotyping, the technique could also be applied for simultaneous expression analysis.
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Affiliation(s)
- Tiira Johansson
- Translational Immunology Research Program and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Finnish Red Cross Blood Service, Helsinki, Finland
| | - Satu Koskela
- Finnish Red Cross Blood Service, Helsinki, Finland
| | - Dawit A Yohannes
- Translational Immunology Research Program and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | | | - Päivi Saavalainen
- Translational Immunology Research Program and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Finnish Red Cross Blood Service, Helsinki, Finland
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11
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Liu C, Yang X, Duffy BF, Hoisington-Lopez J, Crosby M, Porche-Sorbet R, Saito K, Berry R, Swamidass V, Mitra RD. High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells. Hum Immunol 2021; 82:288-295. [PMID: 33612390 DOI: 10.1016/j.humimm.2021.02.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 01/12/2023]
Abstract
Nanopore sequencing has been investigated as a rapid and cost-efficient option for HLA typing in recent years. Despite the lower raw read accuracy, encouraging typing accuracy has been reported, and long reads from the platform offer additional benefits of the improved phasing of distant variants. The newly released R10.3 flow cells are expected to provide higher read-level accuracy than previous chemistries. We examined the performance of R10.3 flow cells on the MinION device in HLA typing after enrichment of target genes by multiplexed PCR. We also aimed to mimic a 1-day workflow with 8-24 samples per sequencing run. A diverse collection of 102 unique samples were typed for HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3/4/5 loci. The concordance rates at 2-field and 3-field resolutions were 99.5% (1836 alleles) and 99.3% (1710 alleles). We also report important quality metrics from these sequencing runs. Continued research and independent validations are warranted to increase the robustness of nanopore-based HLA typing for broad clinical application.
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Affiliation(s)
- Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Xiao Yang
- GeneGenieDx, 160 E Tasman Dr Ste 109, San Jose, CA, USA
| | - Brian F Duffy
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Jessica Hoisington-Lopez
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - MariaLynn Crosby
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rhonda Porche-Sorbet
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Rick Berry
- PlatformSTL, 4340 Duncan Ave. St. Louis, MO, USA
| | | | - Robi D Mitra
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
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12
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Mosbruger TL, Dinou A, Duke JL, Ferriola D, Mehler H, Pagkrati I, Damianos G, Mbunwe E, Sarmady M, Lyratzakis I, Tishkoff SA, Dinh A, Monos DS. Utilizing nanopore sequencing technology for the rapid and comprehensive characterization of eleven HLA loci; addressing the need for deceased donor expedited HLA typing. Hum Immunol 2020; 81:413-422. [PMID: 32595056 PMCID: PMC7870017 DOI: 10.1016/j.humimm.2020.06.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
The comprehensive characterization of human leukocyte antigen (HLA) genomic sequences remains a challenging problem. Despite the significant advantages of next-generation sequencing (NGS) in the field of Immunogenetics, there has yet to be a single solution for unambiguous, accurate, simple, cost-effective, and timely genotyping necessary for all clinical applications. This report demonstrates the benefits of nanopore sequencing introduced by Oxford Nanopore Technologies (ONT) for HLA genotyping. Samples (n = 120) previously characterized at high-resolution three-field (HR-3F) for 11 loci were assessed using ONT sequencing paired to a single-plex PCR protocol (Holotype) and to two multiplex protocols OmniType (Omixon) and NGSgo®-MX6-1 (GenDx). The results demonstrate the potential of nanopore sequencing for delivering accurate HR-3F typing with a simple, rapid, and cost-effective protocol. The protocol is applicable to time-sensitive applications, such as deceased donor typings, enabling better assessments of compatibility and epitope analysis. The technology also allows significantly shorter turnaround time for multiple samples at a lower cost. Overall, the nanopore technology appears to offer a significant advancement over current next-generation sequencing platforms as a single solution for all HLA genotyping needs.
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Affiliation(s)
- Timothy L Mosbruger
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Amalia Dinou
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jamie L Duke
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Deborah Ferriola
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hilary Mehler
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ioanna Pagkrati
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Georgios Damianos
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric Mbunwe
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mahdi Sarmady
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ioannis Lyratzakis
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anh Dinh
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dimitri S Monos
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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13
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Liu C. A long road/read to rapid high-resolution HLA typing: The nanopore perspective. Hum Immunol 2020; 82:488-495. [PMID: 32386782 DOI: 10.1016/j.humimm.2020.04.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 01/18/2023]
Abstract
Next-generation sequencing (NGS) has been widely adopted for clinical HLA typing and advanced immunogenetics researches. Current methodologies still face challenges in resolving cis-trans ambiguity involving distant variant positions, and the turnaround time is affected by testing volume and batching. Nanopore sequencing may become a promising addition to the existing options for HLA typing. The technology delivered by the MinION sequencer of Oxford Nanopore Technologies (ONT) can record the ionic current changes during the translocation of DNA/RNA strands through transmembrane pores and translate the signals to sequence reads. It features simple and flexible library preparations, long sequencing reads, portable and affordable sequencing devices, and rapid, real-time sequencing. However, the error rate of the sequencing reads is high and remains a hurdle for its broad application. This review article will provide a brief overview of this technology and then focus on the opportunities and challenges of using nanopore sequencing for high-resolution HLA typing and immunogenetics research.
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Affiliation(s)
- Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63105, United States.
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14
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Liu C, Duffy BF, Weimer ET, Montgomery MC, Jennemann JE, Hill R, Phelan D, Lay L, Parikh BA. Performance of a multiplexed amplicon-based next-generation sequencing assay for HLA typing. PLoS One 2020; 15:e0232050. [PMID: 32324777 PMCID: PMC7179861 DOI: 10.1371/journal.pone.0232050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/06/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) has enabled efficient high-resolution typing of human leukocyte antigen (HLA) genes with minimal ambiguity. Most commercially available assays amplify individual or subgroup of HLA genes by long-range PCR followed by library preparation and sequencing. The AllType assay simplifies the workflow by amplifying 11 transplant-relevant HLA genes in one PCR reaction. Here, we report the performance of this unique workflow evaluated using 218 genetically diverse samples. METHODS Five whole genes (HLA-A/B/C/DQA1/DPA1) and six near-whole genes (HLA-DRB1/DRB345/DQB1/DPB1; excluding exon 1 and part of intron 1) were amplified in a multiplexed, long-range PCR. Manual library preparation was performed per manufacturer's protocol, followed by template preparation and chip loading on the Ion Chef, and sequencing on the Ion S5 sequencer. Pre-specified rules for quality control and repeat testing were followed; technologists were blinded to the reference results. The concordance between AllType and reference results was determined at 2-field resolution. We also describe the ranges of input DNA and library concentrations, read number per sample and per locus, and key health metrics in relation to typing results. RESULTS The concordance rates were 98.6%, 99.8% and 99.9% at the sample (n = 218), genotype (n = 1688), and allele (n = 3376) levels, respectively. Three genotypes were discordant, all of which shared the same G group typing results with the reference. Most ambiguous genotypes (116 out of 144, 80.6%) were due to the lack of exon 1 and intron 1 coverage for HLA-DRB1/DRB345/DQB1/DPB1 genes. A broad range of input DNA concentrations and library concentrations were tolerated. Per sample read numbers were adequate for accurate genotyping. Per locus read numbers showed some inter-lot variations, and a trend toward improved inter-locus balance was observed with later lots of reagents. CONCLUSION The AllType assay on the Ion Chef/Ion S5 platform offers a robust and efficient workflow for clinical HLA typing at the 2-field resolution. The multiplex PCR strategy simplifies the laboratory procedure without compromising the typing accuracy.
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Affiliation(s)
- Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Brian F. Duffy
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Eric T. Weimer
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Hospitals, Chapel Hill, North Carolina, United States of America
| | - Maureen C. Montgomery
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Hospitals, Chapel Hill, North Carolina, United States of America
| | - Jo-Ellen Jennemann
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Rachel Hill
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Donna Phelan
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Lindsay Lay
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Bijal A. Parikh
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
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15
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Matern BM, Olieslagers TI, Groeneweg M, Duygu B, Wieten L, Tilanus MGJ, Voorter CEM. Long-Read Nanopore Sequencing Validated for Human Leukocyte Antigen Class I Typing in Routine Diagnostics. J Mol Diagn 2020; 22:912-919. [PMID: 32302780 DOI: 10.1016/j.jmoldx.2020.04.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/03/2020] [Accepted: 04/02/2020] [Indexed: 01/23/2023] Open
Abstract
Matching of human leukocyte antigen (HLA) gene polymorphisms by high-resolution DNA sequence analysis is the gold standard for determining compatibility between patient and donor for hematopoietic stem cell transplantation. Single-molecule sequencing (PacBio or MinION) is a newest (third) generation sequencing approach. MinION is a nanopore sequencing platform, which provides long targeted DNA sequences. The long reads provide unambiguous phasing, but the initial high error profile prevented its use in high-impact applications, such as HLA typing for HLA matching of donor and recipient in the transplantation setting. Ongoing developments on instrumentation and basecalling software have improved the per-base accuracy of 1D2 nanopore reads tremendously. In the current study, two validation panels of samples covering 70 of the 71 known HLA class I allele groups were used to compare third field sequences obtained by MinION, with Sanger sequence-based typing showing a 100% concordance between both data sets. In addition, the first validation panel was used to set the acceptance criteria for the use of MinION in a routine setting. The acceptance criteria were subsequently confirmed with the second validation panel. In summary, the present study describes validation and implementation of nanopore sequencing HLA class I typing method and illustrates that nanopore sequencing technology has advanced to a point where it can be used in routine diagnostics with high accuracy.
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Affiliation(s)
- Benedict M Matern
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Timo I Olieslagers
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Mathijs Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Burcu Duygu
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Lotte Wieten
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Marcel G J Tilanus
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Christina E M Voorter
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands.
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16
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Using Nanopore Whole-Transcriptome Sequencing for Human Leukocyte Antigen Genotyping and Correlating Donor Human Leukocyte Antigen Expression with Flow Cytometric Crossmatch Results. J Mol Diagn 2020; 22:101-110. [DOI: 10.1016/j.jmoldx.2019.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/27/2019] [Accepted: 09/11/2019] [Indexed: 01/07/2023] Open
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17
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Abstract
Nanopore sequencing, enabled initially by the MinION device from Oxford Nanopore Technologies (ONT), is the only technology that offers portable, single-molecule sequencing and ultralong reads. The technology is ideal for the typing of human leukocyte antigen (HLA) genes for transplantation and cancer immunotherapy. However, such applications have been hindered by the high error rate of nanopore sequencing reads. We developed the workflow and bioinformatic pipeline, Athlon (accurate typing of human leukocyte antigen by Oxford Nanopore), to perform high-resolution typing of Class I HLA genes by nanopore sequencing. The method features a novel algorithm for candidate allele selection, followed by error correction through consensus building. Here, we describe the protocol of using Athlon packaged in a VirtualBox image for the above application.
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18
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Hammer SE, Ho CS, Ando A, Rogel-Gaillard C, Charles M, Tector M, Tector AJ, Lunney JK. Importance of the Major Histocompatibility Complex (Swine Leukocyte Antigen) in Swine Health and Biomedical Research. Annu Rev Anim Biosci 2019; 8:171-198. [PMID: 31846353 DOI: 10.1146/annurev-animal-020518-115014] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In pigs, the major histocompatibility complex (MHC), or swine leukocyte antigen (SLA) complex, maps to Sus scrofa chromosome 7. It consists of three regions, the class I and class III regions mapping to 7p1.1 and the class II region mapping to 7q1.1. The swine MHC is divided by the centromere, which is unique among mammals studied to date. The SLA complexspans between 2.4 and 2.7 Mb, depending on haplotype, and encodes approximately 150 loci, with at least 120 genes predicted to be functional. Here we update the whole SLA complex based on the Sscrofa11.1 build and annotate the organization for all recognized SLA genes and their allelic sequences. We present SLA nomenclature and typing methods and discuss the expression of SLA proteins, as well as their role in antigen presentation and immune, disease, and vaccine responses. Finally, we explore the role of SLA genes in transplantation and xenotransplantation and their importance in swine biomedical models.
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Affiliation(s)
- Sabine E Hammer
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria
| | - Chak-Sum Ho
- Gift of Hope Organ & Tissue Donor Network, Itasca, Illinois 60143, USA
| | - Asako Ando
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | | | - Mathieu Charles
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Matthew Tector
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.,Current address: Makana Therapeutics, Wilmington, Delaware 19801, USA
| | - A Joseph Tector
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.,Current address: Department of Surgery, University of Miami, Miami, Florida 33136, USA
| | - Joan K Lunney
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, Beltsville, Maryland 20705, USA;
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19
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Fürst D, Tsamadou C, Neuchel C, Schrezenmeier H, Mytilineos J, Weinstock C. Next-Generation Sequencing Technologies in Blood Group Typing. Transfus Med Hemother 2019; 47:4-13. [PMID: 32110189 DOI: 10.1159/000504765] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
Sequencing of the human genome has led to the definition of the genes for most of the relevant blood group systems, and the polymorphisms responsible for most of the clinically relevant blood group antigens are characterized. Molecular blood group typing is used in situations where erythrocytes are not available or where serological testing was inconclusive or not possible due to the lack of antisera. Also, molecular testing may be more cost-effective in certain situations. Molecular typing approaches are mostly based on either PCR with specific primers, DNA hybridization, or DNA sequencing. Particularly the transition of sequencing techniques from Sanger-based sequencing to next-generation sequencing (NGS) technologies has led to exciting new possibilities in blood group genotyping. We describe briefly the currently available NGS platforms and their specifications, depict the genetic background of blood group polymorphisms, and discuss applications for NGS approaches in immunohematology. As an example, we delineate a protocol for large-scale donor blood group screening established and in use at our institution. Furthermore, we discuss technical challenges and limitations as well as the prospect for future developments, including long-read sequencing technologies.
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Affiliation(s)
- Daniel Fürst
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Chrysanthi Tsamadou
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Christine Neuchel
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Hubert Schrezenmeier
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Joannis Mytilineos
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Christof Weinstock
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
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20
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Geneugelijk K, Spierings E. PIRCHE-II: an algorithm to predict indirectly recognizable HLA epitopes in solid organ transplantation. Immunogenetics 2019; 72:119-129. [PMID: 31741009 PMCID: PMC6971131 DOI: 10.1007/s00251-019-01140-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/16/2019] [Indexed: 12/14/2022]
Abstract
Human leukocyte antigen (HLA) mismatches between donors and recipients may lead to alloreactivity after solid organ transplantation. Over the last few decades, our knowledge of the complexity of the HLA system has dramatically increased, as numerous new HLA alleles have been identified. As a result, the likelihood of alloreactive responses towards HLA mismatches after solid organ transplantation cannot easily be assessed. Algorithms are promising solutions to estimate the risk for alloreactivity after solid organ transplantation. In this review, we show that the recently developed PIRCHE-II (Predicted Indirectly ReCognizable HLA Epitopes) algorithm can be used to minimize alloreactivity towards HLA mismatches. Together with the use of other algorithms and simulation approaches, the PIRCHE-II algorithm aims for a better estimated alloreactive risk for individual patients and eventually an improved graft survival after solid organ transplantation.
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Affiliation(s)
- Kirsten Geneugelijk
- Laboratory of Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX, Utrecht, The Netherlands.
| | - Eric Spierings
- Laboratory of Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX, Utrecht, The Netherlands
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21
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Cargou M, Ralazamahaleo M, Blouin L, Top I, Elsermans V, Andreani M, Guidicelli G, Visentin J. Evaluation of the AllType kit for HLA typing using the Ion Torrent S5 XL platform. HLA 2019; 95:30-39. [DOI: 10.1111/tan.13708] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/04/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Marine Cargou
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
- Immuno ConcEpT Bordeaux France
- Université de Bordeaux Bordeaux France
| | - Mamy Ralazamahaleo
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
| | - Laura Blouin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
| | - Isabelle Top
- CHRU de Lille, Institut d'Immunologie‐HLA Lille France
| | | | - Marco Andreani
- Laboratorio d'Immunogenetica dei Trapianti IRCCS Ospedale Pediatrico Bambino Gesù Roma Italy
| | - Gwendaline Guidicelli
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
- Immuno ConcEpT Bordeaux France
- Université de Bordeaux Bordeaux France
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22
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Midha MK, Wu M, Chiu KP. Long-read sequencing in deciphering human genetics to a greater depth. Hum Genet 2019; 138:1201-1215. [PMID: 31538236 DOI: 10.1007/s00439-019-02064-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Through four decades' development, DNA sequencing has inched into the era of single-molecule sequencing (SMS), or the third-generation sequencing (TGS), as represented by two distinct technical approaches developed independently by Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT). Historically, each generation of sequencing technologies was marked by innovative technological achievements and novel applications. Long reads (LRs) are considered as the most advantageous feature of SMS shared by both PacBio and ONT to distinguish SMS from next-generation sequencing (NGS, or the second-generation sequencing) and Sanger sequencing (the first-generation sequencing). Long reads overcome the limitations of NGS and drastically improves the quality of genome assembly. Besides, ONT also contributes several unique features including ultra-long reads (ULRs) with read length above 300 kb and some close to 1 million bp, direct RNA sequencing and superior portability as made possible by pocket-sized MinION sequencer. Here, we review the history of DNA sequencing technologies and associated applications, with a special focus on the advantages as well as the limitations of ULR sequencing in genome assembly.
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Affiliation(s)
- Mohit K Midha
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang District, Taipei, 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Mengchu Wu
- Health GeneTech, 22F No. 99, Xin Pu 6th St., Taoyuan, Taiwan
| | - Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang District, Taipei, 115, Taiwan. .,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan. .,Department of Life Sciences, College of Life Sciences, National Taiwan University, Taipei, Taiwan.
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23
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Oxford nanopore sequencing enables rapid discovery of single-domain antibodies from phage display libraries. Biotechniques 2019; 65:351-356. [PMID: 30477332 DOI: 10.2144/btn-2018-0123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Antibody (Ab) repertoire sequencing using high-throughput massively parallel technologies has contributed substantially to the understanding of Ab responses following infection, vaccination and autoimmunity. Because individual B-cell receptors are recombined and diversified somatically, genomic comparisons are limited, and distinguishing rare variants from sequencing errors is a major challenge. Oxford Nanopore Technologies' MinION is a highly portable and cost-effective third-generation sequencing instrument, but has not been used for Ab repertoire sequencing due to its high error rate (approximately 1/10 bases). Here, we applied nanopore sequencing to single-domain Ab (sdAb) repertoires and phage-displayed sdAb libraries. We show that despite low overall data fidelity, sdAb sequences could be reconstructed above a frequency threshold (∼100 copies); however, distinguishing clonal sdAb variants was not always possible. The data quality was sufficient to enable rapid identification of antigen-specific sdAb sequences enriched during panning of phage display libraries, obviating the need for screening single clones.
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24
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Lazaro A, Hou L, Tu B, Masaberg C, Enriquez E, Gerfen J, Kariyawasam K, Persaud M, Qin X, Simbulan D, Xiao Y, Xun L, Yang R, Ng J, Hurley CK. Full gene HLA class I sequences of 79 novel and 519 mostly uncommon alleles from a large United States registry population. HLA 2018; 92:304-309. [PMID: 30117314 DOI: 10.1111/tan.13377] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/09/2018] [Accepted: 08/13/2018] [Indexed: 12/26/2022]
Abstract
HLA class I assignments were obtained at single genotype, G-level resolution from 98 855 volunteers for an unrelated donor registry in the United States. In spite of the diverse ancestry of the volunteers, over 99% of the assignments at each locus are common. Within this population, 52 novel alleles differing in exons 2 and 3 are identified and characterized. Previously reported alleles with incomplete sequences in the IPD-IMGT/HLA database (n = 519) were selected for full gene sequencing and, from this sampling, another 27 novel alleles are described.
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Affiliation(s)
- Ana Lazaro
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Lihua Hou
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Bin Tu
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Carly Masaberg
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Elizabeth Enriquez
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Jennifer Gerfen
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Kanthi Kariyawasam
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Misti Persaud
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Xihan Qin
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Dannah Simbulan
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Yi Xiao
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Lisa Xun
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Ruyan Yang
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Jennifer Ng
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
| | - Carolyn K Hurley
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Pediatrics and Oncology, Georgetown University, Washington, District of Columbia
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