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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 Aug; 81(8):413-422.HI

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.

Authors+Show Affiliations

Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.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.Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.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.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. Electronic address: monosd@email.chop.edu.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32595056

Citation

Mosbruger, Timothy L., et al. "Utilizing Nanopore Sequencing Technology for the Rapid and Comprehensive Characterization of Eleven HLA Loci; Addressing the Need for Deceased Donor Expedited HLA Typing." Human Immunology, vol. 81, no. 8, 2020, pp. 413-422.
Mosbruger TL, Dinou A, Duke JL, et al. 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(8):413-422.
Mosbruger, T. L., Dinou, A., Duke, J. L., Ferriola, D., Mehler, H., Pagkrati, I., Damianos, G., Mbunwe, E., Sarmady, M., Lyratzakis, I., Tishkoff, S. A., Dinh, A., & Monos, D. S. (2020). Utilizing nanopore sequencing technology for the rapid and comprehensive characterization of eleven HLA loci; addressing the need for deceased donor expedited HLA typing. Human Immunology, 81(8), 413-422. https://doi.org/10.1016/j.humimm.2020.06.004
Mosbruger TL, et al. 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(8):413-422. PubMed PMID: 32595056.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Utilizing nanopore sequencing technology for the rapid and comprehensive characterization of eleven HLA loci; addressing the need for deceased donor expedited HLA typing. AU - Mosbruger,Timothy L, AU - Dinou,Amalia, AU - Duke,Jamie L, AU - Ferriola,Deborah, AU - Mehler,Hilary, AU - Pagkrati,Ioanna, AU - Damianos,Georgios, AU - Mbunwe,Eric, AU - Sarmady,Mahdi, AU - Lyratzakis,Ioannis, AU - Tishkoff,Sarah A, AU - Dinh,Anh, AU - Monos,Dimitri S, Y1 - 2020/06/25/ PY - 2020/04/29/received PY - 2020/06/03/revised PY - 2020/06/03/accepted PY - 2020/7/1/pubmed PY - 2020/7/1/medline PY - 2020/6/30/entrez KW - HLA genotyping KW - Human Leukocyte Antigens KW - NGS KW - Oxford Nanopore sequencing KW - Transplantation SP - 413 EP - 422 JF - Human immunology JO - Hum. Immunol. VL - 81 IS - 8 N2 - 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. SN - 1879-1166 UR - https://www.unboundmedicine.com/medline/citation/32595056/Utilizing_nanopore_sequencing_technology_for_the_rapid_and_comprehensive_characterization_of_eleven_HLA_loci L2 - https://linkinghub.elsevier.com/retrieve/pii/S0198-8859(20)30339-6 DB - PRIME DP - Unbound Medicine ER -
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