A long road/read to rapid high-resolution HLA typing: The nanopore perspective
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 batchin...
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| Published in | Human immunology Vol. 82; no. 7; pp. 488 - 495 |
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| Main Author | |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
01.07.2021
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| Subjects | |
| Online Access | Get full text |
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| 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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| AbstractList | 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.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. 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. |
| Author | Liu, Chang |
| Author_xml | – sequence: 1 givenname: Chang surname: Liu fullname: Liu, Chang email: cliu32@wustl.edu organization: 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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| Keywords | PRG Consensus sequence Next-generation sequencing ONT Nanopore sequencing INC-Seq Human leukocyte antigen SNV SMRT NGS HLA Sequencing error PCR |
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| SubjectTerms | Alleles Consensus sequence Histocompatibility Testing - methods HLA Antigens - genetics Human leukocyte antigen Humans Immunogenetics - methods Nanopore Sequencing Next-generation sequencing Sequencing error |
| Title | A long road/read to rapid high-resolution HLA typing: The nanopore perspective |
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