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Long-Read Nanopore Sequencing Validated for Human Leukocyte Antigen Class I Typing in Routine Diagnostics.
J Mol Diagn. 2020 Jul; 22(7):912-919.JM

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.

Authors+Show Affiliations

Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands.Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands.Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands.Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands.Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands.Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands.Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands. Electronic address: c.voorter@mumc.nl.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32302780

Citation

Matern, Benedict M., et al. "Long-Read Nanopore Sequencing Validated for Human Leukocyte Antigen Class I Typing in Routine Diagnostics." The Journal of Molecular Diagnostics : JMD, vol. 22, no. 7, 2020, pp. 912-919.
Matern BM, Olieslagers TI, Groeneweg M, et al. Long-Read Nanopore Sequencing Validated for Human Leukocyte Antigen Class I Typing in Routine Diagnostics. J Mol Diagn. 2020;22(7):912-919.
Matern, B. M., Olieslagers, T. I., Groeneweg, M., Duygu, B., Wieten, L., Tilanus, M. G. J., & Voorter, C. E. M. (2020). Long-Read Nanopore Sequencing Validated for Human Leukocyte Antigen Class I Typing in Routine Diagnostics. The Journal of Molecular Diagnostics : JMD, 22(7), 912-919. https://doi.org/10.1016/j.jmoldx.2020.04.001
Matern BM, et al. Long-Read Nanopore Sequencing Validated for Human Leukocyte Antigen Class I Typing in Routine Diagnostics. J Mol Diagn. 2020;22(7):912-919. PubMed PMID: 32302780.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Long-Read Nanopore Sequencing Validated for Human Leukocyte Antigen Class I Typing in Routine Diagnostics. AU - Matern,Benedict M, AU - Olieslagers,Timo I, AU - Groeneweg,Mathijs, AU - Duygu,Burcu, AU - Wieten,Lotte, AU - Tilanus,Marcel G J, AU - Voorter,Christina E M, Y1 - 2020/04/14/ PY - 2020/01/10/received PY - 2020/03/03/revised PY - 2020/04/02/accepted PY - 2020/4/18/pubmed PY - 2020/4/18/medline PY - 2020/4/18/entrez SP - 912 EP - 919 JF - The Journal of molecular diagnostics : JMD JO - J Mol Diagn VL - 22 IS - 7 N2 - 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. SN - 1943-7811 UR - https://www.unboundmedicine.com/medline/citation/32302780/Long_Read_Nanopore_Sequencing_Validated_for_Human_Leukocyte_Antigen_Class_I_Typing_in_Routine_Diagnostics_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1525-1578(20)30091-X DB - PRIME DP - Unbound Medicine ER -
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