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Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing.
J Mol Diagn. 2018 07; 20(4):428-435.JM

Abstract

Oxford Nanopore Technologies' MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability. The MinION has the potential to enable expedited point-of-care human leukocyte antigen (HLA) typing, an assay routinely used to assess the immunologic compatibility between organ donors and recipients, but the platform's high error rate makes it challenging to type alleles with accuracy. We developed and validated accurate typing of HLA by Oxford nanopore (Athlon), a bioinformatic pipeline that i) maps nanopore reads to a database of known HLA alleles, ii) identifies candidate alleles with the highest read coverage at different resolution levels that are represented as branching nodes and leaves of a tree structure, iii) generates consensus sequences by remapping the reads to the candidate alleles, and iv) calls the final diploid genotype by blasting consensus sequences against the reference database. Using two independent data sets generated on the R9.4 flow cell chemistry, Athlon achieved a 100% accuracy in class I HLA typing at the two-field resolution.

Authors+Show Affiliations

Department of Pathology and Immunology, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri. Electronic address: cliu32@wustl.edu.Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.Division of Laboratory and Genomic Medicine, and the Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri.DKMS Life Science Lab GmbH, Dresden, Germany.DKMS Life Science Lab GmbH, Dresden, Germany.HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri.Division of Laboratory and Genomic Medicine, and the Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri. Electronic address: rmitra@genetics.wustl.edu.

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

29625249

Citation

Liu, Chang, et al. "Accurate Typing of Human Leukocyte Antigen Class I Genes By Oxford Nanopore Sequencing." The Journal of Molecular Diagnostics : JMD, vol. 20, no. 4, 2018, pp. 428-435.
Liu C, Xiao F, Hoisington-Lopez J, et al. Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing. J Mol Diagn. 2018;20(4):428-435.
Liu, C., Xiao, F., Hoisington-Lopez, J., Lang, K., Quenzel, P., Duffy, B., & Mitra, R. D. (2018). Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing. The Journal of Molecular Diagnostics : JMD, 20(4), 428-435. https://doi.org/10.1016/j.jmoldx.2018.02.006
Liu C, et al. Accurate Typing of Human Leukocyte Antigen Class I Genes By Oxford Nanopore Sequencing. J Mol Diagn. 2018;20(4):428-435. PubMed PMID: 29625249.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing. AU - Liu,Chang, AU - Xiao,Fangzhou, AU - Hoisington-Lopez,Jessica, AU - Lang,Kathrin, AU - Quenzel,Philipp, AU - Duffy,Brian, AU - Mitra,Robi D, Y1 - 2018/04/03/ PY - 2017/09/06/received PY - 2018/01/13/revised PY - 2018/02/13/accepted PY - 2018/4/7/pubmed PY - 2019/9/12/medline PY - 2018/4/7/entrez SP - 428 EP - 435 JF - The Journal of molecular diagnostics : JMD JO - J Mol Diagn VL - 20 IS - 4 N2 - Oxford Nanopore Technologies' MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability. The MinION has the potential to enable expedited point-of-care human leukocyte antigen (HLA) typing, an assay routinely used to assess the immunologic compatibility between organ donors and recipients, but the platform's high error rate makes it challenging to type alleles with accuracy. We developed and validated accurate typing of HLA by Oxford nanopore (Athlon), a bioinformatic pipeline that i) maps nanopore reads to a database of known HLA alleles, ii) identifies candidate alleles with the highest read coverage at different resolution levels that are represented as branching nodes and leaves of a tree structure, iii) generates consensus sequences by remapping the reads to the candidate alleles, and iv) calls the final diploid genotype by blasting consensus sequences against the reference database. Using two independent data sets generated on the R9.4 flow cell chemistry, Athlon achieved a 100% accuracy in class I HLA typing at the two-field resolution. SN - 1943-7811 UR - https://www.unboundmedicine.com/medline/citation/29625249/Accurate_Typing_of_Human_Leukocyte_Antigen_Class_I_Genes_by_Oxford_Nanopore_Sequencing_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1525-1578(17)30430-0 DB - PRIME DP - Unbound Medicine ER -