Rapid high-resolution typing of class I HLA genes by Nanopore sequencing

Chang Liu, Rick Berry

Research output: Chapter in Book/Report/Conference proceedingChapter

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.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages93-99
Number of pages7
DOIs
StatePublished - Jan 1 2020

Publication series

NameMethods in Molecular Biology
Volume2120
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • HLA typing
  • Human leukocyte antigen (HLA)
  • Nanopore sequencing
  • Targeted sequencing

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  • Cite this

    Liu, C., & Berry, R. (2020). Rapid high-resolution typing of class I HLA genes by Nanopore sequencing. In Methods in Molecular Biology (pp. 93-99). (Methods in Molecular Biology; Vol. 2120). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-0327-7_6