Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
PlatformSTL, St. Louis, MO, USA.
Methods Mol Biol. 2020;2120:93-99. doi: 10.1007/978-1-0716-0327-7_6.
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.
纳米孔测序最初由牛津纳米孔技术（ONT）的 MinION 设备实现，是唯一提供便携式、单分子测序和超长读长的技术。该技术非常适合用于移植和癌症免疫治疗的人类白细胞抗原（HLA）基因分型。然而，这种应用受到纳米孔测序reads 高错误率的阻碍。我们开发了工作流程和生物信息学管道 Athlon（通过牛津纳米孔准确进行人类白细胞抗原分型），通过纳米孔测序对 I 类 HLA 基因进行高分辨率分型。该方法的特点是一种新的候选等位基因选择算法，随后通过共识构建进行错误校正。在这里，我们描述了使用 Athlon 的协议，该协议封装在一个 VirtualBox 映像中，用于上述应用。
