Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing

In collaboration with Dr. Liu and Washington University in St. Louis, PlatformSTL is currently developing a kit and software to enable Human Leukocyte Antigen (HLA) typing by Nanopore sequencing. PlatformSTL's product will allow users to perform rapid high-resolution typing of HLA genes to better support organ and stem cell transplantations.

Nanopore sequencing, enabled by the MinION device from Oxford Nanopore Technologies, is the only technology that offers portable, single-molecule sequencing and ultra-long 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.

Reference : https://jmd.amjpathol.org/article/S1525-1578(17)30430-0/abstract

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Chang Liu, MD,PhD
 Assistant Professor, Pathology & Immunology, Washington University in St. Louis

Medical Director, Barnes-Jewish Hospital HLA Laboratory
 Attending Physician, Barnes-Jewish Hospital Transfusion Medicine service

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