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Published July 2018 | Submitted
Journal Article Open

Accurate typing of Human Leukocyte Antigen class I genes by Oxford nanopore sequencing

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 immunological compatibility between organ donors and recipients, but the platform's high error rate makes it challenging to type alleles with accuracy. Here, 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 datasets generated on the R9.4 flow cell chemistry, Athlon achieved a 100% accuracy in class I HLA typing at the 2-field resolution.

Additional Information

© 2018 Published by Elsevier Inc. on behalf of the American Society for Investigative Pathology and the Association for Molecular Pathology. Received 6 September 2017, Revised 13 January 2018, Accepted 13 February 2018, Available online 3 April 2018. Funding: Supported by the Washington University Hematology Scholars K12 award (K12-HL087107-07; C.L.) and grants from the National Institutes of Health (U01MH109133, R01NS076993; R.D.M), and Children's Discovery Institute (MC-II-2016-533 to R.D.M). Disclosures: C.L., R.D.M, K.L., and P.Q. were participants of the MinION Access Program and received the initial MinION instrument and flow cells free of charge.

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August 19, 2023
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