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

Liu, Chang and Xiao, Fangzhou and Hoisington-Lopez, Jessica and Lang, Kathrin and Quenzel, Philipp and Duffy, Brian and Mitra, Robi David (2018) Accurate typing of Human Leukocyte Antigen class I genes by Oxford nanopore sequencing. Journal of Molecular Diagnostics, 20 (4). pp. 428-435. ISSN 1525-1578 . http://resolver.caltech.edu/CaltechAUTHORS:20180416-083506865

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1016/j.jmoldx.2018.02.006DOIArticle
https://www.sciencedirect.com/science/article/pii/S1525157817304300PublisherArticle
https://doi.org/10.1101/178590DOIDiscussion Paper
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.
Funders:
Funding AgencyGrant Number
Washington UniversityK12-HL087107-07
NIHU01MH109133
NIHR01NS076993
Children’s Discovery InstituteMC-II-2016-533
Record Number:CaltechAUTHORS:20180416-083506865
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20180416-083506865
Official Citation:Chang Liu, Fangzhou Xiao, Jessica Hoisington-Lopez, Kathrin Lang, Philipp Quenzel, Brian Duffy, Robi D. Mitra, Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing, The Journal of Molecular Diagnostics, Volume 20, Issue 4, 2018, Pages 428-435, ISSN 1525-1578, https://doi.org/10.1016/j.jmoldx.2018.02.006. (http://www.sciencedirect.com/science/article/pii/S1525157817304300)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:85870
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:16 Apr 2018 21:22
Last Modified:26 Oct 2018 22:29

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