ArticleThe Journal of molecular diagnostics : JMD2018
Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing.
Article in The Journal of molecular diagnostics : JMD, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- A de novo algorithm for allele reconstruction from Oxford nanopore amplicon reads, with application to CYP2D6.Bioinformatics (Oxford, England) · 2026Article
- A computational HLA allele-typing protocol to de-noise and leverage nanopore amplicon data.BMC genomics · 2025Article
- Article
- A walk through the development of human leukocyte antigen typing: from serologic techniques to next-generation sequencing.Clinical transplantation and research · 2024Review
- NanoHLA: A Method for Human Leukocyte Antigen Class I Genes Typing Without Error Correction Based on Nanopore Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Large-Scale Complete Sequencing and Haplotyping of 1-10 kb DNA Molecules Using Short Massively Parallel Reads.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Allele-specific quantification of human leukocyte antigen transcript isoforms by nanopore sequencing.Frontiers in immunology · 2023Article
- Enhancing Molecular Testing for Effective Delivery of Actionable Gene Diagnostics.Bioengineering (Basel, Switzerland) · 2022Review
- Unique Molecular Identifier-Based High-Resolution HLA Typing and Transcript Quantitation Using Long-Read Sequencing.Frontiers in genetics · 2022Article
- Nanopore sequencing technology, bioinformatics and applications.Nature biotechnology · 2021Review
- A long road/read to rapid high-resolution HLA typing: The nanopore perspective.Human immunology · 2021Review
- Targeted RNA-Based Oxford Nanopore Sequencing for Typing 12 Classical HLA Genes.Frontiers in genetics · 2021Article
- Utilizing nanopore sequencing technology for the rapid and comprehensive characterization of eleven HLA loci; addressing the need for deceased donor expedited HLA typing.Human immunology · 2020Article
- PIRCHE-II: an algorithm to predict indirectly recognizable HLA epitopes in solid organ transplantation.Immunogenetics · 2020Review
- Next-Generation Sequencing Technologies in Blood Group Typing.Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie · 2020Review
- Performance of a multiplexed amplicon-based next-generation sequencing assay for HLA typing.PloS one · 2020Article
- Long-read sequencing in deciphering human genetics to a greater depth.Human genetics · 2019Review
- Harnessing the MinION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora.Molecular ecology resources · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
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 immunologic compatibility between organ donors and recipients, but the platform's high error rate makes it challenging to type alleles with accuracy. 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 data sets generated on the R9.4 flow cell chemistry, Athlon achieved a 100% accuracy in class I HLA typing at the two-field resolution.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.