High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells
| Autor: | Katsuyuki Saito, Rhonda Porche-Sorbet, Xiao Yang, Rick Berry, Victoria Swamidass, Brian Duffy, Jessica Hoisington-Lopez, Robi D. Mitra, MariaLynn Crosby, Chang Liu |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Histocompatibility Testing Immunology High resolution High-Throughput Nucleotide Sequencing General Medicine Computational biology Human leukocyte antigen Biology DNA sequencing 03 medical and health sciences Nanopore Nanopore Sequencing Nanopores 030104 developmental biology 0302 clinical medicine HLA Antigens Minion Immunology and Allergy Humans Nanopore sequencing Typing Alleles 030215 immunology |
| Zdroj: | Human immunology. 82(4) |
| ISSN: | 1879-1166 |
| Popis: | Nanopore sequencing has been investigated as a rapid and cost-efficient option for HLA typing in recent years. Despite the lower raw read accuracy, encouraging typing accuracy has been reported, and long reads from the platform offer additional benefits of the improved phasing of distant variants. The newly released R10.3 flow cells are expected to provide higher read-level accuracy than previous chemistries. We examined the performance of R10.3 flow cells on the MinION device in HLA typing after enrichment of target genes by multiplexed PCR. We also aimed to mimic a 1-day workflow with 8-24 samples per sequencing run. A diverse collection of 102 unique samples were typed for HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3/4/5 loci. The concordance rates at 2-field and 3-field resolutions were 99.5% (1836 alleles) and 99.3% (1710 alleles). We also report important quality metrics from these sequencing runs. Continued research and independent validations are warranted to increase the robustness of nanopore-based HLA typing for broad clinical application. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full Text from ScienceDirect