High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells

Chang Liu, Xiao Yang, Brian F. Duffy, Jessica Hoisington-Lopez, Maria Lynn Crosby, Rhonda Porche-Sorbet, Katsuyuki Saito, Rick Berry, Victoria Swamidass, Robi D. Mitra

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)288-295
Number of pages8
JournalHuman Immunology
Volume82
Issue number4
DOIs
StatePublished - Apr 2021

Keywords

  • Human leukocyte antigen
  • Nanopore sequencing
  • Next-generation sequencing
  • R10.3 flow cells

Fingerprint

Dive into the research topics of 'High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells'. Together they form a unique fingerprint.

Cite this