TY - JOUR
T1 - High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells
AU - Liu, Chang
AU - Yang, Xiao
AU - Duffy, Brian F.
AU - Hoisington-Lopez, Jessica
AU - Crosby, Maria Lynn
AU - Porche-Sorbet, Rhonda
AU - Saito, Katsuyuki
AU - Berry, Rick
AU - Swamidass, Victoria
AU - Mitra, Robi D.
N1 - Publisher Copyright:
© 2021 American Society for Histocompatibility and Immunogenetics
PY - 2021/4
Y1 - 2021/4
N2 - 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.
AB - 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.
KW - Human leukocyte antigen
KW - Nanopore sequencing
KW - Next-generation sequencing
KW - R10.3 flow cells
UR - http://www.scopus.com/inward/record.url?scp=85101171128&partnerID=8YFLogxK
U2 - 10.1016/j.humimm.2021.02.005
DO - 10.1016/j.humimm.2021.02.005
M3 - Article
C2 - 33612390
AN - SCOPUS:85101171128
SN - 0198-8859
VL - 82
SP - 288
EP - 295
JO - Human Immunology
JF - Human Immunology
IS - 4
ER -