Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing
Regulatory T Cell Development and Function
Radiology, Nuclear Medicine and Imaging
Genotyping
Therapeutic Antibodies: Development, Engineering, and Applications
Hypersensitivity Reactions to Drugs and Medications
Nanopore sequencing
Genotype
HLA-B*5701
Immunology
Population
QH426-470
Gene
HLA Genotyping
Drug Hypersensitivity
Computational biology
human leukocyte antigen
Health Sciences
Genetics
DNA sequencing
nanopore
Biology
turnaround time
Multiplex
pharmacogenomics
Pharmacology
Immunology and Microbiology
Allele
Human leukocyte antigen
FOS: Clinical medicine
Life Sciences
Typing
Environmental health
FOS: Biological sciences
Antigen
long-read sequencing
Medicine
Thai
DOI:
10.3389/fgene.2023.1213457
Publication Date:
2023-06-24T14:06:23Z
AUTHORS (9)
ABSTRACT
Nanopore sequencing has been examined as a method for rapid and high-resolution human leukocyte antigen (HLA) typing in recent years. We aimed to apply ultrarapid nanopore-based HLA typing for HLA class I alleles associated with drug hypersensitivity, including HLA-A*31:01, HLA-B*15:02, and HLA-C*08:01. Most studies have used the Oxford Nanopore Ligation Sequencing kit for HLA typing, which requires several enzymatic reactions and remains relatively expensive, even when the samples are multiplexed. Here, we used the Oxford Nanopore Rapid Barcoding kit, which is transposase-based, with library preparation taking less than 1 h of hands-on time and requiring minimal reagents. Twenty DNA samples were genotyped for HLA-A, -B, and -C; 11 samples were from individuals of different ethnicity and nine were from Thai individuals. Two primer sets, a commercial set and a published set, were used to amplify the HLA-A, -B, and -C genes. HLA-typing tools that used different algorithms were applied and compared. We found that without using several third-party reagents, the transposase-based method reduced the hands-on time from approximately 9 h to 4 h, making this a viable approach for obtaining same-day results from 2 to 24 samples. However, an imbalance in the PCR amplification of different haplotypes could affect the accuracy of typing results. This work demonstrates the ability of transposase-based sequencing to report 3-field HLA alleles and its potential for race- and population-independent testing at considerably decreased time and cost.
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CITATIONS (7)
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