Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing

• DOI: 10.3389/fgene.2023.1213457
• Publication Date: 2023-06-24T14:06:23Z
• Authors: Nampeung Anukul; Piroon Jenjaroenpun; Chonticha Sirikul; Natnicha Wankaew; Pattaraporn Nimsamer; Ekkapong Roothumnong; Manop Pithukpakorn; Nipapan Leetrakool; Thidathip Wongsur...
• Keywords: Multiplex

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 class I alleles associated with drug hypersensitivity, including HLA-A*31:01, HLA-B*15:0 2 , HLA-C*08:01. Most studies have used the Oxford Ligation Sequencing kit typing, which requires several enzymatic reactions remains relatively expensive, even when samples are multiplexed. Here, we Rapid Barcoding kit, is transposase-based, library preparation taking less than 1 h of hands-on time requiring minimal reagents. Twenty DNA were genotyped HLA-A, -B, -C; 11 from individuals different ethnicity nine Thai individuals. Two primer sets, commercial set published set, amplify HLA-A - B C genes. HLA-typing tools that algorithms applied compared. found without using third-party reagents, transposase-based reduced approximately 9 4 h, making this viable approach obtaining same-day results 24 samples. However, an imbalance PCR amplification haplotypes could affect accuracy results. This work demonstrates ability report 3-field its potential race- population-independent testing at considerably decreased cost.