Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing
Issued Date
2023-01-01
Resource Type
eISSN
16648021
Scopus ID
2-s2.0-85164498621
Journal Title
Frontiers in Genetics
Volume
14
Rights Holder(s)
SCOPUS
Bibliographic Citation
Frontiers in Genetics Vol.14 (2023)
Suggested Citation
Anukul N., Jenjaroenpun P., Sirikul C., Wankaew N., Nimsamer P., Roothumnong E., Pithukpakorn M., Leetrakool N., Wongsurawat T. Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing. Frontiers in Genetics Vol.14 (2023). doi:10.3389/fgene.2023.1213457 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/88010
Title
Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing
Author's Affiliation
Other Contributor(s)
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.