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

The main aim of this study was to develop and evaluate a rapid and cost-effective method for high-resolution HLA class I typing using Oxford Nanopore sequencing. The study focused on detecting HLA alleles that are associated with drug hypersensitivity, such as HLA-B15:02, HLA-A31:01, and HLA-C*08:01. These alleles are significant in pharmacogenomics, especially in predicting severe cutaneous adverse reactions (SCARs) from drugs like carbamazepine and allopurinol. The research aimed to optimize HLA typing for to reducing the time and cost involved in pharmacogenomic evaluation.

The Oxford Nanopore MinION sequencer was used with a transposase-based rapid barcoding kit. This method reduced the library preparation time to less than 1 hour, compared to the more time-intensive ligation-based methods. The study also employed two different HLA primer sets and tested bioinformatics tools for analysing HLA typing results.

The study found that the transposase-based nanopore sequencing method accurately identified HLA alleles with over 90% accuracy, significantly reducing hands-on time and costs compared to traditional ligation-based sequencing. The method was able to detect HLA alleles related to drug hypersensitivity in Thai patients, showing high-resolution 3-field HLA typing. This ultrarapid sequencing method holds promise for clinical settings, as it can provide same-day HLA typing results, improving the safety and efficiency of pharmacogenomic testing.