ORIGINAL RESEARCH article
Front. Genet.
Sec. Pharmacogenetics and Pharmacogenomics
Volume 16 - 2025 | doi: 10.3389/fgene.2025.1649990
Concordance of an in-house 2-Steps PCR-SSP and Nanopore Sequencing for HLA-B*57:01 and HLA-B*58:01 typing: A Comparative Study
Provisionally accepted
Nattapong Intharuangrung1
Chonticha Sirikul1Pattaraporn Nimsamer2
Thidathip Wongsurawat2Auttachai Saejia1
Nampeung Anukul1*- 1Division of Transfusion Science, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai, Thailand
- 2Oxford Nanopore Centre of Excellence, Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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This study reports an optimized in-house 2-step PCR-SSP assay for rapid, cost-effective detection of HLA-B*57:01 and HLA-B*58:01 in routine pharmacogenomics laboratory. This assay employs allele-specific primers positioned within exon 2–3 boundaries, validated in silico against common HLA-B alleles. Using 30 clinical DNA samples, our PCR workflow (<1 h) showed 100% concordance at 2-field resolution with Oxford Nanopore sequencing performed using ligation-based sequencing kit with PCR barcoding. Cohen's kappa was 1.00 with 95% CI. The turnaround time and reagent cost per sample were reduced to 1 hour of hands-on PCR time and USD 7 per sample, respectively. These do not include DNA extraction or gel electrophoresis analysis. This 2-step PCR-SSP offers a robust alternative for pharmacogenomic screening in resource-limited settings for detecting the HLA-B*57:01 and HLA-B*58:01.
Keywords: HLA, pharmacogenomics, nanopore, Health, precision medicine, Adverse Drug Reaction
Received: 19 Jun 2025; Accepted: 03 Sep 2025.
Copyright: © 2025 Intharuangrung, Sirikul, Nimsamer, Wongsurawat, Saejia and Anukul. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Nampeung Anukul, Division of Transfusion Science, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai, Thailand
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