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
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Issued Date
2025-01-01
Resource Type
eISSN
16648021
Scopus ID
2-s2.0-105018683121
Journal Title
Frontiers in Genetics
Volume
16
Rights Holder(s)
SCOPUS
Bibliographic Citation
Frontiers in Genetics Vol.16 (2025)
Suggested Citation
Intharuangrung N., Sirikul C., Nimsamer P., Wongsurawat T., Saejia A., Anukul N. 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. Frontiers in Genetics Vol.16 (2025). doi:10.3389/fgene.2025.1649990 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/112720
Title
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
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Abstract
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 h 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.