Assay-dependent discordance in detecting a rare HLA-DPB1 allele: Long-range PCR vs. hybrid capture NGS

Next-generation sequencing (NGS) has become fundamental to high-resolution HLA typing, but methodological differences between long-range PCR (LR PCR) and hybrid capture (HC) approaches can lead to discrepant results. This study examined cases where an allele identified as DPB1*13:01 by LR PCR was assigned DPB1*107:01 by HC. This discordance was attributed to both primer-site mutations and incomplete coverage of non-coding regions in LR PCR, resulting in allele dropout and preferential amplification. Conversely, typing by HC captures full genomic regions and minimizes PCR-generated errors, enabling accurate allele assignment. Findings indicate that DPB1*107:01 may be more prevalent than current CIWD classifications suggest, while broader implications include the need for proficiency testing programs to incorporate method-specific grading criteria that reflect the diversity of available typing technologies. This study underscores the importance of comprehensive genomic coverage for accurate HLA typing and supports the expanded adoption of HC-based sequencing in clinical laboratories.