Ultrafast Workflow for Accurate Full-length ABO Genotyping using Nanopore Sequencing

Rapid ABO discrepancy resolution is critical for transfusion safety. However, current short-read sequencing cannot resolve phase across the 21.9 kb ABO gene. Here, the aim is to developed a nanopore-based workflow for full-length ABO genotyping. A workflow combining a long-range PCR (LR-PCR) amplicon spanning the ABO gene was generated from genomic DNA from 63 serologically discrepant donors and sequenced using Oxford Nanopore Technologies (ONT) Platform. PacBio HiFi sequencing was used as an orthogonal reference standard. Variant calling and haplotype reconstruction were performed using a unified bioinformatics pipeline. The workflow was further evaluated with another nanopore sequencing platform, PolySeq, where the sequencing accuracy is lower than that of ONT R10.4 chemistry. In this study, 63 discrepant samples of 280,712 donors yielded 126 full-length haplotypes. The nanopore workflow delivered results within 6 hours versus over 46 hours for PacBio. ONT showed 100% concordance with PacBio HiFi outside homopolymer regions. Causal variants were resolved in 92.06% samples. Homopolymer errors were confined to intron 1 without phenotypic impact. PolySeq platform also produced PacBio-comparable consensus accuracy after applying deep learning-based error correction, with superior chimerism sensitivity, confirming the robustness of our workflow. In conclusion, this ultrafast nanopore workflow enables same-day, full-length ABO haplotype resolution, which provided a rapid, cost-effective genotyping solution of complex variants for precision transfusion and aids global haplotype database development.