Resolving MiSeq-generated ambiguities in HLA-DPB1 typing by using the Oxford Nanopore technology

The technical limitations of current next-generation sequencing technologies, combined with an ever-increasing number of human leukocyte antigen (HLA) alleles, forms the basis for the additional ambiguities we encounter in our clinical practice at an increasing rate. HLA-DPB1 characterization, particularly, generates a significant percent of ambiguities (25.5%) posing a challenge for accurate and unambiguous HLA-DPB1 genotyping. Phasing of exonic heterozygous positions between exon 2 and all other downstream exons has been the major cause of ambiguities. In this study, Oxford Nanopore, a third generation sequencing technology, was used to resolve the phasing. The accurate MiSeq sequencing data combined with the long reads obtained from the MinION platform of Nanopore technology allowed for the resolution of the tested ambiguities.