Accurate typing of Human Leukocyte Antigen class I genes by Oxford nanopore sequencing

Oxford Nanopore Technologies’ MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability. The MinION has the potential to enable expedited point-of-care human leukocyte antigen (HLA) typing, an assay routinely used to assess the immunological compatibility between organ donors and recipients, but the platform’s high error rate makes it challenging to type alleles with accuracy. Here, we developed and validated Athlon (Accurate typing of HLA by Oxford nanopore), a bioinformatic pipeline that (i) maps nanopore reads to a database of known HLA alleles, (ii) identifies candidate alleles with the highest read coverage at different resolution levels that are represented as branching nodes and leaves of a tree structure, (iii) generates consensus sequences by remapping the reads to the candidate alleles, and (iv) calls the final diploid genotype by blasting consensus sequences against the reference database. Using two independent datasets generated on the R9.4 flow cell chemistry, Athlon achieved a 100% accuracy in class I HLA typing at the 2-field resolution.