LAUSR

Aim The human MHC region has been shown to be associated with a wide range of diseases.The recent advancement in the next generation sequencing (NGS) technology has definitely helped in increasing the resolution (up to 4-field) of HLA genotyping. However, it remains a challenge in interpreting the results from NGS platform due to biases including systematic sequencing error by sequencing platform, difference in the sensitivity and specificity of HLA calling algorithm, ability to resolve HLA alleles ambiguity by incorporating phasing information, and more importantly incompleteness of the current IMGT database. Methods In order to access the sensitivity and specificity of the NXTypeTM NGS HLA typing kit (One Lambda), a total of 105 Japanese samples were sequenced for HLA class I genes using the Ion Torrent Personal Genome Machine (PGM) following the NXType protocol. HLA calling was performed using the HLATypeStream v1.0.0.86 with IMGT/HLA databses of 3.21.0. Concordance rates were evaluated by comparing HLATypeStream results with Luminex-based HLA typing result for up to 2-field result. Results With the default setting of HLATypeStream and without manual interpretation of the results, the allelic concordance is more than 98% for HLA-A, HLA-B and HLA-C. Other commercially available HLA calling software and open-access software were also evaluated. Conclusions Careful inspection of the final results and occasionally manual interpretations of results are necessary especially for rare or novel HLA alleles.