Accuracy of NGS HLA typing data influenced by STR

Abstract Next Generation Sequencing (NGS) has become a major technology in HLA typing. The expectations are that highly accurate and unambiguous typing results will be obtained. However, HLA typing by NGS has some limitations caused by imperfections in the PCR amplification. The accuracy of NGS data is investigated by analyzing the Short Tandem Repeats (STR) regions. For this analysis HLA-DRB5 is used as the model. The repeat length in a sample highly influences the repeat length distribution present in the reads of NGS data. With a repeat length of 20 only 50% of all reads were of the estimated repeat length, seriously hampering distinguishing allelic differences in this region correctly. Our findings are confirmed by doing the same analysis in HLA-DRB1. Despite the uncertainty of determining the repeat lengths, several new HLA-DRB5 alleles have been identified in this paper.