REVIEW AND COMPARISON OF HLASCAN AND HLAMINER FOR HLA ANALYSIS OF NGS DATA

Abstract

Human leukocyte antigen (HLA), an essential factor for a successful organ transplant, is related to many human diseases. The recent advances in next-generation sequencing technologies (NGS) have led to increased bandwidth and throughput as well as reduced cost for genome sequencing. Several HLA typing algorithms and assays have been developed to take advantage of this new development. However, due to the variety and polymorphisms of HLA loci, HLA typing is still a challenge, even with NGS data. For practical usage of this technology in both research and clinical environments, it is necessary to investigate which software tool could provide better HLA typing results from available sequencing data. We have therefore conducted experiments to assess two HLA typing tools, HLAscan and HLAminer, on whole exome sequencing data (WES). HLAscan predicted 21 HLA genotypes with better accuracy and performance than HLAminer. This result can provide directions for future HLA typing studies on WES data.