Towards allele-level human leucocyte antigens genotyping - assessing two next-generation sequencing platforms: Ion Torrent Personal Genome Machine and Illumina MiSeq.

摘要: Summary Human leucocyte antigens (HLA) typing has been a challenge due to extreme polymorphism of the HLA genes and limitations current technologies protocols used for their characterization. Recently, next-generation sequencing techniques have shown be well-suited technology complete characterization genes. However, comprehensive assessment different platforms typing, describing advantages each them, not presented. We compared Ion Torrent Personal Genome Machine (PGM) Illumina MiSeq, currently two most frequently diagnostic applications, number metrics including total output, quality score per position across reads error rates after alignment which can all affect accuracy genotyping. For this purpose, we one homozygous three heterozygous well-characterized samples, at HLA-A, HLA-B, HLA-C, HLA-DRB1 HLA-DQB1. The output bases produced by MiSeq was higher, they higher scores lower overall rate than PGM. also fidelity when through homopolymer regions up 9 bp in length. need set phase between distant polymorphic sites more readily achieved with using paired-end fragments that are longer those obtained Additionally, assessed workflows complexity sample preparation, sequencer operation turnaround time. effects data quantity impact genotyping results; having an adequate amount good analyse will imperative confident time very comparable platforms; however, preparation is PGM, while actual MiSeq.