HLA-genotyping of clinical specimens using Ion Torrent-based NGS
作者： Jonathan C. Barone , Katsuyuki Saito , Karl Beutner , Maria Campo , Wei Dong
DOI: 10.1016/J.HUMIMM.2015.09.014
关键词:
摘要: We have evaluated and validated the NXType™ workflow (One Lambda, Inc.) accompanying TypeStream™ software on Ion Torrent Next Generation Sequencing (NGS) platform using a comprehensive testing panel. The panel consisted of 285 genomic DNA (gDNA) samples derived from four major ethnic populations contained 59 PT 226 clinical specimens. total number alleles six loci interrogated by NGS was 3420. This validation provided wide range HLA sequence variations including many rare alleles, new variants homozygous alleles. system (reagents software) able to correctly genotype vast majority these concordance rate between SBT-derived genotypes those generated auto-analysis ranged 99.5% 99.8% for HLA-A, B, C, DRB1 DQB1 loci, 98.9% HLA-DPB1. A strategy data review developed that would allow correction most few remaining typing errors. entire gDNA amplification assignment could be completed within 3 working days. Through this study, limitations shortcomings platform, specific assay system, algorithm were also revealed further evaluation improvement.
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