An Integrated Tool to Study MHC Region: Accurate SNV Detection and HLA Genes Typing in Human MHC Region Using Targeted High-Throughput Sequencing

作者：Hongzhi Cao, Jinghua Wu, Yu Wang, Hui Jiang, Tao Zhang, Xiao Liu, Yinyin Xu, Dequan Liang, Peng Gao, Yepeng Sun, Benjamin Gifford, Mark D’Ascenzo, Xiaomin Liu, Laurent C. A. M. Tellier, Fang� Yang, Xin Tong, Dan Chen, Jing Zheng, Weiyang Li, Todd Richmond, Xun Xu, Jun Wang, Yingrui Li · 发表于：PLoS ONE · 年份：2013 · DOI：10.1371/journal.pone.0069388 · 被引用次数：69 · 研究领域：T-cell and B-cell Immunology、Immune Cell Function and Interaction、Renal Transplantation Outcomes and Treatments

The major histocompatibility complex (MHC) is one of the most variable and gene-dense regions of the human genome. Most studies of the MHC, and associated regions, focus on minor variants and HLA typing, many of which have been demonstrated to be associated with human disease susceptibility and metabolic pathways. However, the detection of variants in the MHC region, and diagnostic HLA typing, still lacks a coherent, standardized, cost effective and high coverage protocol of clinical quality and reliability. In this paper, we presented such a method for the accurate detection of minor variants and HLA types in the human MHC region, using high-throughput, high-coverage sequencing of target regions. A probe set was designed to template upon the 8 annotated human MHC haplotypes, and to encompass the 5 megabases (Mb) of the extended MHC region. We deployed our probes upon three, genetically diverse human samples for probe set evaluation, and sequencing data show that ∼97% of the MHC region, and over 99% of the genes in MHC region, are covered with sufficient depth and good evenness. 98% of genotypes called by this capture sequencing prove consistent with established HapMap genotypes. We have concurrently developed a one-step pipeline for calling any HLA type referenced in the IMGT/HLA database from this target capture sequencing data, which shows over 96% typing accuracy when deployed at 4 digital resolution. This cost-effective and highly accurate approach for variant detection ...