Huang Da Wei, Raley Castle, Jiang Min Kang, Zheng Xin, Liang Dun, Rehman M Tauseef, Highbarger Helene C, Jiao Xiaoli, Sherman Brad, Ma Liang, Chen Xiaofeng, Skelly Thomas, Troyer Jennifer, Stephens Robert, Imamichi Tomozumi, Pau Alice, Lempicki Richard A, Tran Bao, Nissley Dwight, Lane H Clifford, Dewar Robin L
Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA; National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
J Data Mining Genomics Proteomics. 2016 Jan;7(1). doi: 10.4172/2153-0602.1000182. Epub 2015 Nov 8.
Development of HIV-1 drug resistance mutations (HDRMs) is one of the major reasons for the clinical failure of antiretroviral therapy. Treatment success rates can be improved by applying personalized anti-HIV regimens based on a patient's HDRM profile. However, the sensitivity and specificity of the HDRM profile is limited by the methods used for detection. Sanger-based sequencing technology has traditionally been used for determining HDRM profiles at the single nucleotide variant (SNV) level, but with a sensitivity of only ≥ 20% in the HIV population of a patient. Next Generation Sequencing (NGS) technologies offer greater detection sensitivity (~ 1%) and larger scope (hundreds of samples per run). However, NGS technologies produce reads that are too short to enable the detection of the physical linkages of individual SNVs across the haplotype of each HIV strain present. In this article, we demonstrate that the single-molecule long reads generated using the Third Generation Sequencer (TGS), PacBio RS II, along with the appropriate bioinformatics analysis method, can resolve the HDRM profile at a more advanced quasispecies level. The case studies on patients' HIV samples showed that the quasispecies view produced using the PacBio method offered greater detection sensitivity and was more comprehensive for understanding HDRM situations, which is complement to both Sanger and NGS technologies. In conclusion, the PacBio method, providing a promising new quasispecies level of HDRM profiling, may effect an important change in the field of HIV drug resistance research.
HIV-1耐药性突变（HDRM）的出现是抗逆转录病毒疗法临床失败的主要原因之一。基于患者的HDRM谱应用个性化抗HIV方案可提高治疗成功率。然而，HDRM谱的敏感性和特异性受到检测方法的限制。传统上，基于桑格测序技术用于在单核苷酸变异（SNV）水平确定HDRM谱，但在患者的HIV群体中敏感性仅≥20%。新一代测序（NGS）技术具有更高的检测敏感性（约1%）和更大的检测范围（每次运行数百个样本）。然而，NGS技术产生的读长太短，无法检测出每个存在的HIV毒株单倍型上各个SNV的物理连锁关系。在本文中，我们证明使用第三代测序仪（TGS）PacBio RS II生成的单分子长读长，连同适当的生物信息学分析方法，能够在更高级的准种水平解析HDRM谱。对患者HIV样本的案例研究表明，使用PacBio方法产生的准种视图具有更高的检测敏感性，并且对于理解HDRM情况更全面，这对桑格测序和NGS技术都是一种补充。总之，PacBio方法提供了一种有前景的新的准种水平的HDRM分析方法，可能会在HIV耐药性研究领域引起重要变革。
