Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism.
Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism.
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使用四个下一代测序平台来确定HIV-1共感受器的向流。
DOI：
10.1371/journal.pone.0049602
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Quiñones-Mateu ME
中科院分区：
文献类型：
--
作者：
Archer J;Weber J;Henry K;Winner D;Gibson R;Lee L;Paxinos E;Arts EJ;Robertson DL;Mimms L;Quiñones-Mateu ME
在使用CCR5拮抗剂治疗之前，需要进行HIV-1共受体趋向性试验以排除cxcr4趋向性（非r5）病毒的存在。表型（例如，Trofile™，Monogram Biosciences）和基因型（例如，与生物信息学算法相关的群体测序）检测是最广泛使用的。虽然有几种下一代测序（NGS）平台可用，但迄今为止，所有已发表的深度测序HIV-1趋向性研究都使用了454™生命科学/罗氏平台。在这项研究中，预测了12名计划开始以马拉韦洛克为基础的抗逆转录病毒治疗方案的患者使用HIV-1共受体。HIV-1 env基因V3区域的测序使用四个NGS平台：454™、PacBio®RS （Pacific Biosciences）、Illumina®和Ion Torrent™（Life Technologies）。评估了跨平台差异，包括读取次数、读取长度和错误率。使用Geno2Pheno、Web PSSM和11/24/25规则推断HIV-1趋向性，并与Trofile™和抗逆转录病毒治疗的病毒学反应进行比较。与实际的HIV-1序列变异相比，四种NGS平台引入的插入/缺失（indels）和核苷酸替换相关的错误率较低。每个平台都以相似的频率检测到HIV-1人群中的所有主要病毒变体。四种平台对非r5病毒的鉴定具有可比性，但用于推断HIV-1趋向性的算法存在微小差异。与Trofile（80%）和种群测序（70%）相比，所有NGS平台对基于马拉韦洛克的方案的病毒学反应显示出相似的一致性（取决于所使用的算法，范围为75%至80%）。总之，所有四个NGS平台都能够在相当水平上检测到少数非r5变异，这表明任何基于NGS的方法都可以用于预测HIV-1共受体的使用。
HIV-1 coreceptor tropism assays are required to rule out the presence of CXCR4-tropic (non-R5) viruses prior treatment with CCR5 antagonists. Phenotypic (e.g., Trofile™, Monogram Biosciences) and genotypic (e.g., population sequencing linked to bioinformatic algorithms) assays are the most widely used. Although several next-generation sequencing (NGS) platforms are available, to date all published deep sequencing HIV-1 tropism studies have used the 454™ Life Sciences/Roche platform. In this study, HIV-1 co-receptor usage was predicted for twelve patients scheduled to start a maraviroc-based antiretroviral regimen. The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences), Illumina®, and Ion Torrent™ (Life Technologies). Cross-platform variation was evaluated, including number of reads, read length and error rates. HIV-1 tropism was inferred using Geno2Pheno, Web PSSM, and the 11/24/25 rule and compared with Trofile™ and virologic response to antiretroviral therapy. Error rates related to insertions/deletions (indels) and nucleotide substitutions introduced by the four NGS platforms were low compared to the actual HIV-1 sequence variation. Each platform detected all major virus variants within the HIV-1 population with similar frequencies. Identification of non-R5 viruses was comparable among the four platforms, with minor differences attributable to the algorithms used to infer HIV-1 tropism. All NGS platforms showed similar concordance with virologic response to the maraviroc-based regimen (75% to 80% range depending on the algorithm used), compared to Trofile (80%) and population sequencing (70%). In conclusion, all four NGS platforms were able to detect minority non-R5 variants at comparable levels suggesting that any NGS-based method can be used to predict HIV-1 coreceptor usage.
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