HIV Drug Resistance Testing by High-Multiplex "Wide" Sequencing on the MiSeq Instrument
HIV Drug Resistance Testing by High-Multiplex "Wide" Sequencing on the MiSeq Instrument
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DOI：
10.1128/aac.01490-15
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发表时间：
2015-11-01
影响因子：
4.9
通讯作者：
Brumme, C. J.
中科院分区：
文献类型：
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作者：
Lapointe, H. R.;Dong, W.;Brumme, C. J.
低收入和中等收入国家获得艾滋病毒耐药性检测的机会有限，阻碍了患者个人层面的临床决策。必须制定一项有效的议定书来解决这一问题，以最大限度地减少在这种情况下对艾滋病毒-1感染者的负面治疗结果。这是一项观察性研究，旨在确定较新的基因组测序平台，如Illumina MiSeq仪器，同时为数百个样本提供准确的艾滋病毒耐药基因型别的潜力。血浆样本来自加拿大患者常规耐药性检测(n=759)和乌干达研究队列(n=349)。用MiSeq测序法和传统的Sanger测序法对跨越HIV逆转录酶密码子90至234的扩增片段进行测序。使用覆盖率和混合参数对方法之间的核苷酸一致性进行评估，以进行质量控制。还分析了在鉴定耐药突变方面的差异的共识序列。Sanger和MiSeq测序分别有881个样本(80%)和892个样本(81%)成功，其中832个样本两种方法都有结果。大多数失败的样本都带有病毒载量
Limited access to HIV drug resistance testing in low-and middle-income countries impedes clinical decision-making at the individual patient level. An efficient protocol to address this issue must be established to minimize negative therapeutic outcomes for HIV-1-infected individuals in such settings. This is an observational study to ascertain the potential of newer genomic sequencing platforms, such as the Illumina MiSeq instrument, to provide accurate HIV drug resistance genotypes for hundreds of samples simultaneously. Plasma samples were collected from Canadian patients during routine drug resistance testing (n = 759) and from a Ugandan study cohort (n = 349). Amplicons spanning HIV reverse transcriptase codons 90 to 234 were sequenced with both MiSeq sequencing and conventional Sanger sequencing methods. Sequences were evaluated for nucleotide concordance between methods, using coverage and mixture parameters for quality control. Consensus sequences were also analyzed for disparities in the identification of drug resistance mutations. Sanger and MiSeq sequencing was successful for 881 samples (80%) and 892 samples (81%), respectively, with 832 samples having results from both methods. Most failures were for samples with viral loads of