A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression.
A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression.
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DOI：
10.1186/s12864-017-4011-0
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发表时间：
2017-08-10
期刊：
影响因子：
4.4
通讯作者：
Grant GR
中科院分区：
文献类型：
--
作者：
Lahens NF;Ricciotti E;Smirnova O;Toorens E;Kim EJ;Baruzzo G;Hayer KE;Ganguly T;Schug J;Grant GR
虽然Illumina在很大程度上主导了RNA-Seq领域，但Ion Torrent的同时可用性让科学家们想知道哪个平台对差异基因表达（DGE）分析最有效。之前对该问题的研究通常使用来自细胞系和脑组织的参考样本，并且不涉及生物学变异性。虽然这些比较可能会为组织特异性表达的研究提供信息，以大规模转录差异为标志，但这并不是常见的用例。在这里，我们采用了一个标准的治疗/对照实验设计，这使我们能够评估这些平台的背景下，在差异基因表达实验中常见的表达差异。具体而言，我们通过用Illumina HiSeq和Ion Torrent Proton测序平台测定来自对照和IL-1β治疗的动物的肝脏RNA来评估小鼠的肝脏炎症反应。我们发现平台之间在读段比对水平上的最大差异，在DGE分析水平上的中等一致性水平，以及在差异影响途径水平上的几乎相同的结果。有趣的是，我们还观察到测序平台和比对器选择之间的强烈相互作用。通过将真实的和模拟的Illumina和Ion Torrent数据与文献中12个最常引用的比对器进行比对，我们观察到不同的比对器和平台组合更适合于探测不同的基因组特征;例如，解开基因-假基因对中的表达来源。综上所述，我们的结果表明，虽然Illumina和Ion Torrent在检测治疗/对照实验的生物学变化方面具有相似的能力，但这些平台可以通过仔细选择比对软件来定制以询问不同的转录现象。本文的在线版本（doi：10.1186/s12864-017-4011-0）包含补充材料，可供授权用户使用。
Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analysis. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. While these comparisons might inform studies of tissue-specific expression, marked by large-scale transcriptional differences, this is not the common use case. Here we employ a standard treatment/control experimental design, which enables us to evaluate these platforms in the context of the expression differences common in differential gene expression experiments. Specifically, we assessed the hepatic inflammatory response of mice by assaying liver RNA from control and IL-1β treated animals with both the Illumina HiSeq and the Ion Torrent Proton sequencing platforms. We found the greatest difference between the platforms at the level of read alignment, a moderate level of concordance at the level of DGE analysis, and nearly identical results at the level of differentially affected pathways. Interestingly, we also observed a strong interaction between sequencing platform and choice of aligner. By aligning both real and simulated Illumina and Ion Torrent data with the twelve most commonly-cited aligners in the literature, we observed that different aligner and platform combinations were better suited to probing different genomic features; for example, disentangling the source of expression in gene-pseudogene pairs. Taken together, our results indicate that while Illumina and Ion Torrent have similar capacities to detect changes in biology from a treatment/control experiment, these platforms may be tailored to interrogate different transcriptional phenomena through careful selection of alignment software. The online version of this article (doi:10.1186/s12864-017-4011-0) contains supplementary material, which is available to authorized users.
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