ICF International at FDA's National Center for Toxicological Research, 3900 NCTR Road, Jefferson, Arkansas 72079, USA.
Chem Res Toxicol. 2011 Sep 19;24(9):1486-93. doi: 10.1021/tx200103b. Epub 2011 Aug 23.
RNA-Seq has been increasingly used for the quantification and characterization of transcriptomes. The ongoing development of the technology promises the more accurate measurement of gene expression. However, its benefits over widely accepted microarray technologies have not been adequately assessed, especially in toxicogenomics studies. The goal of this study is to enhance the scientific community's understanding of the advantages and challenges of RNA-Seq in the quantification of gene expression by comparing analysis results from RNA-Seq and microarray data on a toxicogenomics study. A typical toxicogenomics study design was used to compare the performance of an RNA-Seq approach (Illumina Genome Analyzer II) to a microarray-based approach (Affymetrix Rat Genome 230 2.0 arrays) for detecting differentially expressed genes (DEGs) in the kidneys of rats treated with aristolochic acid (AA), a carcinogenic and nephrotoxic chemical most notably used for weight loss. We studied the comparability of the RNA-Seq and microarray data in terms of absolute gene expression, gene expression patterns, differentially expressed genes, and biological interpretation. We found that RNA-Seq was more sensitive in detecting genes with low expression levels, while similar gene expression patterns were observed for both platforms. Moreover, although the overlap of the DEGs was only 40-50%, the biological interpretation was largely consistent between the RNA-Seq and microarray data. RNA-Seq maintained a consistent biological interpretation with time-tested microarray platforms while generating more sensitive results. However, there is clearly a need for future investigations to better understand the advantages and limitations of RNA-Seq in toxicogenomics studies and environmental health research.
RNA-Seq 已被越来越多地用于转录组的定量和特征描述。该技术的不断发展有望更准确地测量基因表达。然而，它相对于广泛接受的微阵列技术的优势尚未得到充分评估，特别是在毒理学基因组学研究中。本研究的目的是通过比较毒理学基因组学研究中 RNA-Seq 和微阵列数据的分析结果，增强科学界对 RNA-Seq 在基因表达定量中的优势和挑战的理解。采用典型的毒理学基因组学研究设计，比较 RNA-Seq 方法（Illumina Genome Analyzer II）和基于微阵列的方法（Affymetrix Rat Genome 230 2.0 阵列）在检测用马兜铃酸（一种致癌和肾毒性化学物质，主要用于减肥）处理的大鼠肾脏中差异表达基因（DEGs）的性能。我们研究了 RNA-Seq 和微阵列数据在绝对基因表达、基因表达模式、差异表达基因和生物学解释方面的可比性。我们发现，RNA-Seq 更敏感地检测低表达水平的基因，而两种平台观察到的基因表达模式相似。此外，尽管 DEGs 的重叠率仅为 40-50%，但 RNA-Seq 和微阵列数据的生物学解释在很大程度上是一致的。RNA-Seq 在产生更敏感结果的同时，与经过时间考验的微阵列平台保持一致的生物学解释。然而，显然需要进一步研究以更好地理解 RNA-Seq 在毒理学基因组学研究和环境健康研究中的优势和局限性。
