Comparison of microRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues.
Comparison of microRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues.
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DOI：
10.1371/journal.pone.0064393
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Lautenschlaeger T
中科院分区：
文献类型：
--
作者：
Meng W;McElroy JP;Volinia S;Palatini J;Warner S;Ayers LW;Palanichamy K;Chakravarti A;Lautenschlaeger T
MicroRNA调控肿瘤发生和癌症进展的几个方面。大多数癌症组织都是福尔马林固定和石蜡包埋（FFPE）存档的。虽然microRNA是一种更稳定的RNA形式，被认为可以承受FFPE加工和降解，但后一种假设的证据有限。我们检查了是否可以使用基于SOLiD连接的测序在FFPE癌组织上成功地进行microRNA谱分析。与匹配的冷冻样品相比，组织储存时间（2-9年）似乎不影响FFPE样品中检测到的microRNA的数量（配对t检验p>0.7）。在给定样品中，microRNA表达值的相关性在microRNA之间非常高（Pearson's r = 0.71-0.95）。 样本间较高的表达值方差与FFPE和冷冻组织之间较高的相关系数相关。本研究中的一个FFPE样品由于未知原因降解，峰值读取长度为17个核苷酸，而所有其他样品为21个核苷酸。该样品中检测到的microRNA的数量在所有其他样品中检测到的microRNA的范围内。FFPE癌组织上基于连接的microRNA深度测序是可行的，并且在我们的研究中观察到的RNA降解程度似乎不会影响可以量化的microRNA的数量。
MicroRNAs regulate several aspects of tumorigenesis and cancer progression. Most cancer tissues are archived formalin-fixed and paraffin-embedded (FFPE). While microRNAs are a more stable form of RNA thought to withstand FFPE-processing and degradation there is only limited evidence for the latter assumption. We examined whether microRNA profiling can be successfully conducted on FFPE cancer tissues using SOLiD ligation based sequencing. Tissue storage times (2–9 years) appeared to not affect the number of detected microRNAs in FFPE samples compared to matched frozen samples (paired t-test p>0.7). Correlations of microRNA expression values were very high across microRNAs in a given sample (Pearson’s r = 0.71–0.95). Higher variance of expression values among samples was associated with higher correlation coefficients between FFPE and frozen tissues. One of the FFPE samples in this study was degraded for unknown reasons with a peak read length of 17 nucleotides compared to 21 in all other samples. The number of detected microRNAs in this sample was within the range of microRNAs detected in all other samples. Ligation-based microRNA deep sequencing on FFPE cancer tissues is feasible and RNA degradation to the degree observed in our study appears to not affect the number of microRNAs that can be quantified.
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影响因子：
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影响因子：
64.8
作者：
Lu, J;Getz, G;Golub, TR
通讯作者：
Golub, TR
影响因子：
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Moltzahn F;Olshen AB;Baehner L;Peek A;Fong L;Stöppler H;Simko J;Hilton JF;Carroll P;Blelloch R
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Blelloch R
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通讯作者：
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作者：
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通讯作者：
Marra, Marco A.