Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: preliminary assessment of cross-platform concordance.
Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: preliminary assessment of cross-platform concordance.
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DOI：
10.1016/j.ygeno.2013.03.008
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发表时间：
2013-07
期刊：
影响因子：
4.4
通讯作者：
Spentzos, Dimitrios
中科院分区：
文献类型：
--
作者：
Kelly, Andrew D.;Hill, Katherine E.;Correll, Mick;Hu, Lan;Wang, Yaoyu E.;Rubio, Renee;Duan, Shenghua;Quackenbush, John;Spentzos, Dimitrios
下一代测序越来越多地用于生物医学研究。在高质量的标本中，已经报道了微阵列和mRNA-seq水平之间的高度一致性，但缺乏福尔马林固定、石蜡包埋（FFPE）组织的信息，特别是对于microRNA（miRNA）分析。我们对miRNA-seq和cDNA介导的退火、选择、延伸和连接（DASL）miRNA测定之间的一致性进行了初步检查。平台之间的定量一致性中等（斯皮尔曼相关性0.514-0.596），并且对一部分miRNA的检测结果存在不一致。对几种不一致的miRNA进行定量PCR（q-RT-PCR）证实了miRNA-seq检测到的大多数序列的存在，但DASL没有检测到，而且miRNA-seq没有检测到一些序列，DASL确信地检测到了。我们的结果表明，miRNA-seq是特异性的，几乎没有假阳性调用，但它可能无法检测FFPE组织中某些丰富的miRNA。进一步的工作是必要的，以充分解决这些问题是相关的转化研究。
Next-generation sequencing is increasingly employed in biomedical investigations. Strong concordance between microarray and mRNA-seq levels has been reported in high quality specimens but information is lacking on formalin-fixed, paraffin-embedded (FFPE) tissues, and particularly for microRNA (miRNA) analysis. We conducted a preliminary examination of the concordance between miRNA-seq and cDNA-mediated annealing, selection, extension, and ligation (DASL) miRNA assays. Quantitative agreement between platforms is moderate (Spearman correlation 0.514–0.596) and there is discordance of detection calls on a subset of miRNAs. Quantitative PCR (q-RT-PCR) performed for several discordant miRNAs confirmed the presence of most sequences detected by miRNA-seq but not by DASL but also that miRNA-seq did not detect some sequences, which DASL confidently detected. Our results suggest that miRNA-seq is specific, with few false positive calls, but it may not detect certain abundant miRNAs in FFPE tissue. Further work is necessary to fully address these issues that are pertinent for translational research.
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DOI：
10.1093/bioinformatics/btr247
发表时间：
2011-07-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Łabaj PP;Leparc GG;Linggi BE;Markillie LM;Wiley HS;Kreil DP
通讯作者：
Kreil DP
影响因子：
14.9
作者：
Kozomara A;Griffiths-Jones S
通讯作者：
Griffiths-Jones S
影响因子：
14.9
作者：
Chen, Jing;Lozach, Jean;Wickham, Eliza;Barnes, Garcia Bret;Luo, Shujun;Mikoulitch, Ivan;Zhou, Lixin;Schroth, Gary;Fan, Jian-Bing
通讯作者：
Fan, Jian-Bing
DOI：
10.1073/pnas.1019753108
发表时间：
2011-03-01
影响因子：
11.1
作者：
Xu, Weihong;Seok, Junhee;Xiao, Wenzhong
通讯作者：
Xiao, Wenzhong
影响因子：
3
作者：
Wang WC;Lin FM;Chang WC;Lin KY;Huang HD;Lin NS
通讯作者：
Lin NS