An Array-Based Analysis of MicroRNA Expression Comparing Matched Frozen and Formalin-Fixed Paraffin-Embedded Human Tissue Samples

被引:99
作者
Zhang, Xiao
Chen, Jiamin
Radcliffe, Tom [4 ]
LeBrun, Dave P. [2 ,3 ]
Tron, Victor A. [2 ,3 ]
Feilotter, Harriet [1 ,2 ,3 ]
机构
[1] Queens Univ, Richardson Lab, Dept Pathol & Mol Med, Kingston, ON K7L 3N6, Canada
[2] Queens Univ, Queens Lab Mol Pathol, Kingston, ON K7L 3N6, Canada
[3] Queens Univ, Queens Canc Res Inst, Kingston, ON K7L 3N6, Canada
[4] Predict Patterns Software, Kingston, ON, Canada
关键词
D O I
10.2353/jmoldx.2008.080077
中图分类号
R36 [病理学];
学科分类号
100104 ;
摘要
MicroRNAs (miRNAs) are small, noncoding RNAs that suppress gene expression at the posttranscriptional level via an antisense RNA-RNA interaction. miRNAs used for array-based profiting are generally purified from either snap-frozen or fresh samples. Because tissues found in most pathology departments are available only in formalin-fixed and paraffin-embedded (FFPE) states, we sought to evaluate miRNA derived from FFPE samples for microarray analysis. In this study, miRNAs extracted from matched snap-frozen and FFPE samples were profiled using the Agilent miRNA array platform (Agilent, Santa Clara, CA). Each miRNA sample was hybridized to arrays containing probes interrogating 470 human miRNAs. Seven cases were compared in either duplicate or triplicate. Intrachip and interchip analyses demonstrated that the processes of miRNA extraction, labeling, and hybridization from both frozen and FFPE samples are highly reproducible and add little variation to the results; technical replicates showed high correlations with one another (Kendall tau, 0.722 to 0.853; Spearman rank correlation coefficient, 0.891 to 0.954). Our results showed consistent high correlations between matched frozen and FFPE samples (Kendall tau, 0.669 to 0.815; Spearman rank correlation coefficient, 0.847 to 0.948), supporting the use of FFPE-derived miRNAs for array-based, gene expression profiling. (J Mol Diagn 2008, 10:513-519; DOI: 10.2353/jmoldx.2008.080077)
引用
收藏
页码:513 / 519
页数:7
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