An Array-Based Analysis of MicroRNA Expression Comparing Matched Frozen and Formalin-Fixed Paraffin-Embedded Human Tissue Samples Xiao Zhang, Jiamin.

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Presentation transcript:

An Array-Based Analysis of MicroRNA Expression Comparing Matched Frozen and Formalin-Fixed Paraffin-Embedded Human Tissue Samples Xiao Zhang, Jiamin Chen, Tom Radcliffe, Dave P. LeBrun, Victor A. Tron, Harriet Feilotter The Journal of Molecular Diagnostics Volume 10, Issue 6, Pages 513-519 (November 2008) DOI: 10.2353/jmoldx.2008.080077 Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 Effects of formalin fixation and paraffin embedding on miRNA. A: Frozen sample-derived total RNA electrophorogram on Agilent small RNA chip. B: FFPE-derived total RNA electrophorogram on Agilent small RNA chip. The Journal of Molecular Diagnostics 2008 10, 513-519DOI: (10.2353/jmoldx.2008.080077) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 Scatter plots of replica frozen sample arrays (A) and replica FFPE sample arrays (B). x and y axes are on log scale. The Journal of Molecular Diagnostics 2008 10, 513-519DOI: (10.2353/jmoldx.2008.080077) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 Comparison of miRNAs extracted from the same sample. x and y axes are on a log scale. A: Scatter plot of replica frozen sample arrays from separately extracted miRNA. B: Scatter plot of replica FFPE sample arrays from separately extracted miRNA. The Journal of Molecular Diagnostics 2008 10, 513-519DOI: (10.2353/jmoldx.2008.080077) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 4 Comparisons of slide to slide variability. x and y axes are on a log scale. A: Scatter plot of replica frozen sample arrays from separately extracted miRNA on arrays on different slides. B: Scatter plot of replica FFPE sample arrays from separately extracted miRNA on arrays on different slides. The Journal of Molecular Diagnostics 2008 10, 513-519DOI: (10.2353/jmoldx.2008.080077) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 5 Scatter plots of frozen sample array versus matched FFPE sample array. y axis stands for frozen sample intensity on log scale. x axis stands for FFPE sample intensity on log scale. A: Scatter plot of our best correlation sample pair. B: Scatter plot of our worst correlation sample pair. The Journal of Molecular Diagnostics 2008 10, 513-519DOI: (10.2353/jmoldx.2008.080077) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 6 Unsupervised clustering of 14 frozen sample arrays and 14 FFPE sample arrays. The Journal of Molecular Diagnostics 2008 10, 513-519DOI: (10.2353/jmoldx.2008.080077) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 7 Line plot of 30 randomly chosen miRNAs comparing relative signal intensities from matched frozen sample and FFPE samples. Similar results were obtained with all 470 miRNAs profiled on the arrays (data not shown). The Journal of Molecular Diagnostics 2008 10, 513-519DOI: (10.2353/jmoldx.2008.080077) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions