A Novel Method of Amplification of FFPET-Derived RNA Enables Accurate Disease Classification with Microarrays P. Mickey Williams, Rui Li, Nathalie A.

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A Novel Method of Amplification of FFPET-Derived RNA Enables Accurate Disease Classification with Microarrays P. Mickey Williams, Rui Li, Nathalie A. Johnson, George Wright, Joe-Don Heath, Randy D. Gascoyne The Journal of Molecular Diagnostics Volume 12, Issue 5, Pages 680-686 (September 2010) DOI: 10.2353/jmoldx.2010.090164 Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 Kaplan-Meier survival plot of DLBCL samples included in this study. The Journal of Molecular Diagnostics 2010 12, 680-686DOI: (10.2353/jmoldx.2010.090164) Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 Representative electropherogram of total RNA extracted from FFPET archived lymphoma sample and a freshly frozen lymphoma sample as analyzed on an Agilent BioAnalyzer. The Journal of Molecular Diagnostics 2010 12, 680-686DOI: (10.2353/jmoldx.2010.090164) Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 Scatter plots comparing each of the three data sets for a representative sample (FF Nugen versus FFPET Nugen, FF Eberwine versus FF Nugen, and FF Eberwine versus FFPET Nugen) of all probeset signals generated by MAS 5.0 Affymetrix Software. The Journal of Molecular Diagnostics 2010 12, 680-686DOI: (10.2353/jmoldx.2010.090164) Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 4 A: Results of t-tests and false discovery rates of the number of genes that statistically separate GCB and ABC sample groups for each dataset: FF Affy (ie, Eberwine), FF Nugen, and FFPET Nugen. B: Venn diagram depicting the top 100 genes with smallest t-test values for each of the three data sets. The Journal of Molecular Diagnostics 2010 12, 680-686DOI: (10.2353/jmoldx.2010.090164) Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 5 Results of pathway analysis from Ingenuity IPA Software. The horizontal gold bar indicates the threshold of significance. The Signature pathways listed in darkest blue come from the list of genes (published by Wright et al19) that separate ABC from GCB subgroups. The Journal of Molecular Diagnostics 2010 12, 680-686DOI: (10.2353/jmoldx.2010.090164) Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions