Figure 3.
The age of the FFPE block is associated with loss of biological signal. (A) x–y scatterplot showing the ratio of SCC/AC gene signature (y axis) against the age of FFPE block in years (x axis). Pearson correlation coefficient (R) is displayed. (B) x–y scatterplot showing the ratio of SCC/AC gene expression (y axis) against %DABG (x axis). Pearson correlation coefficient (R) is displayed. (C) x–y scatterplot showing median TP63 expression plotted against the age of the FFPE block. Pearson correlation coefficient (R) is displayed. (D) Western blot of p63 protein expression in 16 cervix cancer cell lines. (E) Box-whisker plot showing Exon array probeset expression of TP63 in AC and SCC from three cohorts; cervix cell lines (n=16), CS1; intermediate age FFPE (n=112) and CS2; old FFPE n=48. (F) Box-whisker plot for a subset of FFPE samples where sufficient tissue was available for p63 immunohistochemistry (CS1 n=108, CS2 n=44). y axis shows the median TP63 probeset expression from Exon array data. x axis shows p63 immunohistochemistry status; positive (>5% nuclei) or negative (<5% nuclei) for samples within the younger CS1 and older CS2 cohorts.