Additional file 1: of Genome-wide analysis of DNA methylation in bronchial washings

Figure S1. Validation of 450K array. (A) A quality of 450K array was first checked by analyzing measured values for predefined subsets of methylation levels (0, 33, 66, and 100%). 2-D scatter plots were produced using plotColorBias2D in the Lumi package. The plotColorBias2D function separately plots methylated (green) and unmethylated (red) probe intensities in a 2-D scatter plot, and shows the interrogated CpG sites in red and green dots based on their color channels. (B) Methylation levels obtained by the 450K array were further validated using pyrosequencing. The sequencing output shows methylation levels at a cg27364741 locus at a promoter of OTX1 gene in cancer (top) and control sample (bottom). (C) Methylation levels at the cg27364741 locus were compared between β values from 450K array (Y-axis) and pyrosequencing (X-axis). Pyrosequencing was performed in 12 bronchial washing samples. Methylation levels at the cg27364741 locus were found to be higher in 450K array than in pyrosequencing. (TIF 25467 kb)