Figure 3

(see facing page). Chromosome 8 (panel a) and chromosome 9 (panel b) analysis. The graphs on the left-hand side of panels (a) and (b) represent copy number estimation and genotype information. The x-axis is the chromosomal position (National Center for Biotechnology Information (NCBI) Build 33). For each sample, the genotype information is presented on top of each panel. The downward red line indicates a homozygous genotype, while the upward green line indicates a heterozygous genotype. Each panel shows the copy number estimation on the y-axis. The vertical green and red lines are individual single nucleotide polymorphism copy number estimates. The upward green lines represent an estimate that is larger than the baseline value of 2, while the downward red lines represent an estimate that is lower than 2. The black dotted lines indicate the relative location of the c-MYC and p-16 genes on chromosomes 8 and 9, respectively. The panels on the right-hand side represent the significance results. The x-axis is the chromosomal position (NCBI Build 33) and the black vertical lines represent the location of the c-MYC (panel a) and p-16 (panel b) genes. The y-axis is the log ₁₀ transformed p-value of each given SNP. To distinguish deletions from amplifications, the log₁₀ ( p-value) (upward green lines) is used when the target value is higher than the reference mean (amplifications) and the log₁₀ (p-value) (downward red lines) is used when the target value is lower than the reference mean (deletions).