Figure 6

Selected instances of recurrent cancer-specific ASE. For both panels, columns are samples and rows are genes. Gene status in each sample is plotted. Note that the non-ASE category (blue) may include genes that fall just short of our ASE cutoffs, as well as genes where low coverage reduces our power to detect ASE. Genes in the non-tested category (gray) lack informative SNVs for ASE assessment in that sample. (A) Selected genes that show tumor-specific ASE (black dot) in multiple cancer tissue samples. Genes were chosen based on whether ASE was gained in tumor tissue samples relative to normal tissue samples, according to two-sample MBASED analysis. We require that the gain of ASE occurs in at least 3/7 tumor samples. Genes are grouped by chromosome (rightmost column) and ordered top-to-bottom in order of chromosomal location. Note that gene RNF167 shows ASE in both normal and tumor samples in HCC individual 4; however, different haplotypes are overexpressed in the two samples. (B) Selected genes that show ASE in multiple lung cancer cell lines. Genes were chosen based on whether ASE was detected based on one-sample MBASED analysis. We require that the ASE occurs in at least 4/18 cell lines and does not occur in any of the 7 normal samples (to exclude, for example, imprinted genes). Genes are grouped by chromosome (rightmost column) and ordered top-to-bottom in order of chromosomal location.