Summary of genomic state of genes showing ASE in cancer samples. (A) Proportion of autosomal genome falling into different categories of underlying copy number (CN) and allelic imbalance (AI) states. Cell lines show more CN gains and fewer CN losses than tissue samples. (B) Proportion of ASE autosomal genes falling into different categories of underlying CN and AI states. CN gain (cell lines) and loss (tissues) regions are enriched for ASE genes. The large extent of ASE genes in regions of CN loss in tissues is most likely explained by heterozygosity detection due to normal tissue admixture. The vast majority of ASE genes in tumor tissue samples from NSCLC individual 2 (second from left) fall into CN-neutral, no-AI regions, but the sample exhibits ASE levels comparable to the other two NSCLC patients (compare Figure 4B).