Tandem duplications are involved in amplicon formation in breast cancer. (A) Density plot of expression values of genes located inside and outside tandem duplications (TD) for the four breast tumors for which RNA-seq data is available. A P-value was computed based on 10,000 random gene permutations. (B, upper) frequency of copy number gain around the ERBB2 locus on Chr 17 across a data set of 1174 breast cancers; (lower) genomic coordinates corresponding to tandem duplications spanning the ERBB2 locus identified in nine different breast cancer samples. (C) Amplified oncogenes are significantly enriched for genes that are recurrently spanned by tandem duplications. Bars correspond to the fold enrichment compared to the all-gene population, with error bars indicating the 95% confidence interval. (NS) Not significant; (*) average and standard deviation values based on 100 gene permutations.
