Fig. 3

Genomics landscape of copy number and structural variants in breast cancer cell lines. A Representative circos plot of MCF7 for genomics alterations. Copy number events are summarized in the inner circle with red and blue colour indicates copy number gains and blue respectively, two inner circles are represented two replicates of MCF7 samples (one 30X and one 60X). Arcs connecting two loci of difference chromosomes indicate inter-chromosomal structural variations. B Venn diagram shows the overlap of CNV genes between COSMIC, Ben-David et al. and this study. C Representative genome browser view of copy number alterations covering a common CNV gene, CDKN2A. Tracks from top to bottom: depth of coverage in an NA12878 control (control), all reads in the sample (all reads), or reads with mapping quality >  = 20 (MQ > 20), the average mapping quality of aligned reads from the sample (MQ, if no reads align MQ = 0), coverage standard deviation from 500 controls (Coverage SD, indicating common CNV), overlapping segmental duplications published by Bailey JA et al. 2002 (SEG-DUP, used as control for germline CNVs), discordant pairs (DP), split reads (SR), variants from the Database of Genomic Variants (DGV), and RefSeq genes (Genes). D Representative genome browser view plot of a novel CNV gene LINC00290 in this study