Identified and validated fusion gene candidates.

13 fusion genes were detected from BT-474 and MCF-7 breast cancer cells. A minimum of two paired-end reads and two fusion junction spanning reads were a prerequisite for choosing a fusion gene candidate for further analysis. Copy number amplification, location on a genomic break point (at least one of the fusion partner genes in both cases) and in-frame prediction are indicated. Lower level copy number gains were not included in the analysis. “Previous characterization” -column summarizes the level of information available for the individual fusion transcripts prior to this study. Validation refers to verification at the transcript level by RT-PCR or Northern blotting (for [20]).