Overview of experimental framework to identify fusion transcripts in breast cancer genomes. (FG^R) Transcripts in which exons from two distinct RefSeq genes are fused together in the same direction. (3′T-E^R) Fusion transcripts in which the 3′-terminus portion of a given 5′ partner gene is truncated and fused to a non-RefSeq but annotated segment that has evidence for being part of a transcript. (3′T-N^R) Any genomic segment that is in the anti-sense strand of any known gene/transcript or in an unannotated region that has no evidence for a transcript in current databases (see Supplemental Glossary).