SRP006908 RNA Seq of br ca cell line Global analysis of previously unrecognized alternative splicing in BRCA1- related breast cancers Background: Breast cancers arising from germline BRCA1 mutations are usually high grade, clinically aggressive tumors that are associated with a poor prognosis. Alterations in a number of pathways contribute to this phenotype including genomic stability, cell cycle and cell proliferation. RNA splicing is also often perturbed in cancers but it is not known whether this contributes to tumorigenesis in BRCA1-related breast cancers. Methods: Using next-generation mRNA sequencing (RNA-Seq), we compared the transcriptome of four breast cancer cell lines and three primary breast cancers from BRCA1 germline mutation carriers to five breast cancer cell lines and two breast cancers occurring in non-BRCA mutation carriers. We created a systematic computational pipeline to detect potentially abnormal novel splice junctions (i.e. absent from RefSeq and UCSC) with irregular expression levels in BRCA1¬-related breast cancers compared to the non-BRCA control cancers. Results: We found that a greater number of common splice junctions not annotated in RefSeq or UCSC databases were either up- or down-regulated in the BRCA1-related breast cancers than expected by chance. We present a list of highly recurrent splicing events, with the most discordant expression patterns compared to other breast cancers. Most of these are predicted to disrupt protein domains, cause frameshifts or are located in important regulatory genes. However, we were not able to detect any abnormally spliced transcripts which clearly contribute to the phenotype of the BRCA1-related breast cancers. Conclusions: RNA-Seq is a powerful tool for analyzing abnormal transcripts on a genome-wide scale. With RNA-Seq, several potentially abnormal transcripts were found to be more highly expressed in the BRCA1-related breast cancers than in the non-BRCA1 breast cancer controls. However, we did not find evidence that highly recurrent, highly expressed abnormal alternative splice variants of specific genes are predominant drivers of tumorigenesis in BRCA1-related breast cancers.