Abstract PD05-07: Detection of fusion transcripts among 100 breast cancer samples by next generation sequencing
Authors: Kim J , Han W , Moon H-G , Ahn SK , In Y-H , Kim S , Lee H-S , Lee JW , Kim JY , Kim T , Kim MK , Noh D-Y 
Published: August 2014

Abstract
Introduction Fusions genes and it's products are widely applied as biomarker and therapeutic target in hematopoietic cancers. It's role as a “driver” of oncogenic pathway have also been proved in several epithelial solid cancers including prostate, lung and breast cancer. We performed high throughput next generation sequencing technique (RNA-Seq) to identify the novel fusion transcript(FT) in a large set of primary breast cancer samples.
Materials and Method Total RNA was prepared using the Illumina® TrueSeq™ RNA sample Preparation Kit and TrueSeq mRNA library was constructed. Clustering was done with HiSeq 2000 and Solexa's sequencing was performed. We used tissues extracted from previously collected 100 fresh-frozen primary breast cancer samples obtained after surgical resection. Among 100 samples, 1 failed to pass the process of RNA sequencing and no expression of fusion transcripts were observed in 7 samples resulting in 92 samples with mRNA-Seq data of fusion transcripts. Fourteen(15.2%) samples were cases with distant metastasis during follow up. Estrogen receptor(ER) was positive in 40(43.5%) samples and 23(25%) were triple negative breast cancer.
Results and discussion We detected 958 fusion transcripts among 92 tumors and 58 were chosen for tumor-specific fusion transcript candidate (Fragments per kilo-base of exon per million fragments mapped, FPKM&gt;500 and 3 times higher than average, probability&gt;0.6). Most of the fusion transcripts were “private”, expressed only in one sample. Estrogen receptor(ER) positive breast cancer samples had 29 fusion transcripts and ER negative had 25 fusion transcripts among the 58 tumor-specific candidates. HER2 negative samples exhibited 29 fusion transcripts while 15 were identified in HER2 negative samples. Triple negative sample showed 4 TF candidates. Among the 17 recurrence samples 190 fusion transcripts were identified. Of the 190 fusion transcripts in recurred samples, 24 candidates of recurrence-specific FTs were chosen by it's high expression level (FPKM&gt;300 and 2 times higher than average, probability&gt;0.5). Eight were expressed both in recurred, non-recurred samples and 16 were exclusively expressed in recurred samples. No fusion transcript matched directly with the currently known actionable gene-list owing to the limited number while majority is unexploited. Further validation and functional pathway analysis is under progress to ascertain the role of highly suspected fusion transcripts with oncogenic property. Considering the high incidence of breast cancer world-wide, identification of TF expressed even in only a minor percentage among the whole breast cancer population, if druggable, it can be applicable to large number of patients.
Conclusion We performed a whole-transcriptome sequencing with a large set of primary breast cancer samples and detected abundant fusion transcripts. The majority of breast cancer(92.9%, 92/99) had at least one fusion transcript suggesting it's role during the tumorigenesis and progression process. With scarce evidence and confirmed data of actionable fusion gene and it's product, data interpretation for it's clinical utility is rather complicated. Accumulation of these large set data of fusion transcript must serve as a groundwork for future work.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD05-07.