Identification of gene fusion transcripts by transcriptome sequencing in <it>BRCA1</it>-mutated breast cancers and cell lines

• Main Authors: Ha Kevin CH (Author), Lalonde Emilie (Author), Li Lili (Author), Cavallone Luca (Author), Natrajan Rachael (Author), Lambros Maryou B (Author), Mitsopoulos Costas (Author), Hakas Jarle (Author), Kozarewa Iwanka (Author), Fenwick Kerry (Author), Lord Chris J (Author), Ashworth Alan (Author), Vincent-Salomon Anne (Author), Basik Mark (Author), Reis-Filho Jorge S (Author), Majewski Jacek (Author), Foulkes William D (Author)
• Format: Book
• Published: BMC, 2011-10-01T00:00:00Z.
• Subjects: article
• Online Access: Connect to this object online.

Summary

<p>Abstract</p> <p>Background</p> <p>Gene fusions arising from chromosomal translocations have been implicated in cancer. However, the role of gene fusions in <it>BRCA1</it>-related breast cancers is not well understood. Mutations in <it>BRCA1 </it>are associated with an increased risk for breast cancer (up to 80% lifetime risk) and ovarian cancer (up to 50%). We sought to identify putative gene fusions in the transcriptomes of these cancers using high-throughput RNA sequencing (RNA-Seq).</p> <p>Methods</p> <p>We used Illumina sequencing technology to sequence the transcriptomes of five <it>BRCA1</it>-mutated breast cancer cell lines, three <it>BRCA1</it>-mutated primary tumors, two secretory breast cancer primary tumors and one non-tumorigenic breast epithelial cell line. Using a bioinformatics approach, our initial attempt at discovering putative gene fusions relied on analyzing single-end reads and identifying reads that aligned across exons of two different genes. Subsequently, latter samples were sequenced with paired-end reads and at longer cycles (producing longer reads). We then refined our approach by identifying misaligned paired reads, which may flank a putative gene fusion junction.</p> <p>Results</p> <p>As a proof of concept, we were able to identify two previously characterized gene fusions in our samples using both single-end and paired-end approaches. In addition, we identified three novel in-frame fusions, but none were recurrent. Two of the candidates, <it>WWC1-ADRBK2 </it>in HCC3153 cell line and <it>ADNP-C20orf132 </it>in a primary tumor, were confirmed by Sanger sequencing and RT-PCR. RNA-Seq expression profiling of these two fusions showed a distinct overexpression of the 3' partner genes, suggesting that its expression may be under the control of the 5' partner gene's regulatory elements.</p> <p>Conclusions</p> <p>In this study, we used both single-end and paired-end sequencing strategies to discover gene fusions in breast cancer transcriptomes with <it>BRCA1 </it>mutations. We found that the use of paired-end reads is an effective tool for transcriptome profiling of gene fusions. Our findings suggest that while gene fusions are present in some <it>BRCA1</it>-mutated breast cancers, they are infrequent and not recurrent. However, private fusions may still be valuable as potential patient-specific biomarkers for diagnosis and treatment.</p>

Item Description

10.1186/1755-8794-4-75
1755-8794