Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines.

BACKGROUND: Gene fusions arising from chromosomal translocations have been implicated in cancer. However, the role of gene fusions in BRCA1-related breast cancers is not well understood. Mutations in BRCA1 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). METHODS: We used Illumina sequencing technology to sequence the transcriptomes of five BRCA1-mutated breast cancer cell lines, three BRCA1-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. RESULTS: 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, WWC1-ADRBK2 in HCC3153 cell line and ADNP-C20orf132 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. CONCLUSIONS: In this study, we used both single-end and paired-end sequencing strategies to discover gene fusions in breast cancer transcriptomes with BRCA1 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 BRCA1-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.

Rethinking ovarian cancer: recommendations for improving outcomes.

There have been major advances in our understanding of the cellular and molecular biology of the human malignancies that are collectively referred to as ovarian cancer. At a recent Helene Harris Memorial Trust meeting, an international group of researchers considered actions that should be taken to improve the outcome for women with ovarian cancer. Nine major recommendations are outlined in this Opinion article.

Hypertension treatment and control rates: chart review in an academic family medicine clinic.

OBJECTIVE: To characterize hypertension management in an academic family medicine clinic. DESIGN: Cross-sectional chart review. SETTING: Academic family medicine clinic in Edmonton, Alta. PARTICIPANTS: A total of 210 patients with 1 or more visits for hypertension during the previous 3 years. MAIN OUTCOME MEASURES: Patient characteristics, current antihypertensive therapies, most recent blood pressure measurements, and compelling indications according to the 2006 Canadian Hypertension Education Program recommendations. RESULTS: A total of 185 subjects (88%) were prescribed antihypertensive medications, and 89 (42%) had controlled hypertension. Younger subjects, people with diabetes, and people not receiving antihypertensive medication therapy appeared less likely to have controlled hypertension. There were 76 subjects (36%) prescribed 1 antihypertensive medication, 65 subjects (31%) prescribed 2 antihypertensive medications, and 44 (21%) prescribed 3 or more antihypertensive medications. Angiotensin-converting enzyme inhibitors were prescribed for 51% of the subjects, diuretics for 47%, beta-blockers for 27%, calcium channel blockers for 23%, angiotensin receptor blockers for 20%, and alpha-blockers for 1%. CONCLUSION: Hypertension treatment and control rates in this academic family medicine clinic appear to be better than those in the general population. Following the principles of a continuous quality improvement process, this information will serve as an important foundation for identifying areas to improve hypertension management in the clinic.