Project description:We report the design and implementation of a "breakpoint analysis" pipeline to discover novel gene fusions by tell-tale transcript level or genomic DNA copy number transitions occurring within genes. We use this method to prioritize candidate rearrangements from high density array CGH datasets as well as exon-resolution expression microarrays. We mine both publicly available data as well as datasets generated in our laboratory. Several gene fusion candidates were chosen for further characterization, and corresponding samples were profiled using paired end RNA sequencing to discover the identity of the gene fusion. Using this approach, we report the discovery and characterization of novel gene fusions spanning multiple cancer subtypes including angiosarcoma, pancreatic cancer, anaplastic astrocytoma, melanoma, breast cancer, and T-cell acute lymphoblastic leukemia. Taken together, this study provides a robust approach for gene fusion discovery, and our results highlight a more widespread role of fusion genes in cancer pathogenesis.

2013-05-31 | GSE45133 | GEO

Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types (exon expression)

Project description:Custom Agilent 8 x 15K microarray interrogating exon level expression of a set of genes previously known to be involved in oncogenic rearrangements. The goal of this study was to discover novel gene fusions by screening for exonic expression transitions within individual genes. Sixteen cancer samples and cell lines, including eight positive controls with known gene fusions and eight sarcoma specimens, where gene fusions have yet to be discovered, were hybridized against a common reference mRNA control (pooled from 11 diverse cell lines)

2013-05-31 | E-GEOD-39287 | biostudies-arrayexpress

Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types (RNA-seq)

2013-05-31 | E-GEOD-45133 | biostudies-arrayexpress

NTRK gene fusions as novel targets of cancer therapy across multiple tumour types.

Project description: Not available

| S-EPMC5070277 | biostudies-literature

Genomic characterization and outcome evaluation of kinome fusions in lung cancer revealed novel druggable fusions.

Project description: Not available

| S-EPMC8433182 | biostudies-literature

Comprehensive genomic profiling identifies novel NTRK fusions in neuroendocrine tumors.

Project description: Not available

| S-EPMC6254675 | biostudies-literature