| The study of the transcriptome, which consists of all RNA molecules in a cell, has been important for elucidating the underlying mechanisms involved in the regulation and expression of genes. Here we describe two studies that apply current high-throughput techniques to investigate two genetic phenomena at the transcriptome level in humans: alternative splicing using whole-transcript gene expression microarrays, and gene fusions using massively parallel transcriptome sequencing (RNA-Seq). Alternative splicing is a post-transcriptional mechanism that allows for the production of multiple transcript isoforms of the same gene, resulting in increased transcriptome diversity. Recently, the global analysis of AS has been facilitated by the Exon Array, which feature oligonucleotide probes that target individual exons across the length of the gene. A similarly designed array, the Gene Array, was later released for measuring whole gene expression. In our first study, we questioned whether it could be used to study AS. We analyzed previously published data to show that expression profiling at both the gene and exon level was highly concordant between both platforms. This suggests that the Gene Array is capable of making AS observations like the Exon Array. Another profiling tool that has emerged is RNA-Seq, which enables the profiling of the entire transcriptome at single-base resolution. In the second study, we describe an RNA-Seq approach to detect gene fusions, which have been frequently implicated in cancer. The role of gene fusions in BRCA1-mutated breast cancers has not been well explored. BRCA1 is involved in tumour suppression by regulating DNA repair pathways and thus mutations in this gene can lead to increased chromosomal instability. While we hypothesized that this may lead to the creation of gene fusions, we did not find them to be significantly enriched. We identified, however, one novel gene fusion that was non-recurrent. With these two studies, we demonstrate how the continued advancement of investigative tools can aid in making biological discoveries. |
