The advent of next-generation sequencing (NGS) technologies has enabled the rapid identification of unknown fusion genes. To detect gene fusions by NGS, genomic DNA can be used for whole genome or whole exome sequencing, or RNA can be used for whole transcriptome sequencing (RNA-Seq). In comparison to whole genome sequencing, which interrogates large intronic segments that likely contain biologically irrelevant fusions, whole exome sequencing only assays the exons. However, the additional exon enrichment step (hybrid capture) involved in whole exome sequencing adds to the overall cost and time to perform these assays. RNA-Seq, which interrogates only expressed fusions, is a faster, more cost-effective approach to detect biologically relevant gene fusions. Though RNA-Seq is somewhat limited in its ability to detect low expression levels of transcripts, target-enrichment strategies can be used to increase read depth over target regions of interest, thereby enhancing detection sensitivity.
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