Abstract
Fusion genes are known to be key drivers of tumor growth in several types of cancer. Traditionally, detecting fusion genes has been a difficult task based on fluorescent in situ hybridization to detect chromosomal abnormalities. More recently, RNA sequencing has enabled an increased pace of fusion gene identification. However, RNA-Seq is inefficient for the identification of fusion genes due to the high number of sequencing reads needed to detect the small number of fusion transcripts present in cells of interest. Here we describe a method, Single Primer Enrichment Technology (SPET), for targeted RNA sequencing that is customizable to any target genes, is simple to use, and efficiently detects gene fusions. Using SPET to target 5701 exons of 401 known cancer fusion genes for sequencing, we were able to identify known and previously unreported gene fusions from both fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue RNA in both normal tissue and cancer cells.
Highlights
Cancer cells frequently contain chromosomal rearrangements that lead to the formation of fusion genes expressed in the cell [1]
While the BCR-ABL fusion gene leads to uncontrolled cell growth, when the fusion gene is identified in a patient, chronic myelogenous leukemia [2] (CML) can be treated successfully with tyrosine kinase inhibitors
The Ovation Fusion Panel Target Enrichment System only requires a single primer to hybridize to a fusion transcript in order to identify both gene partners, allowing any potential fusions involving targeted genes to be interrogated in a single tube assay
Summary
Cancer cells frequently contain chromosomal rearrangements that lead to the formation of fusion genes expressed in the cell [1]. These fusion genes can act as drivers for cell growth. The Philadelphia Chromosome rearrangement, originally identified in chronic myelogenous leukemia [2] (CML), is the result of a translocation between chromosomes 9 and 22 which leads to the expression of a fusion gene combining the BCR and ABL kinases [3]. While the BCR-ABL fusion gene leads to uncontrolled cell growth, when the fusion gene is identified in a patient, CML can be treated successfully with tyrosine kinase inhibitors. FISH has many problems as a technique including being a difficult, low throughput procedure, required knowledge of both
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
