Scientists studying cancer often look at DNA mutations to identify the changes occurring within different tumor types. But to gain a functional understanding of what is happening within cancer samples, it has become critically important to understand which mutated genes are actually expressed. Illumina has launched a new targeted panel that provides cost effective access to this information on a desktop sequencer.
We sat down with John Leite, Ph.D., Vice President, Oncology Market Development at Illumina and Gianni Cazzaniga, Head of the Diagnostic Laboratory at Centro Ricerca Tettamanti, Univ. Milano Bicocca in Italy, who beta tested the TruSight® RNA Pan-Cancer Panel to discuss how this panel is enabling cancer researchers.
What is the value of using RNA in cancer research?
John Leite, Ph.D.: Analysis of RNA is desirable for the simple reason that it provides us a view to what genetic alterations are being expressed and drive the malignant phenotype. Targeted RNA sequencing allows for gene expression analysis, variant detection, and identification of fusion genes, which is particularly important in cancer research.
Gianni Cazzaniga: We first used DNA panels, which were difficult to interpret because repetitive sequences prevented us from understanding which gene was involved in the translocation. The new TruSight RNA Pan-Cancer Panel simplifies the screening for variants and requires only a low amount of RNA input.
Tell us about the new TruSight RNA Pan-Cancer Panel and how it enables cancer research.
JL: The TruSight® RNA Pan-Cancer Panel offers insight into what is actively happening in cancer samples, giving researchers better coverage of low expressed genes and providing deeper coverage of relevant regions. In addition, it is specifically designed to detect fusions in over 500 genes frequently involved in malignancy.
By providing deeper coverage of relevant genes with fewer overall reads required, this new panel enables efficient, highly sensitive RNA sequencing (RNA-Seq) on a desktop sequencer. The panel can be used for gene expression analysis, variant detection, and for the detection of gene fusions including novel fusion gene partners, providing discovery power on a desktop sequencer.
Gianni, can you give a brief summary as to what your institution does, and the ultimate goal of your study?
GC: My Institution is the largest center treating childhood leukemia in Italy, with our laboratory being one of the two used for referrals for all young Italian patients. We are proud to be unique in having diagnostics, research and cure in the same Institute, with bi-directional interactions, with the final aim to transfer our research findings into diagnostics and to directly answer outstanding clinical questions.
What are you using TruSight RNA-Pan-Cancer for?
GC: We are using the panel mainly for detecting fusion genes deriving from chromosomal translocations, a structural variation in genes that contributes to leukemia in both children and adults. Some translocations are prognostic for disease outcome, and the gene fusion status can help to assess both the risk of relapse and the possibility of a cure.
What was your experience using the new TruSight RNA Pan-Cancer Panel?
GC: The new TruSight RNA Pan-Cancer Panel simplifies the screening for variants, allowing us to focus our research on candidate genes that are frequently involved yet to detect any gene fusion partner. It requires only a low amount of RNA input and the targeted approach simplifies the data analysis compared to more complex whole genome, exome or transcriptome approaches. The relatively short processing time has been an added benefit and the methodology is highly reproducible and has been consistent between different operators.
How has the panel helped your research?
GC: TruSight RNA Pan-Cancer has been helpful because it allows us to use the same NGS platform to comprehensively detect clinically important gene variants present at different levels. This avoids using multiple tests in the laboratory which can be time consuming and demanding. This panel provides a broader capacity to detect different variants with the same prognostic power as other approaches.
Were you able to discover any novel findings using the panel?
GC: Yes! With our first use of the panel we identified an important new gene fusion partner, and we have also identified known variants that were not detected by standard methods. We are very excited by the potential of our novel research findings as they could ultimately represent new targets for tailored treatment in poor risk patients.
How do you think this panel will help the field of cancer research?
JL: We hope to streamline gene fusion detection by providing cancer researchers access to focused oncology content with the power to discover new cancer-associated fusion genes. By providing this solution on a desktop sequencer, we hope to enable researchers who may be new to the power of RNA sequencing.
TruSight RNA Pan-Cancer is now available for pre-order and will begin shipping in January 2015.
For Research Use Only. Not for use in diagnostic procedures.