Abstract 5603
Background
Gene fusions caused by chromosomal rearrangements play an important role in oncogenesis, the progression of cancer and the selection of targeted therapies. Next-generation sequencing (NGS) using RNA enables sensitive, specific and precise detection of potentially clinically relevant gene fusions, especially when the fusion breakpoint is known. We have developed an NGS solution appropriate for FFPE tissues to detect fusion biomarkers in routine clinical research.
Methods
Fusion content was selected based on prioritization of actionability, verified fusion isoforms reported in the literature and collaborations, as well as prevalence of solid tumor fusion driver genes. The assay was designed to use Ion AmpliSeq multiplex PCR chemistry using manual or automated library preparation, automated templating on the Ion Chef, and sequencing on the Ion Torrent GeneStudioTM S5 sequencing platform. The analysis was supported by fully automated analysis software that performs sample QC, read-filtering, fusion calling and reporting. Streamlined access to decision support software was enabled by Oncomine™ Reporter.
Results
Over 1200 targeted isoforms from over 50 known fusion driver genes were incorporated into the assay that included prominent fusion drivers such as ALK, RET, ROS1, NTRK1/2/3 and FGFR1/2/3, and intragenic fusion events in MET, EGFR, BRAF and AR. The assay also reported non-targeted fusion events in relevant driver genes by using a novel statistically significant expression imbalance algorithm comparing 5’- and 3’- end gene expression. A preliminary development study was performed using commercially available total RNA for a Tri-Fusion control and Seraseq™ Fusion RNA Mix v3 where all of the expected fusions were detected with 100% sensitivity and specificity. Results were also concordant when characterized FFPE tumor samples with known fusion targets were tested using the assay.
Conclusions
A comprehensive NGS assay was developed to support clinical research in oncology for detecting relevant RNA structural alterations from solid tumor FFPEs. An update on assay performance will be presented.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
Thermo Fisher Scientific.
Funding
Has not received any funding.
Disclosure
V.K. Mittal: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. S.P. Myrand: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. D. Cyanam: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. P.D. Williams: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. G.G. Bee: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. A. Marcovitz: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. R. Gottimukkala: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. F. Hyland: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. C. Allen: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. E. Wong-Ho: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. S. Sadis: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. C. Van Loy: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. J. Kilzer: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. N. Khazanov: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific.
Resources from the same session
4096 - Patient experience and use of an intervention combining nurse-led telephone and technologies for the monitoring of oral cancer medication
Presenter: Marie Ferrua
Session: Poster Display session 3
Resources:
Abstract
6042 - Harnessing nurse leadership to implement a project for electronic scheduling of chemotherapy
Presenter: Emma Masters
Session: Poster Display session 3
Resources:
Abstract
3123 - Turkish Cancer Patients’ Preference for Information and Communication Technologies
Presenter: Esra ildes
Session: Poster Display session 3
Resources:
Abstract
6062 - Unmet Needs in Oncology Research related to radiological response evaluation: a multi-center survey in three European countries
Presenter: Sophie Nisse Durgeat
Session: Poster Display session 3
Resources:
Abstract
6109 - A program implementation to facilitate intraoperative brachytherapy between hospitals
Presenter: Marc Garcia Casellas
Session: Poster Display session 3
Resources:
Abstract
1772 - Using Mobile-Based Health Care Applications Outcomes: Mini Systematic Review
Presenter: Aydanur Aydin
Session: Poster Display session 3
Resources:
Abstract
2792 - Evaluation of an education program for cancer patients receiving chemotherapy
Presenter: Iraqi Amina
Session: Poster Display session 3
Resources:
Abstract
3715 - iGestSaúde: Application for self-management of symptoms during chemotherapy treatment
Presenter: Bruno Magalhaes
Session: Poster Display session 3
Resources:
Abstract
3854 - Palliative care requirements of cancer patients and investigation of knowledge and expectations related to palliative care of the patients and their families
Presenter: Ozlem Topkaya
Session: Poster Display session 3
Resources:
Abstract
4997 - Hospice care, what to expect? An exploration of the expectation of future hospice patients
Presenter: Merel van Klinken
Session: Poster Display session 3
Resources:
Abstract