Abstract 314P
Background
Infectious agents account for 13-20% of new cancer cases worldwide and may have a role in the origin and progression of cancers and pathogenesis. Unfortunately, most commercially available genomic NGS assays neglect this increasingly important information. Herein, we describe next-generation sequencing (NGS) assays, OncoKey SL60 Plus and SL 525 Plus, that identifies DNA and RNA variants, as well as microbial signatures in various tumor types.
Methods
The automated hybridization capture-based NGS tests, OncoKey SL60 Plus and SL525 Plus, target 60 and 525, respectively, clinically relevant genes for small variants, MSI, splice variants, CNV and fusions, including 6 oncogenic viruses: EBV, HCV, HBV, MCPyV, KSHV and 30 subtypes of HPV, and 4 oncogenic bacteria: H. pylori, S. Typhi, S. gallolyticus and C. pneumoniae. Various commercial FFPE reference materials, cell lines harboring oncogenic viruses, and 32 FFPE clinical samples were characterized with the assays and sequenced on both the Illumina® MiSeq and NextSeq Systems.
Results
All expected DNA variants and RNA fusions in reference standards from as little as 40 ng of DNA/RNA input. In clinical samples, NGS results generally concurred with previous FISH/IHC and other molecular characterization thus demonstrating and equivalent accuracy. MCPyV and HBV were detected in MKL-1 and PLC/PRF/5 cell lines respectively, both of which are known carriers. Of the 32 FFPE samples, HPV16 and EBV were identified in 2 head and neck samples thus suggesting possible etiological roles. The presence of HPV and EBV was subsequently confirmed with IHC. In the EBV positive sample, BRCA2 p.G602fs mutation was also detected thus suggesting the patient may be a suitable candidate for PARP inhibitor therapies. In the HPV16 positive sample, PIK3CA p.R88Q was detected thus suggesting the patient may benefit from enroling into PIK3CA inhibitor trials.
Conclusions
Identifying virus and bacteria as etiological agents aids our understanding of the microbiome and cancer, diagnosis and treatment. NGS tools, such as the OncoKey SL60/525 Plus, provide rapid, high throughput and cost-effective strategies for comprehensive microbial and genomic profiling.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
Vela Research Singapore.
Funding
Vela Research Singapore.
Disclosure
M.Q. Yee, Y.L. Kok, P. Ariyaratne, Y. Yu, O. Scully, D. Tay, C. Tang, T. Ong, H. Suhardi, K.K.M. Aye, A.W. Kyaw, E.Wee, C. Lee: Full/Part-time employment: Vela Research Singapore Pte. Ltd.
Resources from the same session
253P - Non-Epithelial Tumours of Ovary, An Experience from Qatar
Presenter: Ammar Madani
Session: e-Poster Display Session
260P - A phase I study of copanlisib, a pan-class I phosphatidylinositol 3-kinase (PI3K) inhibitor, in Chinese patients with relapsed indolent non-Hodgkin lymphoma (iNHL)
Presenter: Yuqin Song
Session: e-Poster Display Session
261P - Clinical outcomes of early-progressed follicular lymphoma in Korea: A multicenter, retrospective analysis
Presenter: Jun Ho Yi
Session: e-Poster Display Session
262P - Correlation between phosphorylated pI3K expression, phosphorylated AKT, and phosphorylated MTOR with serum dehydrogenase lactate level in non-Hodgkin lymphoma
Presenter: Hary Gustian
Session: e-Poster Display Session
263P - Good response to chemotherapy in primary CNS lymphoma may not translate into significant neurocognitive improvement in comatose patients
Presenter: Ryan Lim
Session: e-Poster Display Session
264P - Treatment outcome of primary testicular lymphoma patients treated in tertiary care centre in Chennai
Presenter: Sivasubramaniam Kumaravelu
Session: e-Poster Display Session
271P - Cost-effectiveness of pembrolizumab as monotherapy or in combination with chemotherapy versus EXTREME regimen for the first-line treatment of recurrent or metastatic head and neck squamous cell carcinoma in Taiwan
Presenter: Cheng Hsu Wang
Session: e-Poster Display Session
272P - Early metabolic changes in PET metrics over initial 8 weeks of treatment in patients with advanced head neck squamous cell carcinomas treated with chemotherapy
Presenter: Ashish Vaidya
Session: e-Poster Display Session
273P - Long term outcomes of locally advanced & borderline resectable esthesioneuroblastoma and sinonasal tumour with neuroendocrine differentiation treated with neoadjuvant chemotherapy
Presenter: Vikas Talreja
Session: e-Poster Display Session
274P - Comparing comorbidity indices in predicting 90-day mortality after radical radiotherapy for head and neck cancer
Presenter: Therese Tsui
Session: e-Poster Display Session