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.
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.
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.
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.
Vela Research Singapore.
Vela Research Singapore.
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.