The applications of circulating cell-free DNA for oral squamous cell carcinoma patients as non-invasive diagnostics of structural variants and fusions

Circulating cell-free DNA (cfDNA) has been widely used as a prognostic marker for different cancers. In this study, we used cfDNA from oral squamous cell carcinoma (OSCC) patients to study various correlation factors that could improve the disease early-stage diagnostics and/or prognosis. We found that OSCC patient cfDNA concentration can serve as an indicator of tumor stage, malignancy, and survival prognosis. Deep genome sequencing of cfDNA revealed genomic alterations, such as copy number variations, fusion gene identification, and viral integrations. Copy number variation analysis suggested correlation with amplification and deletion in chromosome 1 at loci 1q, 2q, 3p, 3q and 8q22. Moreover, at these loci, amplification of TP53, PIK3CA and other genes related to keratinization in OSCC patients were observed. In addition, we identified the novel fusion gene, TRMO-TRNT1 ‘chimera’, in seven high-grade tumor samples. The parental genes of this chimera, TRMO and TRNT1, are known to play roles in tRNA modification and DNA repair, respectively. Therefore, our study indicates that liquid biopsy may thus serve as a sensitive tool to study OSCC patient genomic alterations by exploring cfDNA circulating in the plasma, by means of an easy-to-use blood test. Finally, we detected integrations of human papilloma virus, simian virus, and enterovirus in the OSCC samples, that may point to the origins of OSCC.