Objectives Oral squamous cell carcinoma (OSCC) and oropharyngeal squamous cell carcinoma (OPSCC) are the two major subtypes of head and neck cancer (HNC) that can go undetected resulting in late detection and poor outcomes. We describe the development and validation of a convenient and easy-to-use test, called CancerDetect for Oral & Throat cancerTM (CDOT), to detect markers of OSCC and/or OPSCC within a high-risk population using salivary metatranscriptomics. Materials and Methods We collected saliva samples from 1,175 unique individuals who were 50 years or older, or adults who had a history of tobacco use. All saliva samples were processed through a metatranscriptomic method to isolate microbial organisms and functions, as well as human transcripts. Of the 1175 samples, 945 were used to train a classifier using machine learning methods, resulting in a salivary RNA metatranscriptomic signature. The classifier was then independently validated on the 230 remaining samples unseen by the classifier, consisting of 20 OSCC (all stages), 76 OPSCC (all stages), and 134 negatives (including 14 pre-malignant). Results On the validation cohort, the specificity of the CDOT test was 94%, sensitivity was 90% for participants with a histopathological diagnosis of OSCC, and 84.2% for participants with a diagnosis of OPSCC. Similar classification results were observed among people in early stage (stages I & II) vs late stage (stages III & IV) of OSCC and OPSCC. Conclusions CDOT is a non-invasive test that can be easily administered in dentist offices, primary care centers and specialized cancer clinics for early detection of OPSCC and OSCC. This test, having received breakthrough designation by the US Food and Drug Administration (FDA), will broadly enable early diagnosis of OSCC and OPSCC, saving lives and significantly reducing healthcare expenditure.

Several authors (GB, OO, CJ, RT, FC, PJT, LK, ND, LH and MV) are employees of Viome Life Sciences, Inc. CP is currently receiving funding from the National Health and Medical Research Council (APP 2002576 and APP 2012560), Cancer Australia (APP1145657), Garnette Passe and Rodney Williams Foundation, NIH R21 and the RBWH Foundation. GB, OO, RT, MV, CP are co-inventors on a patent for a metatranscriptomics-based saliva test for OSCC and OPSCC.

Several authors (GB, OO, CJ, RT, FC, PJT, LK, ND, LH and MV) are employees of Viome Life Sciences, Inc. CP is currently receiving funding from the National Health and Medical Research Council (APP 2002576 and APP 2012560), Cancer Australia (APP1145657), Garnette Passe and Rodney Williams Foundation, NIH R21 and the RBWH Foundation.

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The study was approved by the Queensland University of Technology and University of Queensland Medical Ethical Institutional Boards (HREC no.: 1400000617 and HREC no.: 2017000662 respectively) and the Royal Brisbane and Womens Hospital (HREC no.: HREC/12/QPAH/381) Ethics Review Board. All participants gave their consent to participate in the study.

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