NYMC Faculty Publications

Detecting Salivary Host and Microbiome RNA Signature for Aiding Diagnosis of Oral and Throat Cancer

Guruduth Banavar, Viome Research Institute, Viome Life Sciences Inc, New York City, NY, and Seattle, WA, USA. Electronic address: guru@viome.com.
Oyetunji Ogundijo, Viome Research Institute, Viome Life Sciences Inc, New York City, NY, and Seattle, WA, USA.
Cristina Julian, Viome Research Institute, Viome Life Sciences Inc, New York City, NY, and Seattle, WA, USA.
Ryan Toma, Viome Research Institute, Viome Life Sciences Inc, New York City, NY, and Seattle, WA, USA.
Francine Camacho, Viome Research Institute, Viome Life Sciences Inc, New York City, NY, and Seattle, WA, USA.
Pedro J. Torres, Viome Research Institute, Viome Life Sciences Inc, New York City, NY, and Seattle, WA, USA.
Lan Hu, Viome Research Institute, Viome Life Sciences Inc, New York City, NY, and Seattle, WA, USA.
Tarun Chandra, EmpriQA LLC, Long Grove, IL, USA.
Andrew Piscitello, EmpriQA LLC, Long Grove, IL, USA.
Liz Kenny, Royal Brisbane and Women's Hospital and The School of Medicine, University of Queensland, Brisbane, QLD, Australia.
Sarju Vasani, Department of Otolaryngology, Royal Brisbane and Women's Hospital and Faculty of Medicine, University of Queensland, Herston, QLD, Australia.
Martin Batstone, Oral and Maxillofacial Surgery Department, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia.
Nevenka Dimitrova, New York Medical College, Valhalla, NY, USA.
Momchilo Vuyisich, Viome Research Institute, Viome Life Sciences Inc, New York City, NY, and Seattle, WA, USA.
Salomon Amar, New York Medical College, Valhalla, NY, USA.Follow
Chamindie Punyadeera, The Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia. Electronic address: c.punyadeera@griffith.edu.au.

Author Type(s)

Faculty

DOI

10.1016/j.oraloncology.2023.106480

Journal Title

Oral Oncology

First Page

106480

Document Type

Article

Publication Date

10-1-2023

Department

Pathology, Microbiology and Immunology

Second Department

Pharmacology

Abstract

OBJECTIVE: Oral squamous cell carcinoma (OSCC) and oropharyngeal squamous cell carcinoma (OPSCC) can go undetected resulting in late detection and poor outcomes. We describe the development and validation of CancerDetect for Oral & Throat cancer™ (CDOT), to detect markers of OSCC and/or OPSCC within a high-risk population. MATERIAL AND METHODS: We collected saliva samples from 1,175 individuals who were 50 years or older, or adults with a tobacco use history. 945 of those were used to train a classifier using machine learning methods, resulting in a salivary microbial and human metatranscriptomic signature. The classifier was then independently validated on the 230 remaining samples prospectively collected and 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 OSCC, and 84.2 % for participants with OPSCC. Similar classification results were observed among people in early stage (stages I & II) vs late stage (stages III & IV). CONCLUSIONS: CDOT is a non-invasive test that can be easily administered in dentist offices, primary care centres and specialised cancer clinics for early detection of OPSCC and OSCC. This test, having received FDA's breakthrough designation for accelerated review, has the potential to enable early diagnosis, saving lives and significantly reducing healthcare expenditure.

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