Ultrasensitive detection of tumor‐specific mutations in saliva of patients with oral cavity squamous cell carcinoma. Issue 10 (21st December 2020)

• Record Type: Journal Article
• Authors: Shanmugam, Ashwini; Hariharan, Arun K.; Hasina, Rifat; Nair, Jayalakshmi R.; Katragadda, Shanmukh; Irusappan, Sivaraj; Ravichandran, Aarthi; Veeramachaneni, Vamsi; Bettadapura, Radhakrishna; Bhati, Muddasir; Ramaswamy, Veena; Rao, Vishal U. S.; Bagadia, Ritvi K.; Manjunath, Ashwini; Manjunath, N. M. L.; Solomon, Monica Charlotte; Maji, Shiuli; Bahadur, Urvashi; Bettegowda, Chetan; Papadopoulos, Nickolas; Lingen, Mark W.; Hariharan, Ramesh; Gupta, Vaijayanti; Agrawal, Nishant; Izumchenko, Evgeny
• Is Part Of: Cancer. Volume 127:Issue 10(2021)
• Page Start: 1576
• Page End: 1589
• Publication Date: 2020-12-21
• Subjects: early detection -- liquid biopsy. mutation -- next‐generation sequencing (NGS) -- oral cavity squamous cell carcinoma (OCSCC) -- oral rinse -- saliva; Cancer -- Periodicals; Cancer -- Cytopathology -- Periodicals; 616.99405
• DOI: 10.1002/cncr.33393
• Languages: English
• ISSNs: 0008-543X

Abstract

Abstract : Background: Oral cavity squamous cell carcinoma (OCSCC) is the most common head and neck malignancy. Although the survival rate of patients with advanced‐stage disease remains approximately 20% to 60%, when detected at an early stage, the survival rate approaches 80%, posing a pressing need for a well validated profiling method to assess patients who have a high risk of developing OCSCC. Tumor DNA detection in saliva may provide a robust biomarker platform that overcomes the limitations of current diagnostic tests. However, there is no routine saliva‐based screening method for patients with OCSCC. Methods: The authors designed a custom next‐generation sequencing panel with unique molecular identifiers that covers coding regions of 7 frequently mutated genes in OCSCC and applied it on DNA extracted from 121 treatment‐naive OCSCC tumors and matched preoperative saliva specimens. Results: By using stringent variant‐calling criteria, mutations were detected in 106 tumors, consistent with a predicted detection rate ≥88%. Moreover, mutations identified in primary malignancies were also detected in 93% of saliva samples. To ensure that variants are not errors resulting in false‐positive calls, a multistep analytical validation of this approach was performed: 1) re‐sequencing of 46 saliva samples confirmed 88% of somatic variants; 2) no functionally relevant mutations were detected in saliva samples from 11 healthy individuals without a history of tobacco or alcohol; and 3) using a panel of 7 synthetic loci across 8 sequencing runs, it was confirmed that the platform developed is reproducible and provides sensitivity on par with droplet digital polymerase chain reaction. Conclusions: The current data highlight the feasibility of somatic mutation identification in driver genes in saliva collected at the time of OCSCC diagnosis. Abstract : A custom next‐generation sequencing test with unique molecular identifiers was designed that covers the coding regions of 7 frequently mutated genes in oral cavity squamous cell carcinoma (OCSCC). The minimal gene set predicted the incidence of at least 1 somatic aberration in 88% of patients with OCSCC, and the results demonstrate that this quick, sensitive, and noninvasive method can be used for the detection of low‐frequency, tumor‐associated mutations in saliva specimens collected from patients with OCSCC.