Abstract 483: Detection of circulating tumor DNA in oral rinses and plasma from head and neck cancer cases in Argentina
Authors: Perdomo Sandra , Avogbe Patrice , Vilensky Marta , Mckay James , Brennan Paul 
Published: July 2016

Abstract
In 2012, almost 700,000 new head and neck cancer (HNSCC) cases were estimated to occur worldwide with two thirds of those cases occurring in developing countries. Within the geographic areas in Latin America, characterized by high incidence rates of head and neck cancer, the region comprising Argentina, southern Brazil and Uruguay has the highest levels of incidence. Despite current therapy approaches, the survival rate is around 50%, and the main reason for treatment failure is the frequent development of regional recurrences, affecting around 30% of patients. In this context the use of ctDNA (specific biomarker for tumors) using techniques of mass sequencing (high sensitivity and specificity) is presented as a promising tool for noninvasive diagnosis and monitoring of HNSCC cases.
Our primary goal was to provide a comprehensive evaluation of the presence of ctDNA in both plasma and oral rinses from a series of HNSCC cases without previous knowledge of tumor mutational status. 43 cases diagnosed as head and neck squamous cell carcinoma were selected from a multi center case-control study conducted in Argentina between 1998 and 2002. Subsite and stage distribution was as follows: 14 oral cavity, 6 oropharynx, 1 hypopharynx, 15 larynx and 7 overlapping lesions. 6 cases were stage III and 17 stage IV. Additionally, 50 controls matched by center, age, sex, smoking and alcohol status were included to assess a threshold of the background noise after sequencing.
Targeted sequencing was performed independently in duplicate on plasma, oral rinses, germline DNA and the tumor material using the Ion Proton™ System. Sequencing included the entire coding region of TP53 as the most frequently mutated gene in HNSCC. Both Plasma and oral rinses samples were sequenced at an average depth of 10000X. For somatic variant calling we used a recently developed new statistical model and a bioinformatics pipeline based on Poisson distribution for estimation of sequencing errors distribution to accurately identify variants above the sequencing background. Statistical tests were carried out in R statistical programming environment.
74% of tumor samples sequenced harboured at least one TP53 somatic mutation. 10 TP53 variants were identified in the corresponding plasma samples and 1 of these variants matched the tumor mutation, possibly reflecting high tumor heterogeneity. In contrast, 90% of the variants detected in the tumor were also found in in the oral rinses with allelic frequencies ranging from 0.002 to 0.05 showing higher specificity of oral rinses as a surrogate sample for mutation detection.
The detection and analysis of ctDNA in noninvasive samples might be included as a potential biomarker to improve early diagnosis and patient monitoring in HNSCC cases.
Citation Format: Sandra Perdomo, Patrice Avogbe, Marta Vilensky, James Mckay, Paul Brennan. Detection of circulating tumor DNA in oral rinses and plasma from head and neck cancer cases in Argentina. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 483.