Next generation sequencing of cell free circulating tumor DNA in blood samples of recurrent and metastatic head and neck cancer patients

Abstract

Background Effective targeted therapy is lacking in head and neck cancer (HNC). The use of next generation sequencing (NGS) has been suggested as a way to potentially expand therapeutic options and improve outcomes. This study was performed in order to further characterize blood sample cell-free circulating tumor DNA (ctDNA) in advanced HNC patients, to determine its ability to identify actionable mutations, and to elucidate its potential role in patient management. Methods Retrospective analysis of 60 patients with recurrent and metastatic (R/M) HNCs who underwent molecular profiling of blood samples utilizing Guardant360, a 70-gene ctDNA NGS platform. ctDNA sequencing data was compared to tumor NGS data, when available. Best response to therapy was assessed using RECIST measures. Results The most common tumor type was oropharyngeal squamous cell carcinoma (n=21). Other cancer types included salivary gland (n=8) and thyroid (n=4). The most common mutations identified by blood analysis were TP53 (68% of patients), PIK3CA (34% of patients), NOTCH1 (20% of patients), and ARID1A (15% of patients). These findings were consistent with results from tumor sequencing data (n=30) where TP53 (48%) and PIK3CA (24%) were also the most common. Seventy-three percent (n=22) of patients had alterations identified in blood that were not present in tumor specimens. In patients with squamous cell carcinoma, 66% had an off-label option identified and 90% had a trial option identified, while 50% of patients with salivary primaries had off-label option identified and 75% had trial options identified. All patients (n=3, 100%) with thyroid primaries had off-label and clinical trial options identified. Of patients with actionable mutations, 13% (n=8) received matched targeted therapy (MTT). Three patients had stable disease (37.5%), 3 had progressive disease (37.5%), and 2 (25%) were not evaluated at the time of follow up. Of those who did not receive targeted therapy (n=21), 11 patients had stable disease (52.4%), 9 had progressive disease (42.9%), and 1 had a complete response (4.8%). Conclusions Alterations identified by ctDNA may help inform management decisions in advanced HNC. The majority of patients had unique mutations identified on ctDNA. The role of NGS of ctDNA should be explored in future studies.

Gene Mutations in Circulating Tumour DNA as a Diagnostic and Prognostic Marker in Head and Neck Cancer—A Systematic Review

“…According to the TNM staging system, patients across the spectrum of stages, with prevailing advanced cases, participated in the studies. In some of the studies, the tumour stage was not specified [27,[33][34][35]. One size of the patient group; 2 tumour sites: OSCC-oral squamous cell carcinoma, OPSCC-oropharyngeal squamous cell carcinoma, HPSCC-hypopharyngeal squamous cell carcinoma, LSCC-laryngeal squamous cell carcinoma, SG-salivary glands, TG-thyroid gland, HN-head and neck carcinoma without further specification.…”

“…In all of these studies, patients with HNSCC across anatomical locations were included (oral cavity, oropharyngeal, hypopharyngeal or laryngeal SCC). In one study, the primary site was not specified [ 35 ], and one group also included the patients with salivary gland and thyroid cancers [ 27 ]. This sub-group of patients was, however, not included in specific analyses of ctDNA.…”

“…According to the TNM staging system, patients across the spectrum of stages, with prevailing advanced cases, participated in the studies. In some of the studies, the tumour stage was not specified [ 27 , 33 , 34 , 35 ].…”

“…Among the conventional techniques are real-time PCR (qPCR), digital PCR-based methods, such as BEAM (bead-based emulsion PCR), ARMS (amplification-refractory mutation system) or and ddPCR (digital droplet PCR) [ 24 , 25 ]. Another option is sequencing, specifically next generation sequencing (NGS) with various modifications, which, thanks to reduced costs and relatively rapid turnaround time, is currently being put under the spotlight [ 26 , 27 ].…”

“…There are still many unresolved issues regarding the preanalytical phase of liquid biopsy sample processing, such as the time between blood collection and isolation, centrifugation methods, options of sample freezing and the freezing time, and ctDNA source selection [ 28 , 29 , 30 ]. In connection with HNSCC and liquid biopsy, cfDNA sources, such as whole blood, plasma or saliva, are discussed in the literature [ 3 , 8 , 27 , 31 , 32 , 33 , 34 , 35 ]. For ctDNA analysis, blood plasma is preferred over serum due to the lower background level of cfDNA, which is 2–24 fold higher in serum [ 36 ].…”