The Optimal Sequencing Depth of Tumor Biopsies for Identifying Clonal Cell Populations

The tumor content of a biopsy and the average depth of coverage are two essential aspects when performing DNA sequencing using next-generation sequencing technologies. The heterogeneous nature of cancer necessitates the identification of distinct clonal cell populations to better understand and treat cancer. Deep sequencing enables researchers to identify these populations, but no consensus on an optimal depth exists for identifying clonal populations. Data from eight deep sequenced oral squamous cell carcinoma biopsies obtained from three stage IV patients, with various degrees of tumor content, were used to randomly down sample the depth before being subjected to cluster analysis.
Source: Journal of Molecular Diagnostics - Category: Pathology Authors: Tags: Regular Article Source Type: research

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Objective Oral cancer ranks in the top three of all cancers in India, accounting for over 30% of all cancers reported. Elective neck dissection (END) is the mainstay of treatment in early disease. Performing ENDs for node negative (N0) patients can result in significant morbidity with questionable benefit and impair the patients’ quality of life. Sentinel Lymph Node Biopsy (SLNB), is an emerging investigation helping in risk stratification of patients with early oral cancer and node negative disease. SLNB is a simple, easy to perform investigation with a high sensitivity and plays a major role in avoiding neck diss...
Source: Nuclear Medicine Communications - Category: Nuclear Medicine Tags: Original Articles Source Type: research
Conclusions: This study successfully constructed a ceRNA network and a PPI network which play a crucial role in OSCC. A risk model was established to predict the prognosis, and four DERNAs are revealed with overall survival in patients with OSCC, suggesting that they may be potential biomarkers in tumor diagnosis and treatment.
Source: Frontiers in Oncology - Category: Cancer & Oncology Source Type: research
D, Braz-Silva PH Abstract Despite its effectiveness, radiochemotherapy treatment in the head and neck region is accompanied by acute oral complications such as oral mucositis, dysphagia, xerostomia, and dysgeusia. The aim of this study was to analyze and prospectively assess the frequency and evolution of acute oral complications during radiochemotherapy in patients diagnosed with squamous cell carcinoma in the head and neck region. We have analyzed oral complications of 20 patients during 6 weeks of radiochemotherapy treatment for squamous cell carcinoma. Oral mucositis was evaluated according to the World Healt...
Source: Ear, Nose and Throat Journal - Category: ENT & OMF Authors: Tags: Ear Nose Throat J Source Type: research
This study evaluated predictive factors for the feasibility of oral intake in adjuvant CCRT for patients with LASCCHN.MethodsThis study retrospectively analyzed 117 LASCCHN patients who underwent surgery followed by adjuvant CCRT with cisplatin at Shizuoka Cancer Center between April 2008 and December 2018. To investigate predictive factors for the feasibility of oral intake, tumor factors, treatment factors and social factors were included in multivariate analyses.ResultsOf the 117 patients, 25 received total laryngectomy and 92 received other surgery. In multivariate analysis, total laryngectomy [HR (hazard ratio) 0.09,P...
Source: International Journal of Clinical Oncology - Category: Cancer & Oncology Source Type: research
AbstractIdentification of effective targeted therapies for recurrent/metastatic head and neck squamous cell carcinoma (HNSCC) remains an unmet medical need. A patient with platinum‐refractory recurrent oral cavity HNSCC underwent comprehensive genomic profiling (CGP) that identified an activating MET mutation (R1004). The patient was treated with the oral MET tyrosine kinase inhibitor crizotinib with rapid response to treatment.Based on this index case, we determined the frequency of MET alterations in 1,637 HNSCC samples, which had been analyzed with hybrid capture‐based CGP performed in the routine course of clinical...
Source: The Oncologist - Category: Cancer & Oncology Authors: Tags: Head and Neck Cancers Precision Medicine Clinic: Molecular Tumor Board Source Type: research
ConclusionThe modified in-continuity resection is valuable for application in clinical practice for cT2N0M0 oral tongue squamous cell carcinoma.
Source: Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology - Category: ENT & OMF Source Type: research
Authors: Wu Q, Cao R, Chen J, Xie X Abstract Oral squamous cell carcinoma (OSCC) is a major type of malignant tumor of the oral cavity. Despite marked advances in the management and diagnosis of OSCC, the associated overall survival ratio has only exhibited a modest increase in recent years. The present study aimed to identify potential crucial genes associated with clinical features and prognosis for OSCC, and to provide a basis for further investigation. RNA-sequencing data and corresponding clinical information were downloaded from The Cancer Genome Atlas database and differentially expressed mRNAs (DEmRNAs) wer...
Source: Experimental and Therapeutic Medicine - Category: General Medicine Tags: Exp Ther Med Source Type: research
Source: OncoTargets and Therapy - Category: Cancer & Oncology Tags: OncoTargets and Therapy Source Type: research
We report an unprecedented case of squamous cell carcinoma (SCC) in the floor of mouth of a 23-year-old woman with XP. The patient was referred to the oncologist and, two months after surgical resection, underwent a single chemotherapy and radiotherapy session. However, she died 73 hours after undergoing her first chemotherapy session. Considering the unexpected outcome of this case, we also investigated possible exacerbated adverse effects of antineoplastic treatments (especially cisplatin-based chemotherapy) in XP patients, and discussed the main characteristics of the disease, especially cases with oral manifestations d...
Source: Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology - Category: ENT & OMF Source Type: research
Abstract AP-1 is a dimeric complex that is composed of JUN, FOS, ATF and MAF protein families. FOS-related antigen 1 (FRA1) which encoded by FOSL1 gene, belongs to the FOS protein family, and mainly forms an AP-1 complex with the protein of the JUN family to exert an effect. Regulation of FRA1 occurs at levels of transcription and post-translational modification, and phosphorylation is the major post-translational modification. FRA1 is mainly regulated by the mitogen-activated protein kinases signaling pathway and is degraded by ubiquitin-independent proteasomes. FRA1 can affect biological functions, such as tumor...
Source: Molecular Biology Reports - Category: Molecular Biology Authors: Tags: Mol Biol Rep Source Type: research
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