Newer Therapeutic Targets in Head and Neck Cancers

Study Overview
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Brief Summary
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Based on the recently identified mutations in HNSCCs, the major pathologic pathways implicated in the tumorigenesis of HNSCC include dysregulation of four processes: cellular survival and proliferation (e.g., TP53, EGFR, MET, and PIK3CA); cell-cycle control (e.g., CDKN2A and CCND1); cellular differentiation (e.g., NOTCH1); and Adhesion and invasion signaling (e.g., FAT1).7 TP53, EGFR, PIK3CA, CDKN2A, CCND1, and MET participate in several common signaling pathways. Alterations of these genes are most frequently seen in alcohol and tobacco-related HNSCC. However their role in prognostication and selection of therapeutics is not known

Detailed Description
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Sample size: Patients with squamous cell carcinoma of oral cavity fulfilling the inclusion and exclusion criteria and willing to participate will be included in this study. Method: Comprehensive history and physical examination of the patients will be carried out and all the details will be recorded in the preset proforma. All routine investigations as indicated including a biopsy to establish a diagnosis and CT of the head and neck to measure the tumor dimensions and stage the disease before initiation of treatment will be recorded. The paraffin embedded tissue will be studied for expression of various genetic mutations using NGS platform. Brush cytology will be collected in liquid medium for HPV typing using PCR. The Ion AmpliSeq™ Cancer Hotspot Panel v3 will be used to detect hotspot regions of 161 oncogenes and tumor suppressor genes This research panel, with improved primer design, contains 4,648 total 4 pools (DNA pool 1: 1,891 amplicons. DNA pool 2: 1,890 amplicons. RNA pool 1: 447 amplicons. RNA pool 2: 420 amplicons.), enabling researchers to sequence challenging samples of formalin-fixed, paraffin-embedded (FFPE) tissue. Copy Number Variants (CNVs), Gene Fusions, Insertions-Deletions (indels), Single Nucleotide Polymorphisms (SNPs), Somatic Variants are identified. HPV DNA PCR METHODOLOGY DNA will be isolated by using QIAamp DNA mini kit (Qiagen, Hilden, Germany). The presence of HPV will be detected by using the digene® HC2 HPV DNA Test- The digene HC2 HPV DNA Test uses Hybrid Capture 2 technology to detect high-risk and low-risk HPV genotypes. It uses in vitro microplate assay based on signal-amplified nucleic acid hybridization that uses chemiluminescence for the qualitative detection of 18 types of human papillomavirus (HPV) (13 high risk and 5 low risk) DNA in cervical specimens. The test uses an RNA probe cocktail that detects 13 high-risk HPV types (16/18/31/33/35/39/45/51/52/56/58/59/68) and 5 low-risk types (6/11/42/43/44).

Official Title
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A Cohort Study to Identify Newer Therapeutic Targets in Head and Neck Cancers

Conditions
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Head Neck Cancer, Oral Cancer

Intervention / Treatment
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* Other: Next generation Sequencing


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: Histologically proven cases of primary head and neck cancers. Exclusion Criteria: Patients under 18 years of age Pregnant and lactating women Multiple cancers or patients with cancer of other sites.

Ages Eligible for Study
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Minimum Age: 18 Years
Maximum Age: 100 Years

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| Head neck cancer<br>Histologically diagnosed cases of head and neck cancer | Other: Next generation Sequencing<br>* Next generation sequencing for 161 genes<br>|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Over all survival | Survival time from the diagnosis to death | 10 years | 
| Relapse free survival | survival time from diagnosis to recurrence or metastasis | 10 years | 

Secondary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Progression free survival | The time from the diagnosis to progression of disease | 5 years | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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Next generation sequencing, predictive biomarker