Identification of Prognostic Biomarkers for Progression of Invasive Squamous Cell Carcinoma

Study Overview
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Brief Summary
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The study will utilize both retrospective and prospective data collection from patients that already had a bronchoscopy and lung resection or will have a bronchoscopy and lung resection for squamous cell carcinoma. The investigators plan to prospectively collect 5 bronchoscopic biopsies, 10ml blood and one tumor and adjacent normal samples from 200 qualified patients who meet the study criteria.

Detailed Description
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The study will utilize both retrospective and prospective data collection from patients that have already had a bronchoscopy and lung resection or will have a bronchoscopy and lung resection for squamous cell carcinoma. The investigators plan to prospectively collect 5 bronchoscopic biopsies, 10ml blood and one tumor and adjacent normal samples from 200 qualified patients who meet the study criteria. If a patient has already had a bronchoscopy and has consented to have samples stored for research at the Mayo Clinic Rochester we will access them for the research study if available. Otherwise, if the patient has already had surgery and tissue has not been stored for research the investigators will consent patients to use their clinical specimens for the research study. The investigators will then extract DNA from tissue sections and blood and use a custom targeted sequencing panel of 23 cancer driver genes with significant mutations in squamous cell carcinoma that they have developed to find the prognostic biomarkers. The DNA will be used in a PCR reaction to generate amplicons for library preparation using Illumina Nextera XT library preparation protocol and targeted sequencing on the Illumina Hiseq sequencer. The reads will be aligned to the HG19 using BWA aligner and variant detection performed with Agilent SureCall and GATK analytic tools.

Official Title
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Identification of Prognostic Biomarkers for Progression of Invasive Squamous Cell Carcinoma

Conditions
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Carcinoma, Squamous Cell, Carcinoma, Squamous, Squamous Cell Carcinoma, Lung Neoplasms, Cancer of Lung, Cancer of the Lung, Lung Cancer, Neoplasms, Lung, Neoplasms, Pulmonary, Pulmonary Cancer, Pulmonary Neoplasms

Intervention / Treatment
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* Genetic: DNA Extraction


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: known or suspected squamous cell carcinoma of the lung able to provide consent could have already had a bronchoscopy or surgical resection with tissue saved at the Mayo Clinic Rochester will be undergoing a bronchoscopy and having a surgical resection at the Mayo Clinic Rochester Exclusion Criteria: unable to provide consent pregnant

Ages Eligible for Study
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Minimum Age: 18 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 |
| --- | --- |
| Tissue Collection<br>We plan to prospectively collect 5 bronchoscopic biopsies, 3ml blood and one tumor and adjacent normal samples from 200 qualified patients who meet the study criteria. If a patient has already had a bronchoscopy and has samples available that were previously collected and stored for research at the Mayo Clinic we will use those samples. | Genetic: DNA Extraction<br>* We will then extract DNA from tissue sections and blood and use a custom targeted sequencing panel of 23 cancer driver genes with significant mutations in squamous cell carcinoma that we have developed to find the prognostic biomarkers. The DNA will be used in a PCR reaction to generate amplicons for library preparation using Illumina Nextera XT library preparation protocol and targeted sequencing on the Illumina Hiseq sequencer. The reads will be aligned to the HG19 using BWA aligner and variant detection performed with Agilent SureCall and GATK analytic tools.<br>|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Number and types of recurrent genomic alterations evaluated by a custom targeted sequencing panel. | The aim of this study is to identify and characterized recurrent genomic alteration found in invasive squamous cell carcinoma that are present in the precursor airway epithelial tissues but absent in normal tissues examined from samples taken during a lung procedure. | 2 years |