Identification of Prognostic Biomarkers for Progression of Invasive Squamous Cell Carcinoma

Study Results

Results pending

The study team has not published outcome measurements, participant flow, or safety data for this trial yet. Check back later for updates.

Basic Information

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Recruitment Status

TERMINATED

Total Enrollment

22 participants

Study Classification

OBSERVATIONAL

Study Start Date

2015-04-08

Study Completion Date

2020-04-23

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.

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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.

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

Study Design

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Observational Model Type

CASE_ONLY

Study Time Perspective

PROSPECTIVE

Study Groups

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Tissue Collection

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.

DNA Extraction

Intervention Type GENETIC

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.

Interventions

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DNA Extraction

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.

Intervention Type GENETIC

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