NCT02549638

Identification of Prognostic Biomarkers for Progression of Invasive Squamous Cell Carcinoma

• Status: Terminated
• Phase: —
• Study type: Observational
• Enrollment: 22 (actual)
• Sponsor: Mayo Clinic · Academic / Other
• Sex: All
• Age: 18 Years
• Healthy volunteers: Not accepted

Summary

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

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

• 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

Interventions

Type	Name	Description
GENETIC	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.

Timeline

• Start date: 2015-04-08
• Primary completion: 2020-04-23
• Completion: 2020-04-23
• First posted: 2015-09-15
• Last updated: 2025-10-14

Locations

1 site across 1 country: United States