Identification of Prognostic Biomarkers for Progression of Invasive Squamous Cell Carcinoma

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.

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