Clinical trial NCT02549638: Identification of Prognostic Biomarkers for Progression of Invasive Squamous Cell Carcinoma
Official title: Identification of Prognostic Biomarkers for Progression of Invasive Squamous Cell Carcinoma
Study type: OBSERVATIONAL
Overall status: ACTIVE_NOT_RECRUITING
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
Lead sponsor: Mayo Clinic
Sponsor class: OTHER
First posted: 2015-09-15
Enrollment: 200
Sex: ALL
Minimum age (years): 18
Standard ages: ADULT
OLDER_ADULT
Accepts healthy volunteers: no
Observational model: CASE_ONLY
Time perspective: PROSPECTIVE
Sampling method: NON_PROBABILITY_SAMPLE
Study population: Mayo Clinic Thoracic Surgery Patients

Brief 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.

Eligibility criteria: 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

Primary outcomes:
measure: Number and types of recurrent genomic alterations evaluated by a custom targeted sequencing panel.
timeFrame: 2 years
Secondary outcomes:
Other outcomes:
Locations:
city: Rochester
country: United States
facility: Mayo Clinic in Rochester
state: Minnesota
Study officials:
affiliation: Mayo Clinic
name: Dennis Wigle, MD, PhD
role: PRINCIPAL_INVESTIGATOR
References: