Neoplasms

All Conditions

Respiratory Tract (Lung and Bronchial) Diseases

Symptoms and General Pathology

Carcinoma

Carcinoma, Squamous Cell

Lung Neoplasms

Disease Progression

Neoplasms, Glandular and Epithelial

Neoplasms by Histologic Type

Neoplasms, Squamous Cell

Respiratory Tract Neoplasms

Thoracic Neoplasms

Lung Diseases

Respiratory Tract Diseases

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.

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.

DNA Extraction

Karlyn Pierson, MAN, RN

Karlyn E Pierson, RN

Dennis A Wigle, MD, PhD

Dennis Wigle, MD, PhD

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.

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.

5 bronchoscopic biopsies, 10ml blood and one tumor and adjacent normal samples

Identification of Prognostic Biomarkers for Progression of Invasive Squamous Cell Carcinoma

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.

Mayo Clinic

Rare Diseases

Glioma

Neoplasms, Neuroepithelial

Neuroectodermal Tumors

Neuroectodermal Tumors, Primitive

Neoplasms, Germ Cell and Embryonal

Neoplasms, Nerve Tissue

Neuroepithelioma

Once the pathological diagnosis is confirmed (WHO 2016), a tumor fragment will be selected and frozen for each lobe. DNA extraction will be performed for each fragment. The samples (4 different DNAs per GDBG corresponding to the DNA extracted from each of the 3 lobes and the blood DNA) will be sent to the Montpellier Genomix platform for sequencing of the complete exome.

sequencing of the complete exome

Catherine Gozé, PharmD, PhD

Catherine GOZE, Pharm-D; PhD

Hugues DUFFAU, PU-PH

Low-grade diffuse glioma (GDBG) are rare tumors of young adults, whose ontogenesis is poorly understood. Patient management is based on the molecular profile defined by two molecular markers : mutations of the IDH genes and chromosomal 1p19q co-deletion. To date, the IDH and 1p19q statuses are determined on a single fragment collected from the tumor. In the case of GDBGs infiltrating several brain lobes, the sampling is done randomly on only one of the infiltrated lobes. An intra-tumoral heterogeneity of genetic alterations has been suggested and would impact management.

Phylogenetic analysis of genetic alterations found, by high throughput sequencing, in each lobe invaded by the same GDBG will make it possible to assess intra-tumoral heterogeneity and to discuss, at a fundamental level, the hypothesis of a single tumor site with secondary diffusion or that of the convergent progression of two or three distinct tumor sites. Clinically, understanding the ontogenesis of GDBGs will improve their management because of the known link between brain location, dominant molecular profile, and prognosis.

In this pilot study we chose the fronto-temporal-insular GDBG model to study the intra-tumoral heterogeneity of the low-grade gliomas by exhaustive high throughput sequencing of each of the 3 infiltrated lobes, followed by comparative phylogenetic analysis of the genetic profiles obtained in the 3 locations

Molecular Heterogeneity in Multilobar Low-grade Gliomas

Phylogenetic Analysis of Intra-tumor Molecular Heterogeneity on a Pilot Series of Diffuse Low-grade Multilobar Gliomas: Tumor Ontogenesis and Therapeutic Implications

exhaustive high throughput sequencing of each of the 3 infiltrated lobes, followed by comparative phylogenetic analysis of the genetic profiles obtained in the 3 locations

Study title	NCT ID	Conditions	Interventions	Eligibility	Organization
Identification of Prognostic Biomarkers for Progression of Invasive Squamous Cell Carcinoma	NCT02549638	Carcinoma, Squa... Carcinoma, Squa... Squamous Cell C... Lung Neoplasms Cancer of Lung Cancer of the L... Lung Cancer Neoplasms, Lung Neoplasms, Pulm... Pulmonary Cance... Pulmonary Neopl...	DNA Extraction	18 Years -	Mayo Clinic
Identification of Prognostic Biomarkers for Progression of Invasive Squamous Cell Carcinoma	NCT02549638	Carcinoma, Squa... Carcinoma, Squa... Squamous Cell C... Lung Neoplasms Cancer of Lung Cancer of the L... Lung Cancer Neoplasms, Lung Neoplasms, Pulm... Pulmonary Cance... Pulmonary Neopl...	DNA Extraction	18 Years -	Mayo Clinic
Molecular Heterogeneity in Multilobar Low-grade Gliomas	NCT04000048	Low-grade Diffu...	sequencing of t...	18 Years -	University Hospital, Montpellier
Molecular Heterogeneity in Multilobar Low-grade Gliomas	NCT04000048	Low-grade Diffu...	sequencing of t...	18 Years -	University Hospital, Montpellier

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