Tumor Type

United States
Lung Cancer - Squamous cell carcinoma
The Cancer Genome Atlas (TCGA)  HTML
Project Profile
Funding Organizations
Research Organizations
Research Activities
Publication Policy

1:   ICGC Goals, Structure, Policies and Guidelines Section E.3 - Publication Policy HTML 
2:   Template Letters to Facilitate Communications HTML 
to ensure appropriate dialogue between data users and generators and for authors to contact ICGC members and editors
Clinic & Pathology

Biospecimen Core Resources (BCRs):
United States: International Genomics Consortium
Nationwide Children's Hospital

The Cancer Genome Atlas Biospecimen Core Resources are centralized laboratories that review and process blood and tissue samples and their associated data using optimized standard operating procedures for the entire TCGA Research Network.
The work of the BCRs include the following important functions:
• Serving as the interface between the TCGA program and the different Tissue Source Sites collecting tumor and matched normal controls
• Ensuring and verifying that TCGA human subjects protections and guidelines are adhered to and that all regulations are followed at each Tissue Source Site
• Including use of language consistent with the TCGA informed consent documents
• Examining of all biospecimens to ensure they meet rigorous standards for each tumor type (including percent necrosis and percent tumor nuclei)
• Reviewing of pathology to ensure accurate diagnosis and inclusion in TCGA
• Collecting clinical information for each tissue and applying standardized terminology, definitions and formats that are caBIG compliant
• Extracting DNA and RNA from tissue samples and and distributing to each of the genomic characterization and sequencing centers

1:   Informed Consent Documents HTML 
NIH
2:   Human Subjects Protection Guideline Documents HTML 
NIH
Sequencing & Analysis

Genome Characterization Centers (GCCs):
Canada: BC Cancer Agency
United States: Baylor College of Medicine
Brigham & Women's Hospital and Harvard Medical School
Broad Institute
Johns Hopkins University
University of North Carolina
University of Southern California
Genome Data Analysis Centers (GDACs):
United States: Broad Institute
Institute for Systems Biology
Lawrence Berkeley National Laboratory
Memorial Sloan-Kettering Cancer Center
University of California, Santa Cruz
University of North Carolina
University of Texas M. D. Anderson Cancer Center
Genome Sequencing Centers (GSCs):
United States: Baylor College of Medicine
Broad Institute
Washington University School of Medicine

TCGA Genome Characterization Centers (GCCs) are responsible for characterizing all of the genomic changes found in the tumors studied as part of the TCGA program. The GCCs will use multiple platforms, including array technologies and second generation sequencing, to provide data to the cancer research community on alterations in miRNA and gene expression, single nucleotide polymorphisms and copy number changes.
TCGA Genome Sequencing Centers (GSCs) perform large-scale genomic sequencing using the most current technologies. The GSCs have the opportunity to continually improve existing technology and invest in implementation of new sequencing technologies to enable whole genome sequencing of tumors for complete genomic analysis at an increasingly reduced cost.
TCGA Genome Data Analysis Centers (GDACs) work with the Genome Characterization Centers to develop state-of-the-art tools that assist researchers with processing and integrating data analyses across the entire genome.

Complementary Studies

Data Storage, Analysis & Management

Data Coordinating Center (DCC):
United States: NCI Center for Bioinformatics
SRA International, Inc.
Genome Data Analysis Centers (GDACs):
United States: Broad Institute
Institute for Systems Biology
Lawrence Berkeley National Laboratory
Memorial Sloan-Kettering Cancer Center
University of California, Santa Cruz
University of Texas M. D. Anderson Cancer Center

The informatics component of TCGA involves developing best ways to collect, store, and distribute the clinical and genomic data generated by the project.
The Genome Data Analysis Centers work with the Genome Characterization Centers to develop state-of-the-art tools that assist researchers with processing and integrating data analyses across the entire genome.

Project Summary

The National Cancer Institute and the National Human Genome Research Institute launched The Cancer Genome Atlas program to create a comprehensive atlas of the genomic changes involved in more than 20 common types of cancer. This large-scale, high-throughput effort is being carried out by a network of more than 100 researchers at many organizations across the United States. The overarching goal of TCGA is to further scientific understanding of the genomic changes in cancer, thereby improving the ability to diagnose, treat and prevent this devastating disease. All data generated by the TCGA research network are made rapidly available to the research community through the TCGA Data Portal.

Principal Investigators

TCGA Program Directors: Jean C. ZenKlusen, M.S., Ph.D. (NCI) and Carolyn Hutter, Ph.D. (NHGRI)

Biospecimen Core Resources (BCRs)
Julie Gastier-Foster, Ph.D.
Robert Penny, M.D., Ph.D.

Genome Characterization Centers (GCCs)
Stephen Baylin, M.D.
Rui Chen, Ph.D.
Lynda Chin, M.D.
Stacey Gabriel, Ph.D
Richard Gibbs, M.D, Ph.D.
Neil Hayes, M.D., M.P.H.
Raju Kucherlapati, Ph.D.
Peter Laird, Ph.D.
Jason Lieb, Ph.D.
Marco Marra, Ph.D.
Matthew Meyerson, M.D., Ph.D.
Chuck Perou, Ph.D.
Jonathan Seidman, Ph.D
David Wheeler, Ph.D.

Genome Sequencing Centers (GSCs)
Richard Gibbs, Ph.D.
Eric Lander, Ph.D.
Richard Wilson, Ph.D.

Data Coordinating Center (DCC)
David Pot, Ph.D., Project Director

Genome Data Analysis Centers (GDACs)
Christopher Benz, M.D
Lynda Chin, M.D.
Gaddy Getz, Ph.D.
David Haussler, Ph.D.
Neil Hayes, M.D., M.P.H.
Marc Ladanyi, M.D
Gordon Mills, M.D., Ph.D.
Chris Sander, Ph.D.
Ilya Shmulevich, Ph.D.
Terrence Speed, Ph.D.
Paul Spellman, Ph.D.
John Weinstein, M.D., Ph.D.
W.K. Alfred Yung, M.D.
Wei Zhang, Ph.D.

Lead Jurisdiction