We propose to operate a Genome Characterization Center for The Cancer Genome Atlas (TCGA) of the National Cancer Institute. Our goal is to characterize the genomes and transcriptomes of 10,000 human cancers over 5 years, together with the collaborators of TCGA Research Network. Given the ongoing revolution in genome analysis, our Center will transition from current-generation microarray technologies to next-generation sequencing technologies for cancer genome characterization. We will accomplish this by benchmarking the next-generation technologies against state-of-the-art array technologies used in the pilot project of TCGA. Our Center is uniquely qualified for this effort, because of our expertise in next-generation sequencing as well as current-generation microarray production and technology development, our knowledge and demonstrated accomplishments in cancer genomics, and our commitment to and experience with multi-institutional collaborations including the pilot project of TCGA. Specifically, we intend to accomplish the following aims for TCGA:
Aim 1. Using microarray technologies: Characterize DNA and RNA from 2000 cancer samples and appropriate controls during year 1.
Aim 2. Using next-generation sequencing: (i) Perform direct comparison and validation of the three alternative platforms during year 1, by characterizing DNA from 300 cancer/normal sample pairs and RNA from 100 cancer samples. (ii) Select the most cost-effective sequencing platform at the end of year 1, based on the results and in conjunction with NCI staff. (iii) Implement this sequencing platform to characterize DNA and RNA from 2000 cancer samples and appropriate controls in Years 2-5. (iv) Continue to decrease cost and increase resolution of genomic analysis.

Public Health Relevance

Cancer is a genomic disease, caused by somatic and germ-line alterations in DNA and RNA. By discovering and enumerating these alterations, we can improve the diagnosis and treatment of cancer: this is the goal of The Cancer Genome Atlas. Our proposed Genome Characterization Center could contribute significantly to TCGA by advancing genomic technology and by rapidly accomplishing cancer genome discoveries.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Resource-Related Research Projects--Cooperative Agreements (U24)
Project #
Application #
Study Section
Special Emphasis Panel (ZCA1-SRLB-U (O1))
Program Officer
Tarnuzzer, Roy W
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Broad Institute, Inc.
United States
Zip Code
Berger, A H; Imielinski, M; Duke, F et al. (2014) Oncogenic RIT1 mutations in lung adenocarcinoma. Oncogene 33:4418-23
Cancer Genome Atlas Research Network (2014) Integrated genomic characterization of papillary thyroid carcinoma. Cell 159:676-90
Hoadley, Katherine A; Yau, Christina; Wolf, Denise M et al. (2014) Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell 158:929-44
Cancer Genome Atlas Research Network (2014) Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507:315-22
Cancer Genome Atlas Research Network (2014) Comprehensive molecular characterization of gastric adenocarcinoma. Nature 513:202-9
Helman, Elena; Lawrence, Michael S; Stewart, Chip et al. (2014) Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing. Genome Res 24:1053-63
Cancer Genome Atlas Research Network (2014) Comprehensive molecular profiling of lung adenocarcinoma. Nature 511:543-50
Brooks, Angela N; Choi, Peter S; de Waal, Luc et al. (2014) A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events. PLoS One 9:e87361
Parfenov, Michael; Pedamallu, Chandra Sekhar; Gehlenborg, Nils et al. (2014) Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A 111:15544-9
Bar-Peled, Liron; Chantranupong, Lynne; Cherniack, Andrew D et al. (2013) A Tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1. Science 340:1100-6

Showing the most recent 10 out of 25 publications