Office of Cancer Genomics (OCG)
Established: 1996
The mission of the NCI’s Office of Cancer Genomics (OCG) is to enhance understanding of the molecular mechanisms of cancer, with the ultimate goal of improving the prevention, early detection, diagnosis, and treatment of cancer.
The OCG interfaces genomics and cancer research through the establishment of information platforms, material resources, and technology infrastructure. The OCG has made numerous contributions to the research enterprise during its first decade; many of the clones produced by OCG programs are publicly available today.
The role of the OCG is to:
- Provide information, technology, methods, informatics tools, and reagents to serve the needs of the cancer research community.
- Support, lead, and/or manage five major research programs, listed in order of their inception:
- Establish and maintain relationships with advisory groups for each of the above programs.
To learn more about the Office of Cancer Genomics, please visit http://ocg.cancer.gov/.
Cancer Genome Anatomy Project (CGAP)
Established: 1997
The NCI CGAP is an online resource designed to characterize biological tissues and provide cDNA clones to the research community. To support these outcomes, CGAP provides a wide range of genomic data that include gene expression profiles of normal, precancerous, and cancerous cells (based on expressed sequence tags (EST) and serial analysis of gene expression (SAGE)), single nucleotide polymorphism (SNP) analysis of cancer-related genes, and the 50,000-plus-case Mitelman database of chromosomal aberrations in cancer.
By collaborating with scientists worldwide, CGAP seeks to increase its scientific expertise and expand its databases for the benefit of all cancer researchers. Access to all CGAP data, clones, and analytic tools is made available to the research community through the CGAP website and distribution system.
To learn more about the Cancer Genome Anatomy Project (CGAP), visit http://cgap.nci.nih.gov/.
Mammalian Gene Collection (MGC)
Established: 1999
The goal of the Mammalian Gene Collection (MGC), a trans-NIH initiative, is to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes. The MGC recently organized an international consortium of seven participants to create “expression-ready” clones for all Homo sapiens genes, which can be used by the research community for expression of proteins for large-scale proteomic analyses.
In 2005, the project added the cow cDNAs generated by Genome Canada. Alternative methods based on gene-specific amplification have recently been developed to target the recovery of human and mouse genes absent from the MGC collection.
To learn more about the Mammalian Gene Collection (MGC), visit http://mgc.nci.nih.gov/.
Initiative for Chemical Genetics (ICG)
Established: 2002
Synthetic chemistry has enabled the creation of large collections of complex and diverse small molecules, patterned after natural products, which are tested for the ability to induce specific biological phenotypes. The NCI’s Initiative for Chemical Genetics provides a systematic approach to study biology using such small molecules, to develop new screening tools and compounds, and to accelerate the development of new cancer strategies and therapies. As detailed below, the ICG focuses efforts on a number of deliverables, including biological assays, chemical libraries, a repository of chemical probes, and a scientific database. Discoveries made through the ICG program to date have resulted in more than 100 publications and 17 patents.
Biological Assays. To date, more than 130 unique, individual biological projects have been analyzed through the ICG. Many of these screens have been developed by external investigators using assistance and supplies provided by the ICG. All results are deposited into ChemBank no later than one year after the completion of the screen.
Chemical Synthesis. Since its inception, the ICG has synthesized more than 10,000 novel compounds. In addition, ICG staff members have enriched the breadth of compounds available for screening by creating recombinant libraries to produce unique natural products and acquiring additional compounds from external sources.
Scientific Database. ChemBank, an online database, includes chemical data on 700,000 small molecules, a subset of which have also been characterized further using additional assays. Investigators can use ChemBank’s tools to query and analyze available data and export raw information for subsequent analysis. ChemBank thus enables researchers to identify promising drug candidates for further development and to gain new knowledge of human disease.
To learn more about the Initiative for Chemical Genetics (ICG), visit http://www.broad.harvard.edu/chembio/icg/index.html.
The Cancer Genome Atlas (TCGA)
Established: 2005
The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing. TCGA is a joint effort of the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), which are both part of the National Institutes of Health.
NCI and NHGRI launched TCGA as a collaborative three-year pilot project to test the feasibility of using large-scale genome analysis technologies to determine all of the important genomic changes involved in cancer. When fully operational, TCGA will consist of four integrated components: a Biospecimen Core Resource (BCR); Cancer Genome Characterization Centers; Genome Sequencing Centers; and a Principal Bioinformatics Resource.
Success factors for the TCGA Pilot Project include completion of genomic analysis of three initial cancer types; identification of specific alterations in genes associated with cancer; and differentiation of cancer subtypes based on genomic changes. In addition, the pilot project will establish a publicly available integrated database that scientists can use to generate new knowledge through research. TCGA data will be made available through public databases supported by NCI’s cancer Biomedical Informatics Grid™ (caBIG™) and the National Library of Medicine’s National Center for Biotechnology Information (NCBI). TCGA data will be provided in a manner that meets the highest standards for protection and respect of the research participants.
To learn more about The Cancer Genome Atlas, please visit http://cancergenome.nih.gov.
For more information about TCGA funding, click here.
Cancer Genetic Markers of Susceptibility (CGEMS)
Established: 2005
CGEMS is a three-year, $14 million-dollar initiative to conduct whole-genome association studies to identify genes that confer susceptibility to prostate and breast cancer. Coordinated through the NCI’s Division of Cancer Epidemiology and Genetics, the Core Genotyping Facility, and the OCG, the project capitalizes on new knowledge of single nucleotide polymorphisms (SNPs) in human genetic variation and technical advances in ultra-high-throughput genotyping.
SNPs are the most common form of human genomic variation; most of the approximately ten million SNPs with a minor allele frequency greater than 5 percent occur in genomic segments in which they correlate highly with each other (i.e., they are in linkage disequilibrium). Data from the International HapMap Project Phase 2 indicate that a minimum of 550,000 carefully-chosen SNPs will be required to conduct a comprehensive whole-genome SNP scan.
CGEMS is designed to conduct whole-genome scans in nested case-control studies of prostate and breast cancer from ongoing population-based cohort studies. Each whole-genome scan will analyze approximately 1,200 cases and 1,200 controls. Because the large number of SNP comparisons in a whole-genome scan will likely generate many false positive signals, follow-up sequential replication studies will be used to validate true positive associations. Using this procedure, CGEMS will assess the 15,000-20,000 top candidate SNPs from the whole-genome scans in follow-up case-control studies. Rapid public access to data generated by CGEMS will be facilitated by caBIG™.
To learn more about the Cancer Genetic Markers of Susceptibility Program, visit http://cgems.cancer.gov.
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