Toward a Comprehensive Genomic Analysis of Cancer - NCI/NHGRI Workshop: Questions and Answers
1. What is the status of efforts to characterize the human cancer genome?
The National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) recognize the potential benefit that a comprehensive collection of genetic and epigenetic alterations for major cancers could provide to the cancer community.
NCI and NHGRI have agreed to examine the best approaches to achieve the goal of building a comprehensive collection and analysis of mutations found in human cancers. Through a multi-phase approach, NCI and NHGRI are examining the major issues and barriers associated with compiling a complete catalog of the genetic changes that characterize cancer.
Many biological, technological and scientific hurdles must be resolved in order to attempt a large-scale project to accomplish this goal. To address these issues, NCI and NHGRI sponsored a workshop in July 2005 to seek input from members of the scientific community who have expertise in cancer and clinical research, genomics, technology development, bioinformatics and bioethics, as well as those who represent the public, non-profit, advocacy and private sectors. Attendees will be asked to provide guidance and expertise on a number of issues, including the types of cancer that should be studied, optimal technology strategies and bioethical issues. These discussions will be important as NCI and NHGRI develop plans for a pilot project.
2. How were these efforts conceived?
NCI and NHGRI began examining the feasibility of undertaking such a collaborative program in a workshop held in April 2004 (www.cgap.nci.nih.gov). Later in 2004, the NCI's National Cancer Advisory Board (NCAB) convened a subcommittee to examine the role of advanced technologies in addressing mission-critical problems in cancer. This subcommittee, the Advanced Biomedical Technology Working Group of the NCAB, presented its recommendations in February 2005 for the development of the Human Cancer Genome Project (http://deainfo.nci.nih.gov/Advisory/ncab/sub-bt/NCABReport_Feb05.pdf), an ambitious program that would develop a comprehensive description of the genetic basis of human cancer, and specifically, the complete identification and characterization of genetic alterations present in a large number of major types of cancer.
NCI initiated a collaboration with NHGRI to develop a pilot project to test the feasibility of a large-scale effort to characterize all the genetic changes that occur in cancer. Many experts believe that analysis of changes that occur at the genetic level has the potential to provide valuable insights into the causes of cancer. Epigenetic analysis also offers the potential to understand how modifications of DNA molecules can turn genes on or off, without changing the DNA sequence. The identification of these changes will lead to improved means of diagnosing, treating and preventing cancer.
3. How will the characterization of the human cancer genome advance and accelerate cancer research?
Fundamentally a genetic disease, cancer begins with one or more genetic alterations within a single cell. As these alterations accumulate, the cell begins to grow abnormally and can become malignant. Escaping the normal signals that control cell growth, the mutated cells proliferate and can spread to other parts of the body
Scientists have identified many genes that are involved in human cancer. The malfunctions of these genes occur by distinct mechanisms, and a systematic characterization of these changes and their role in causing cancer could lead to an increased understanding of the disease.
A comprehensive effort to examine changes in the cancer genome may offer an effective way to identify all of the relevant genetic changes and malfunctions that can contribute to cancer. The detailed analysis of the genomes in cancer cells holds the promise to provide key information about many cellular pathways involved in cancer. This new effort could provide researchers with specific molecular targets for drug development. For example, GleevecTM is a molecularly targeted drug and has proven effective in the treatment of chronic myelogenous leukemia, gastrointestinal stromal tumor and several other cancers.
4. How is this effort different from the Human Genome Project?
The Human Genome Project, an international project led in the United States by NHGRI and the Department of Energy, was completed in April 2003 and provided a reference DNA sequence of the human genome. The Human Genome Project also helped to advance sequencing technologies, which continue to improve.
The proposed project will take advantage of these remarkable developments to address cancer. Cancer is now understood to include more than 200 different diseases, in which specific molecular transformations at the DNA level cause disruptions within intracellular pathways, spurring cells to grow uncontrollably. Because of the complexity of cancer, a comprehensive approach may hold the key to characterize fully the many genes in which molecular variations can occur.
5. Why are NCI and NHGRI pursuing the characterization of the human cancer genome now?
The Human Genome Project provided a model for approaching large-scale biomedical research projects. The experience and technological advances resulting from the Human Genome Project have made it feasible to consider large-scale science projects. While conceptually feasible, a large-scale cancer genomic characterization project will require new research into cancer biology as well as additional technological improvements. To demonstrate the practicality of this approach, a pilot project will be a very important first step. The pilot project will drive development of more cost-effective and efficient technologies that will be needed to examine cancer genomes in sufficient detail.
Genomics, along with the development of advanced imaging methods, nanotechnology, new drug discovery and development, improved biomarkers and proteins, and extensive clinical research, potentially will change the way cancers are prevented, diagnosed and treated.
6. How will the initial phases of this effort to characterize the human cancer genome be structured?
The pilot phase of this effort will focus on addressing the wide range of challenges in cancer biology and technology that must be met in order to implement a successful large-scale human cancer genome project. The initial phases also will analyze whether the comprehensive cataloguing of the sequence changes in cancer will prove useful in understanding cancer and lead to new methods of diagnosis and treatment.
A pilot program, which will determine the feasibility of a full-scale effort, is scheduled to begin in fiscal year 2006. It is expected to take at least three years to complete. The pilot project will be funded jointly by NCI and NHGRI, and the management structure for the pilot will take advantage of the scientific knowledge and management expertise of both institutes. In addition, an external scientific committee of experts has been established to provide guidance on all aspects of the design and evaluation of the pilot project. The committee will work with NCI and NHGRI staff to evaluate progress and revise scientific strategies, where necessary, to meet pilot project goals and milestones.
7. How much will a pilot project cost and how will it be funded?
The pilot project is a major undertaking and will require considerable preparation to address all of the technical and scientific issues. It also will establish parameters that will demonstrate the feasibility of a large-scale project. Although the recommendation proposed to the National Cancer Board in February 2005 included cost projections, NIH has not at this time determined the exact cost of the pilot project. NCI and NHGRI have recently committed to each contribute up to $50 million for the pilot, pending approval from their respective scientific advisory boards and councils.
8. Will any other organizations be involved in these efforts?
NCI and NHGRI are actively seeking the involvement of partners from the public and private sectors, as well as international collaborators.
9. What remains to be done between now and the start of the pilot project?
Based on input received from the scientific community during the July 2005 workshop, NCI and NHGRI have begun the planning phase of the pilot project. Plans for a competitive approach to
supporting the pilot project then will be presented for approval by the National Cancer Advisory Board, NCI's Board of Scientific Advisors and the National Advisory Council for Human Genome Research. A set of Requests for Applications will be issued following the necessary institute approvals. The applications will be evaluated by a rigorous peer-review process and then funded according to standard NIH procedures.
10. Will the data generated by this effort be publicly available? How will researchers access the data?
NCI and NHGRI will develop a data release policy that will continue the efforts in the field of genomics to make data available as rapidly as possible to the entire scientific community and public -- with little to no restrictions on scientific use. The specific details of the data release policy will be developed during the planning and implementation of the pilot project and will be designed to achieve the joint goals of rapid public availability, protection of privacy of patient information and appropriate use of intellectual property to further the goal of widespread access to the benefits of this research. These issues were discussed in greater detail during the July workshop.
11. Is this effort affiliated with other cancer projects, such as the Wellcome Trust Sanger Institute's Cancer Genome Project in England?
NCI and NHGRI are reaching out to researchers and investigators to discuss the successes and challenges of similar efforts around the world. NCI and NHGRI program staff recently met with scientists from the Wellcome Trust Sanger Institute and officials in the Wellcome Trust, as well as with the European Commission, to discuss their current activities in sequencing and analyzing cancer genomes. These discussions have provided valuable feedback to help guide the direction of the NCI/NHGRI pilot project.
12. Where can I get more information?
A report form the July workshop is forthcoming.
For more information about cancer, visit the NCI Web site at http://www.cancer.gov or call NCI's Cancer Information Service at 1-800-4CANCER (1-800-422-6237).
For more information on genomics and the Human Genome Project, visit the NHGRI Web site at http://www.genome.gov.