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The Large-Scale Genome Sequencing Program
Scientific OrganizationThe Large-Scale Genome Sequencing Program is composed of several broad research programs. The National Human Genome Research Institute (NHGRI) engages in specific initiatives and sequencing projects that comply with the aims of these research programs. The scientific organization of the Large-Scale Genome Sequencing Program is depicted below.
Program OverviewThe National Human Genome Research Institute (NHGRI) funds large-scale genome sequencing capacity at several centers located in the U.S. This program undertakes large-scale sequencing projects to provide critical genomic information that can be of significant value to the scientific community in areas of very broad scientific interest. NHGRI issues competitive solicitations for cooperative agreements for large-scale sequencing centers. Applications are reviewed by the normal NIH peer-review mechanism. The funding of sequencing capacity is done separately from the selection of new sequencing projects. FY 2006 funding was approximately $130M or over 150 billion raw Q20 base pairs per year. The sequencing centers are organized into a research network, with oversight by NHGRI program staff in conjunction with the Scientific Advisors to the Large-Scale Sequencing Program. The current funded sequencing centers are:
In addition to these outside centers, the NHGRI Division of Extramural Research funds sequencing capacity at the National Institutes of Health Intramural Sequencing Center (NISC). The most recent competitive solicitation, funded in December 2006, can be viewed at: RFA-HG-O6-001.html: Genome Sequencing Centers (U54) [grants.nih.gov] Major ProgramsThe NHGRI Large-Scale Genome Sequencing Program grew from the effort to sequence the human genome. Please see Program History to learn more about the development and aims of the program. At the present time, the Large-Scale Genome Sequencing Program focuses on generating sequence information under five general rationales. Each rationale corresponds to a separate program, under which there are individual initiatives and projects.
In addition, individual sequencing centers may allocate resources to Center Initiated Projects. Please see Allied Sequencing Programs to learn about programs that NHGRI engages in with other institutes. The Large-Scale Sequencing Program is under continuous programmatic evaluation. New scientific opportunities arise with some regularity as technology and the state of knowledge change. The program will change over time to address those opportunities.
Active Sequencing Projects
How to Access Sequencing Data
Process for Selecting New Sequencing TargetsSelection and approval of new sequencing targets Typically, new sequencing targets are selected through target selection working groups that have been assembled to advise NHGRI on each of the individual programs of the Large-Scale Sequencing Program. These working groups propose broad initiatives within their areas of interest, and specific projects within those broad areas. A project could be a single organismal genome, or could be more extensive, for example, sequencing a set of closely related organisms related to a specific scientific aim. In some cases, the working groups propose general initiatives that result in solicitation of individual projects from the scientific community to address the goals of those initiatives, which are evaluated by the working groups. See Instructions for Submitting a Proposal for the Sequencing of a New Target Genome for instructions on submitting new project proposals. Several projects will be selected as part of focused workshops initiated by NHGRI on specific topics. Two that are currently under development are in the areas of human eukaryotic pathogens and vectors (Coming Soon) and Sequencing of Reference Genomes of Human Microbiotas. All recommendations from the working groups are assessed by a Coordinating Committee for Sequencing Target Selection (CC) which evaluates the relative merit and priority of the individual projects, and also comments more broadly on the scientific direction and structure of the target selection process. CC recommendations are subsequently reviewed by the National Advisory Council on Human Genome Research (NACHGR), which advises NHGRI on which projects should be approved, and also provides general advice about programmatic priorities. Please see Group Rosters for a list of current members of the working groups and the CC. Meeting reports and workshop summaries are located at Archive of Meeting Reports and Workshop Summaries.Prioritizing and implementing specific approved projects Once a specific sequencing target has been approved, NHGRI staff assigns the project to a sequencing center. NHGRI works with the sequencing centers and (where appropriate) members of the scientific community that have proposed specific projects to enter those projects into sequencing pipelines in an efficient manner, to ascertain that the project as proposed is technically tractable, and to ensure that any human samples comply with NHGRI Medical Sequencing policies. Approved projects are entered into sequencing pipelines based on available space in the pipelines, their overall priority compared to other approved projects as determined in the review process, and availability of appropriate samples. Approved projects that have not been started yet are routinely re-prioritized by NHGRI in consultation with target selection advisors for entry into sequencing pipelines. Please see Sequencing Program Priorities for further information on current priorities. Depending on the project, the delay from approval to the beginning of work can range from a few months to a year, occasionally longer. In rare cases, approved projects can be delayed indefinitely for technical reasons (for example, where it is impossible to get good samples, or where a biological feature of the genome makes it significantly less tractable than anticipated), scientific reasons (new facts become available that diminish the significance of a previously approved target, or make it clear that the project will be much more expensive than initially anticipated), human subjects reasons (adequacy of consent) or major changes in overall program priorities and availability of funding for the Large-Scale Genome Sequencing Program.
Sequencing PoliciesAll major policies are reviewed by the National Advisory Council for Human Genome Research. General policies for data release were determined at a series of meetings of the genomics community. NHGRI is committed to the rapid release of all sequence data from community resource projects. All trace data are released rapidly (within a week) of their production into the public Trace Archive [ncbi.nlm.nih.gov]. Genome assemblies are released as soon as they have been validated. Specific technical policies for sequencing (for example, the quality standards for human and mouse sequence) are determined by the sequencing centers, together with the funding agencies. Medical Sequencing policies (informed consent, data deposition, data access) are created with advice from the Medical Sequencing Working Group and additional outside advisors. Because human research participants are involved, access to some Medical Sequencing data is controlled. See Medical Sequencing Policies for instructions on how to access Medical Sequencing Data.
Outside ResourcesThe NHGRI Large-Scale sequencing program sponsors several activities related to large-scale sequencing. One is the construction and distribution of BAC libraries. Another is the Human Genome Reference Consortium (HGRC), a collaborative effort between NHGRI, the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI), and the Wellcome Trust Sanger Institute (WTSI). The HGRC aims to maintain, update, and curate the human genome reference sequence. Currently Funded Sequencing Centers
Other Major Centers
Resources
Other
Program ContactsAdam Felsenfeld, Ph.D. (Medical Sequencing, Annotating the Human Genome, General Information)
Lu Wang, Ph.D. (Human Microbiome Project, Pathogens and Vectors, General Information) Brad Ozenberger, Ph.D. (Cancer Sequencing, The Cancer Genome Atlas) Kris Wetterstrand, M.S. (BAC Libraries) Jane Peterson, Ph.D. (Human Microbiome Project, General Information) AddressNational Human Genome Research Institute
Last Updated: June 19, 2008 |
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. Using basic sequence information as a research tool to allow a better understanding of the most significant eukaryotic human disease pathogens and their vectors.
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