Proposal instructions for sequencing a new target organism
National Human Genome Research Institute
National Institutes of Health U.S. Department of Health and Human Services
Instructions for Submitting a Proposal for the Sequencing of a New Target Genome
Programmatic emphasis within the Large-Scale Genome Sequencing Program changes over time. If you are interested in submitting a white paper, we strongly urge you to contact the Program Director for large-scale genome sequencing as early in the process as possible.
The request to have the genome of an organism (or group of organisms) sequenced may be submitted to the NHGRI in the form of a "white paper." The original white paper concept was developed at an NHGRI-sponsored workshop on Developing Guidelines for Choosing New Genomic Sequencing Targets (July 9-10, 2001). While the current working group mechanism described above supercedes the specific recommendations of that workshop, many of the principles remain relevant. The most important difference is that white papers should only be submitted for requests in cases where the major rationale for obtaining genome sequence clearly does not fall into the areas of one of the two working groups described above.
The white paper should present a clear justification for the sequencing of the organism (or group of organisms). There are several factors that will influence the selection of a new organism for genomic sequencing; these factors fall into two distinct groups. One is biological and includes considerations of the ways in which the sequence information will contribute to advances in biomedical and biological research. The second is strategic and concerns pragmatic issues that are relevant to sequence acquisition. Both sets of factors (see item 3, Points to Address, below) must be addressed in the white paper to effectively allow the review process (see item 2) to establish the priority for obtaining the sequence of an organism on a cost-benefit basis.
The white paper should discuss the relevant scientific community's depth of interest in having the sequence of the particular organism, and should describe any process, if there has been one, by which that research community has come to consensus on the request being made.
A white paper may be submitted by a sequencing center, by a collaborative group involving both a sequencing center and a research community or an individual, or by a research community or individual that has not already made a connection with a specific sequencing center. In the latter case, the paper should describe any efforts that have been made to contact sequencing centers.
White papers will be accepted twice a year, on January 10 and July 10.
The white paper should not exceed a total of ten pages. There is no specific form necessary for submission of a white paper nor is any specific format required, but all of the issues listed in item 6 should be addressed.
Although not a criterion for consideration by NHGRI, the developer(s) of a white paper is (are) also encouraged to disseminate it and/or its ideas broadly within the scientific community. For example, the white paper may be published or made available through a Web site or list serve. Such dissemination will not in any way compromise the consideration of the request by the NHGRI.
White paper proposals will first receive preliminary assessment by the coordinating committee overseeing the selection process. The coordinating committee will recommend future action in one of the following two ways:
If the proposed organism meets some or all of the goals of the two working groups ("Annotating the Human Genome" and "Comparative Genome Evolution,") the coordinating committee may recommend that the white paper be submitted for discussion at the next scheduled meeting of the appropriate working group. The working group will then have the option of including the proposed organism in its sequencing plan. It is expected that there will be very few white papers submitted that fall under the purview of either of the working groups since those interested in suggesting such sequencing targets should contact the working groups directly.
If the proposed organism cannot easily be placed within the scope of either working group but is scientifically meritorious of consideration in its own right, the coordinating committee may review the paper internally. The committee will consider where to include the proposed organism in the prioritized list of sequencing targets. If the coordinating committee believes the nomination is meritorious, it will receive a priority relative to all other candidate organisms. Alternately, the committee may defer deliberations and direct the sequencing centers to obtain preliminary data if that will resolve an outstanding scientific issue. Finally, the committee may also return the proposal unranked. It is important to note that the committee may re-prioritize organisms for sequencing as new candidates are proposed by the community and the working groups. We emphasize that a place on a prioritized list does not guarantee that the organism will be sequenced. Among other things, scientific and programmatic priorities may change during the lifetime of the program. Indeed, part of the intent of this program is to better accommodate changing priorities in a rapidly moving area of research. Submitters of white papers will receive verbal feedback form NHGRI staff.
As sequencing capacity becomes available, NHGRI large-scale sequencing centers will choose target organisms from the prioritized list. The center Principal Investigator will prepare a detailed plan describing the strategy selected for the sequencing of that particular genome and include a timetable for the determination of the sequence.
Points to Address in a White Paper
A. Specific biological/biomedical rationales for the utility of new sequence data
Improving human health. How will the genomic sequence of an organism inform our understanding of human disease or hold the potential for improving human health? What, if any, is the relevance to the development of innovative and improved methods of diagnosis, treatment or prevention?
Informing human biology. How will the genomic sequence of a particular organism lead to a better understanding of biological function in the human?
Expanding our understanding of basic biological processes relevant to human health, e.g. cell or developmental biology, neurobiology.
Providing additional surrogate systems for human experimentation, e.g. new disease models, improved opportunities for drug testing, or other medical procedures, such as transplantation.
Facilitating the ability to do experiments, e.g "direct" genetics or positional mapping, in additional organisms.
B. Strategic issues in acquiring new sequence data
The demand for the new sequence data. What is the size of the research community that will use it? What is the community's enthusiasm for having the sequence? Will the new sequence data stimulate the expansion of the research community?
The suitability of the organism for experimentation. What are the basic properties of the organism that affect its ability to be studied in the laboratory (e.g. availability, ability to be cultured and propagated in the laboratory, generation time)? Are mutants available with defined phenotypes? How will the new sequence data enhance the experimental use of the organism? What other genomic resources and technologies (e.g. gene transfer, ability to go from molecule to mutation) are available that will allow the new sequence information to be effectively used?
The rationale for the complete sequence of the organism. Why would the complete sequence be more useful than the sequences of specific regions, or only the coding sequences, or only ESTs? Are there alternative ways to get the necessary information?
The cost of sequencing the genome and the state of readiness of the organism's DNA for sequencing. What is the size of the genome? Will the repeat structure or other biological features pose challenges for genome sequencing? What quality of sequence product is needed (finished sequence? draft? full shotgun?)? What sequencing strategy will be used? Is suitable DNA readily available?
Are there other (partial) sources of funding available or being sought for this sequencing project? NHGRI is willing to consider requests to sequence disease vectors but priority will be given to requests that relate to the programmatic interests of NHGRI and where co-funding from other entities has either been identified or discussions about such funding is underway.
All proposals of new organisms for genomic sequencing by the NHGRI-supported sequencing centers must address both sets of issues. If one or more of the issues listed above is not applicable to the specific request that should be stated clearly rather than left unmentioned.
For additional information about the sequencing program, please contact:
Dr. Adam Felsenfeld
Program Director, Large-scale Sequencing
National Human Genome Research Institute
5635 Fishers Lane, Suite 4076
Bethesda, MD 20852-9305
Phone: (301) 496-7531
Fax: (301) 480-2770