Revolutionary genome sequencing technologies: the $1,000 genome.

The purpose of this request for applications (RFA) is to solicit grant applications to develop novel technologies that will enable extremely low-cost genomic DNA sequencing. Current technologies are able to produce the sequence of a mammalian-sized genome of the desired data quality for $10-50 million; the goal of this initiative is to reduce costs by at least 4 orders of magnitude, so that a mammalian-sized genome could be sequenced for approximately $1,000. Substantial fundamental research is needed to develop the scientific and technological knowledge underpinning such a major advance, Therefore, it is anticipated that the realization of the goals of this RFA is a long-range effort that is likely to require as much as 10 years to achieve. The parallel RFA HG04-002 (details at http://grants.nih.gov/grants/ guide/rfa-files/RFA-HG-04-002.html) solicits grant applications to develop technologies to meet the shorter-term goal of achieving a 2 orders of magnitude cost reduction in about 5 years.

The ability to sequence complete genomes and the flee dissemination of the sequence data have dramatically changed the nature of biological and biomedical research. Sequence and other genomic data have the potential to lead to remarkable improvements in many facets of human life and society, including the understanding, diagnosis, treatment, and prevention of disease; advances in agriculture, environmental science, and remediation; and the understanding of evolution and ecological systems.

At current prices, the cost of sequencing a mammalian-sized genome means we must still be very selective when choosing new genomes to sequence. In particular, we remain very far away from being able to afford to use comprehensive genomic sequence information in individual health care. For this and many other reasons, the rationale for achieving the ability to sequence entire genomes very inexpensively is very strong.

Given the broad utility and high importance of dramatically reducing DNA sequencing costs, the National Human Genome Research Institute (NHGRI) is launching two parallel technology development programs. For both programs, the cost targets are defined in terms of a mammalian-sized genome, about 3 gigabases (Gb), with a target sequence quality equivalent to, or better than, that of the mouse assembly published in December 2002 [Nature 420:520 (2002)].

The ultimate goal of this program is to obtain technologies that can produce an assembled sequence (i.e., de nova sequencing). However, an accompanying shorter-term goal is to obtain highly accurate sequence data at the single base level, i.e., without assembly information, that can be overlaid onto a reference sequence for the same organism (i.e., resequencing). This could be achieved, for example, with short reads that have no substantial information linking them to other reads. While the sequence product of this kind of technology would lack some important information, such as information about genomic rearrangements, it would nevertheless potentially be available more rapidly and produce data of great value for certain uses in studying disease etiology and in individualized medicine. Therefore, both programs' objectives include a balanced portfolio of projects developing both de nova and resequencing technologies.

The goal of research supported under this RFA is to develop new or improved technology to enable rapid, efficient genomic DNA sequencing. New sensing and detection modalities will likely be needed to achieve these goals. New fabrication technologies may also be required. It is therefore anticipated that proposals responding to this RFA will need to involve fundamental and engineering research conducted by multidisciplinary teams of investigators. The guidance for budget requests accommodates the formation of groups having investigators at several institutions, in cases where that is needed to assemble a team of the appropriate balance, breadth, and experience.

Although the ultimate goal is to develop full-scale sequencing systems, independent research on essential components will also be considered responsive to this RFA. However, it will be important for applicants proposing research on system components or concepts to describe how the knowledge gained as a result of their project would be incorporated into a full system that they might subsequently propose to develop, or that is being developed by other groups. Such independent proposals are an important path for pursuing novel high-risk/high-payoff ideas.

Research conducted under this RFA may include development of the computational tools associated with the technology, e.g., to extract sequence information, including signal processing, and to evaluate sequence quality and assign confidence scores, It may also address strategies to assemble the sequence from the information being obtained from the technology or by merging the sequence data with information from parallel technology. However, this RFA will not support development of sequence assembly software independent of technology development to obtain the sequence.

The quality of sequence to be generated by the technology is of paramount importance for this solicitation. Two major factors contributing to genomic sequence quality are per-base accuracy and contiguity of the assembly. Much of the utility of comparative sequence information will derive from characterization of sequence variation between species, and between individuals of a species. Therefore, per-base accuracy must be high enough to distinguish polymorphism at the single-nucleotide level (substitutions, insertions, deletions). Experience and resulting policy have established a target accuracy of not more than 1 error per 10,000 bases. All applications in response to this RFA, whether to develop resequencing or de nova sequencing technologies, must propose achieving per-base quality at least to this standard.

The NHGRI intends to commit approximately $6 million in fiscal year 2004 to fund 3-10 new and/or competitive continuation grants in response to this RFA, and an additional $5 million in fiscal year 2005. For the R21 mechanism, an applicant may request a project period of up to 3 years and a budget of up to $200,000 in direct costs per year. For R21/R33 applications, the total project period may not exceed 5 years, distributed as required for the project; the R21 phase may request a budget up to $200,000 in direct costs and the R33 phase up to $2 million in direct costs per year. For R01 and P01 mechanisms, an applicant may request a project period of up to 5 years and a budget of up to $2 million in direct costs per year. Budgets may exceed this guidance only to accommodate indirect costs to subcontracts. Applicants should be aware that the NHGRI intends to fund as many promising projects, of varying scope, as possible in order to pursue multiple approaches to solving these difficult problems and mitigate risk. Therefore, awards may not be made at the maximum budget level.

Applicant institutions may be for-profit or nonprofit organizations; public or private institutions, such as universities, colleges, hospitals, and laboratories; units of state and local governments; eligible agencies of the federal government; or domestic or foreign institutions/organizations. Any individual with the skills, knowledge, and resources necessary to carry out the proposed research is invited to work with his/her institution to develop an application for support. Individuals from underrepresented racial and ethnic groups as well as individuals with disabilities are always encouraged to apply for NIH programs.

Applications must be prepared using the PHS 398 research grant application instructions and forms (rev. 5/2001). Applications must have a Dun and Bradstreer Data Universal Numbering System (DUNS) number as the Universal Identifier when applying for federal grants or cooperative agreements. The DUNS number can be obtained by calling 1-866-705-5711 or through the website at http://www.dunandbradstreet.com/. The PHS 398 document is available at http://grants.nih.gov/ grants/funding/phs398/phs398.html in an interactive format. For further assistance, contact GrantsInfo, 301-435-0714, e-mail GrantsInfo@ nih.gov.

Letters of intent must be received by 14 September 2004. Applications are due 14 October 2004. The earliest anticipated start date is 1 June 2005.

Contact: Jeffery A. Schloss, Ph.D. Division of Extramural Research, NHGRI, Bldg 31, Rm B2B07, Bethesda, MD 20892-2033 USA, 301-496-7531, fax: [phone], e-mail: [e-mail]. Reference: RFA No. RFA-HG-04-003