Q2C@nihcu.bitnet (09/05/90)
FEASIBILITY STUDIES FOR LARGE-SCALE DNA SEQUENCING OF REGIONS OF HIGH BIOLOGICAL INTEREST RFA AVAILABLE: HG-90-03 P.T. 34; K.W. 0755045, 1004000, 0755018 National Center For Human Genome Research Letter of Intent Receipt Date: October 15, 1990 Application Receipt Date: December 3, 1990 The National Center for Human Genome Research (NCHGR) invites applications for assistance awards to support feasibility studies using advanced state-of-the-art DNA sequencing technology to accomplish large-scale sequencing projects at a higher rate and lower cost than is currently possible. This program is described in the Catalog of Federal Domestic Assistance No. 13.172. Awards will be made under the authority of the Public Health Service Act, Sections 301 (Public Law 78-410, as amended 42 U.S.C. 241) and administered under PHS grants policies and Federal Regulations 42 CFR Part 52 and 45 CFR Part 74. This program is not subject to the intergovernmental review requirement of Executive Order 12373 or to Health System Agency review. BACKGROUND The NCHGR sponsors basic and applied research concerned with the development and application of new technologies for the characterization and analysis of the human genome and the genomes of important model organisms. The activities encompassed by the NCHGR program include genetic and physical mapping, DNA sequencing, and informatics related to mapping and sequencing. The NCHGR, in conjunction with the Department of Energy, recently formulated a five-year plan that identifies areas where further research, including new technology development, is needed before the characterization of the human and other genomes can proceed to the degree envisioned by the scientific community. With respect to sequencing megabase regions of DNA, it is clear that rates of sequence acquisition achievable today must be increased at least 10- to 100-fold, and DNA sequencing costs must be reduced at least 10-fold before large-scale sequencing, on the order of a human chromosome, can be considered. Current technology for DNA sequencing includes both manual and automated methods. Sequencing DNA by these methods is estimated to cost between $2 and $5 (total cost) per base pair. However, currently available sequencing techniques and strategies have not been tested on a large scale. Thus, it is possible that current or improved methods, when used at the megabase level, and when combined with economies of scale, new strategies, improved automation, and/or new technologies, will significantly lower the cost of DNA sequencing. The purpose of this Request for Applications (RFA) is to support investigator-initiated research projects that will extend the limits of advanced state-of-the-art technology considerably further than has yet been attempted. DEFINITION OF LARGE-SCALE SEQUENCING The Program Advisory Committee on the Human Genome has suggested that, at the present time, a reasonable definition of a "large-scale sequencing project" is one that attempts to determine on the order of three megabase pairs of (largely) contiguous sequence in three years (by comparison, the largest DNA sequence completed to date is a viral genome of 240 kilobase pairs, work that took several years to complete). Continuity is an important characteristic of the DNA sequence to be obtained; the scientific problems that arise in considering sequencing a one-megabase region are different from those involved in sequencing 1000 one- kilobase regions. The Committee estimated that a rate of 2- 5 megabase pairs of DNA sequence per year in the subsequent years should be attainable. Similarly, reduction of the cost of DNA sequencing to approximately $0.75 per base pair within three years and to $0.50 per base pair within five years was recommended to be a reasonable guide. As these levels are well beyond anything that has been achieved to date, applicants are encouraged to consider them as guidelines. The NCHGR encourages discussion of these guidelines by applicants, including an estimate of whether they can be achieved. DATA MANAGEMENT Another essential component of DNA sequencing projects that also needs to be investigated on a large scale is data management. Although software and database packages are currently available for acquisition and assembly of DNA sequence, they have been developed for relatively small- scale applications. Thus, it is not known whether any of these will be adequate for use in megabase sequencing projects. It is understood that different sequencing strategies will have different data handling needs and, therefore, no one solution to data management problems for large-scale sequencing is likely. While, in the long run, software may have to be developed for interpretation of the large segments of DNA sequence generated by the human genome project, the informatics priorities for this RFA will be primarily directed toward the design, development, and testing of software for data acquisition, assembly, and management. RESEARCH SCOPE Projects responsive to this RFA should test hypotheses and new research strategies designed to yield information on the feasibility of determining large amounts of DNA sequence rapidly and in a cost-effective manner. It is anticipated that such projects will involve an integrated approach that addresses a number of identifiable aspects of the problem, including: o The biological materials to be sequenced, e.g., genomic DNA or overlapping clones representing a megabase-sized region. Applicants are encouraged to select DNA comprising regions of high biological interest; o Scale-up of DNA sequencing technology to allow large-scale, high-throughput, and low-cost acquisition of DNA sequence data. Note: in order to have a uniform approach for estimating the cost of sequencing, applicants should calculate the cost per base of finished DNA sequence ready for publication and/or submission to a public database. The cost figure should include all direct and indirect expenses, starting either directly with the DNA of the organism or with appropriately large fragments (YAC or cosmid clones) and ending with the final finished sequence. Neither the costs of any necessary laboratory renovation nor the costs associated with the interpretation of DNA sequence data should be considered as a part of the per base cost of sequence determination; o Types of errors and rates of error that will occur in large-scale DNA sequencing, and a discussion of what level of error will be acceptable; o Overall strategies, including quality control systems, and plans for organizing the research group; o Systems for data acquisition, data management, sequence assembly, and error estimation. DATA RELEASE The policy of the U.S. Public Health Service (PHS) states that "when resources are developed with PHS funds and the associated research findings have been published . . . it is essential that they be made readily available for research purposes to the scientific community." Applicants will be expected to follow this policy. Generating large amounts of DNA sequence will raise additional questions with respect to data release and public accessibility to DNA sequence data because much of this data will never be published in journals or will not be published in its entirety. The NCHGR considers the timely release of data to the scientific community to be critical and encourages applicants to release all sequence data, including those that are not published, to a public database in a timely fashion. This is an area of active discussion within the scientific community. Although it will not be used as a review criteria, the NCHGR is interested in the investigator's analysis and evaluation of issues related to the timely release of data, such as a timetable for data release, the criteria for "finished" DNA sequence (i.e., sequence that is ready to be publicly released), and the intervals (e.g., number of nucleotides or number of months) at which data will be released. MECHANISM OF SUPPORT Support for this program will be through research grants (R01s). Applicants may request up to five years of support. For grants awarded for more than three years, competitive renewals will be due at the end of the third year to allow a determination of whether the project is satisfactorily meeting its stated objectives. As a result of that review, funds may be continued at the level recommended or reduced to phase out the project by the end of the original project period. An annual meeting is being planned to assist grantees receiving funds under this RFA in maintaining communication with other investigators working on the development of large-scale DNA sequencing methods and in obtaining rapid access to those developments. Funds for travel to this meeting for as many as two investigators can be requested. The total amount of support available for grants under this RFA (approximately $6 million) is contingent upon the appropriation of funds for this purpose. It is anticipated that up to three awards will be made during fiscal year 1991. There is no set limit on the size of each award. Rather, each investigator should propose a budget adequate to accomplish the work proposed. The number of awards is contingent upon the quality of the applications received; if there are a large number of meritorious applications, consideration will be given to increasing the number of awards. It is possible that additional RFAs soliciting applications on this topic may be published in the future. LETTER OF INTENT It is strongly recommended that potential applicants contact NCHGR staff to discuss research objectives. Potential applicants are asked to submit a letter of intent by October 15, 1990. This letter should include a descriptive title of the proposed research, names of principal investigators and other key investigators and their institutions. The letter of intent is requested in order to provide an indication of the number and scope of applications to be reviewed. The letter of intent does not commit the sender to submit an application, nor is it a requirement for submission of an application. Letters of intent should be sent directly to: Dr. Jane L. Peterson Chief, Research Centers Branch National Center for Human Genome Research Building 38A, Room 610 National Institutes of Health Bethesda, MD 20892 Telephone: (301) 496-7531 E-mail: jp2@nihcu.bitnet; jp2@cu.nih.gov APPLICATION AND REVIEW PROCEDURES Applications in response to this announcement will be reviewed in accordance with the usual NIH peer review procedures. If the application submitted in response to this RFA is substantially similar to a research grant application already submitted to the NIH for review, but has not yet been reviewed, the applicant will be asked to withdraw either the pending application or the new one. Simultaneous submission of identical applications will not be allowed, nor will essentially identical applications be reviewed by different review committees. Therefore, an application cannot be submitted in response to this RFA which is essentially identical to one that has already been reviewed. This does not preclude the submission of substantial revisions of applications already reviewed, but such applications must include an Introduction addressing the previous critique. Applications will first be screened for responsiveness to this RFA by NIH staff. Those deemed nonresponsive will be returned to the applicant. If a large number of responsive applications is received, they will undergo a preliminary peer review to identify the most meritorious ones. Applications that are deemed non-competitive by this peer review will receive only a brief critique and will not be reviewed further. The remaining applications will be reviewed for scientific and technical merit by an initial review group (IRG) assembled by the Office of Scientific Review, NCHGR. A second level of review will be conducted by a national advisory council. Review criteria include the following: o Overall scientific and technical merit of the research; o The potential for the proposed work for attaining the research objectives outlined in this RFA; o Training, experience, research competence, and dedication of the investigator(s); o Adequacy of available facilities; o Provision for the protection of human subjects and the humane care of animals; and o Appropriateness of the requested budget for the work proposed. Applications should be submitted using the form PHS 398 (rev. 10/88). The RFA label available in the revised application kit MUST be affixed to the bottom of the face page. Failure to use this label could result in delayed processing of the application such that it may not reach the review committee in time for review. Application kits are available in the business or grants office at most academic or research institutions, or from the Division of Research Grants, National Institutes of Health. Applications will be accepted in accordance with the following schedule: TIMETABLE: Receipt Date: December 3, 1990 IRG Review: Feb/March, 1991 Council Review: May 1991 Earliest Funding Date: July 1991 It is essential that applicants type "Feasibility Studies for Large Scale DNA Sequencing of Regions of High Biological Interest" and the RFA number HG-90-03 on line 2 on the face page of the application form. The original and four copies of the application should be submitted to the following office: Grant Application Receipt Office Division of Research Grants National Institutes of Health Westwood Building, Room 240 Bethesda, MD 20892** To expedite the review process, it is important to submit two copies of your application directly to: Office of Scientific Review National Center for Human Genome Research Building 38A, Room 604 National Institutes of Health Bethesda, MD 20892 Funding decisions will be based on recommendations of the initial review group and the advisory council regarding the scientific merit and program relevance. For more information and the complete RFA, please contact: Dr. Jane L. Peterson Chief, Research Centers Branch National Center for Human Genome Research Building 38A, Room 610 National Institutes of Health Bethesda, MD 20892 Telephone: (301) 496-7531 E-mail: jp2@nihcu.bitnet; jp2@cu.nih.gov