Pilot Projects for Sequencing of the Human Genome

Pilot Projects for Sequencing of the Human Genome

NIH Guide, Vol. 24, No. 9, March 10, 1995

RFA: HG-95-005

Letter of Intent Receipt Date: June 1, 1995
Application Receipt Date: August 4, 1995

National Human Genome Research Institute

Purpose

The National Human Genome Research Institute (NHGRI) invites applications to develop and implement pilot projects to test strategies that have the potential to lead to full-scale production sequencing of mammalian DNA, resulting in achieving the goal of the complete, accurate, finished sequence of human DNA by the year 2005.

Healthy People 2000

The Public Health Service (PHS) is committed to achieving the health promotion and disease prevention objectives of "Healthy People 2000," a PHS-led national activity for setting priority areas. This Request for Applications (RFA), Pilot Projects for Sequencing of Human DNA, is related to several priority areas, including cancer, heart disease and stroke, diabetes and chronic disability conditions, maternal and infant health, and others. Potential applicants may obtain a copy of "Healthy People 2000" (Full Report: Stock No. 017-001-00474-0) or "Healthy People 2000" (Summary Report: Stock No. 017-001-00473-1) through the Superintendent of Documents, Government Printing Office, Washington, DC 20402-9325 (telephone 202-783-3238).

Eligibility Requirements

Applications may be submitted by domestic for-profit and non-profit organizations, public and private, such as universities, colleges, hospitals, laboratories, units of state and local governments, and eligible agencies of the federal government. Applications from social/ethnic minority individuals, women, and persons with disabilities are encouraged. Applications from foreign institutions will not be accepted. However, subcontracts to foreign institutions are allowable with sufficient justification.

Collaborations and consortia are encouraged. In such collaborations, the respective contributions should be well-integrated into the design of the application to encourage cross-fertilization of ideas and rapid application of the research to practical purposes.

Mechanism of Support

This RFA will use the National Institutes of Health (NIH) individual research grant (R01), pilot project/feasibility study (R21), research program project (P01), exploratory grant (P20) and center (P50) grant mechanisms. The R21 mechanism is used to support highly creative approaches for which substantial preliminary data are not yet available. R21 awards will be limited to $100,000 direct costs per year for a maximum of two years. The P20 mechanism is used to support groups of outstanding investigators who wish to develop interdisciplinary research programs. P20 awards will be limited to $750,000 direct costs per year. R21 and P20 grants are not renewable, but future project continuation is possible through other grant mechanisms such as R01 or P01. Responsibility for the planning, direction and execution of the proposed project will be solely that of the applicant. Awards will be administered under PHS grants policy as stated in the Public Health Service Grants Policy Statement. The total project period for applications submitted in response to the present RFA may not exceed three years (with the exception of the R21 noted above).

Future unsolicited competing continuation applications will compete with all investigator-initiated applications and be reviewed according to the customary peer review procedures. The anticipated award date is April 1, 1996.

Funds Available

Given the importance of both further technology improvement for DNA sequencing and the need to gain more experience in large-scale sequencing of human DNA, the NHGRI is implementing a bipartite plan to advance the capability of large-scale sequencing of human DNA and to strike a balance between these two program areas. This RFA represents one part of this plan and solicits applications to initiate pilot projects for large-scale sequencing that will increase the experience in production issues such as improved strategies, substrate preparation, data analysis, and project management and organization. The other, complementary part of the plan is announced in RFA HG-95-004, "Improved Electrophoretic DNA Sequencing Technology". The scientific goals of these two RFAs are very different but applications submitted for both RFAs will be funded out of a single set-aside of up to $20 million. Applicants may respond to each RFA, if desired, but should not address the two RFAs in a single application. The anticipated outcome of the plan is to support a set of applications that will provide the balance needed in the NHGRI program to enhance progress toward attainment of the sequence of the human genome.

NHGRI anticipates that projects of widely varying size may be responsive to this RFA and therefore expects to consider for funding projects ranging in cost from $100,000 to several million dollars per year. Only applications found to be of high scientific merit will be considered for funding and all of the funds will not be spent if there are not enough highly meritorious applications. Funding in future years is subject to the availability of funds.

Research Objectives

Background

The NHGRI sponsors basic and applied research concerned with the characterization and analysis of the human genome and the genomes of selected model organisms. The activities encompassed by the NHGRI program include genetic and physical mapping, DNA sequencing, informatics related to mapping and sequencing, gene identification and technology development that will facilitate all of these efforts. The NHGRI, in conjunction with the Department of Energy (DOE), recently formulated a new five-year plan (Science Vol. 262, pp. 43-46, 1993) in which the goals for DNA sequencing were two-fold: 1) development of new technologies to facilitate DNA sequencing and 2) the production of DNA sequence, primarily that of model organisms.

In the past year, there has been significant progress in developing the capability for large-scale DNA sequencing. Several laboratories have generated at least one, and as much as ten, megabases of DNA sequence each. Through this experience, strategic and organizational lessons, such as how to manage large laboratory efforts devoted to rapid data production, have been learned. The capacity of automated sequencing instruments has increased, and newer, higher throughput sequencing instruments are close to a stage at which they could be introduced into a large-scale sequencing environment. However, sequencing technology and sequencing capability must still be improved considerably to achieve the DNA sequencing capability necessary to determine the sequence of the three billion base pairs of human DNA within the time and cost goals for the HGP.

The technological progress and project management experience that have already been achieved warrant the initiation of human DNA sequencing at increased scale. Obtaining more experience in larger scale sequencing of human DNA is also necessitated by the recognition that important issues will be encountered in large-scale sequencing of human DNA that will not be addressed in current large-scale projects directed to sequencing non-human DNA.

One such issue is the large-scale generation of sequencing substrates, which in most cases will be based on high resolution maps. The current human physical mapping goal calls for maps with STSs every 100 kb, on average. Current DNA sequencing methods require maps of considerably higher resolution but, except for relatively short intervals, such high resolution maps are not available for human DNA. The quantity and type of repetitive sequences present in human DNA, and the sheer size of the genome, will present challenges to map construction. Therefore, large-scale human DNA sequencing requires that strategies to convert low resolution maps to sequencing substrates be developed and tested. However, preparation of high resolution physical maps is not in and of itself, a goal of the NHGRI; for reasons of efficiency and quality control, it is noted in the extended five-year plan, that "preparation of sequence-ready sets of clones should be closely associated with an imminent intent to sequence."

A second issue requiring study is the effect of highly conserved, highly repetitive sequences on the assembly of DNA sequence. Large data sets of human DNA sequence will be useful in studying this question. Such data sets will also be useful in developing improved base-calling algorithms.

In recognition of the importance of both further technology improvement and the need to gain more experience in large-scale sequencing of human DNA, the NHGRI is implementing a bipartite plan to advance the capability of large-scale sequencing of human DNA and to strike a balance between these two program areas. This RFA represents one part of this plan and solicits applications to initiate pilot projects for large-scale sequencing that will increase the experience in production issues such as improved strategies, substrate preparation, data analysis, project management and organization. The other, complementary part of the plan is announced in RFA HG-95-004, "Improved Electrophoretic DNA Sequencing Technology". Its purpose is to invite applications for research projects to develop novel automated sequencing technology suitable for large-scale genomic sequencing through the reduction in scale and increased parallelization of existing methods that utilize Sanger sequencing reactions coupled with electrophoretic separation of fragments.

Objectives and Scope

The purpose of this RFA is to solicit proposals for pilot projects to increase the capacity of the NHGRI program for the sequencing of human DNA, i.e., to develop realistic paths that have the potential to lead to full-scale production sequencing of human DNA, resulting in achieving the goal of the complete, accurate, finished sequence of human DNA by the year 2005. Applications are sought that will propose an integrated strategy that will span the entire large-scale sequencing problem, from the up-front preparation of sequencing substrates through the assembly and analysis of the data. The applicant must propose to sequence at least 1 Mb of contiguous DNA over the three year pilot project period.

If the models tested in these pilot projects are to truly contribute to the ultimate goal of the HGP, they will have to be capable of scaling up effectively. Therefore, applicants should clearly address the question of how the proposed approach will scale for efficient, rapid large-scale human DNA sequencing. Importantly, the issues of organization and managing large-scale sequencing should be addressed in so far as is possible, i.e., the pilot project and a tentative plan for a scaled-up project should be presented.

The primary focus of this RFA is to gain experience in sequencing human DNA. However, the inclusion of parallel sequencing of mouse DNA is acceptable, with appropriate justification.

Applicants should address the following issues:

• How the pilot-scale project will scale up and lead to the efficient, cost-effective sequencing of the human genome and attainment of the year 2005 goal.
  
  
• The "up-front" aspects of high throughput sequencing, specifically, the preparation of sequencing substrate. At present, the density of the markers (STSs) on the human physical mapping varies widely on different chromosomes. The HGP goal for the physical map, to be completed by 1998, is to have one STS marker every 100 kb, on average. While such a map is extremely valuable for many uses, additional effort will be needed to either produce a much higher resolution map in regions to be sequenced or to develop a strategy that can use the low resolution map directly in order to generate the DNA substrates for sequencing. Thus it is critical for the applicant to address the transition from the relatively low resolution map information that is available now to a map of the resolution required to support sequencing, or to propose an alternative means of substrate (template) generation. The proposed strategy for doing so should be tested on a region of not less than 5 Mb of DNA. This requirement is intended to ensure that the problem of converting 100 kb maps to sequencing substrates will be done on a region large enough to provide information about the problems that will be encountered in dealing with large-scale substrate preparation. If, on the other hand, the project proposes to sequence regions where only minimal substrate preparation is needed, because the high resolution map has already been constructed, applicants must address how substrate preparation for sequencing the entire human genome will be accomplished.
  
  
• New Technological Developments: Successful applications will need a clear-cut scientific and budgetary strategy for maintaining state-of-the-art sequencing capability. Applicants must address the ways in which the proposed strategy will allow incorporation of the new technological developments in DNA sequencing that will surely arise during the term of the grant. The exportability of any technology or strategies to be developed in the pilot project must also be addressed.
  
  
• Sequence quality: While the ultimate goal of the HGP is to produce DNA sequence of high quality, some applicants may wish to propose, as a viable path toward attaining the final high quality sequence, scenarios that produce sequence that is of lower quality than that expected for the year 2005 product, such as sequence that has gaps and/or a relatively high error rate. In such cases, the applicants must indicate how the pilot project will contribute to attaining the ultimate goal of accurate and complete sequence. Applicants must also estimate the value of any such "lower accuracy" product to the community. Thus, an applicant's overall vision and strategy for how the HGP will accomplish its goal of producing an accurate and complete sequence, is of central importance. Additionally, the applicant must discuss the cost-effectiveness of a strategy that involves an investment in lower accuracy sequencing.
  
  
• Another aspect of sequence quality that applicants must address is the description of confidence levels for the sequence produced in the pilot project.
  
  
• Other cost factors: It is recognized that the cost of sequencing in different pilot projects will vary, depending upon several factors including the laboratory's strategy, state of the starting map, and current level of experience in sequencing. However, as the long-range vision of successful pilot projects must be toward sequencing the entire human genome, applicants must address both their costs through the life of the proposed (3 year) project and projected long-term costs, as part of their overall vision for efficiently accomplishing the goal of a complete and accurate human sequence.
  
  
• Selection of the genomic region(s) to serve as substrate for the pilot project: Because of the small number of projects that will be funded, it will be important that the region(s) chosen for sequencing accurately represent the breadth of "problems" likely to be encountered in the sequence of the entire genome.
  
  
• The U.S. HGP has adopted a policy of encouraging rapid release of mapping and sequencing data into public databases. Guidelines developed by NHGRI and DOE advisors recommend that data be made publicly available within six months of the time they are verified. Applicants should fully describe their plans for data release.

Post-Award Management

During the course of the grant period, mapping and cloning technologies will improve, genomic technologies will evolve, and the rate of progress and focus of work supported by the grant(s) may change. It is expected that the Principal Investigator will make any necessary adjustment in scientific direction to accommodate the changing environment. In order to ensure that the project(s) remains focused on appropriate goals, incorporates new technological advances and makes sufficient progress, scientific and programmatic visits to the grantee will be conducted at a frequency to be negotiated with the awardee.

Letter of Intent

Prospective applicants are asked to submit, by June 15, 1995, a letter of intent that includes a descriptive title of the proposed research, the name, address, and telephone number of the Principal Investigator, the identities of other key personnel and participating institutions, and the number and title of the RFA in response to which the application may be submitted. Any applicant planning to submit an application for more than $500,000 direct cost per year must have contacted staff, listed below, before submitting the application or it will be returned to the applicant.

Although a letter of intent is not required, is not binding, and does not enter into the review of subsequent applications, the information that it contains allows IC staff to estimate the potential review workload and to avoid conflict of interest in the review.

The letter of intent is to be sent to:

Jane L. Peterson, Ph.D. or
Jeffery A. Schloss, Ph.D.
Mammalian Genomics Branch
National Human Genome Research Institute
Building 38A, Room 610
38 Library Drive MSC 6050
Bethesda, MD 20892-6050
Phone: (301) 496-7531
Fax: (301) 480-2770
E-mail: petersoj@odder.nhgri.nih.gov
E-mail: schlosj@odder.nhgri.nih.gov

Application Procedures

The research grant application form PHS 398 (rev. 9/91) is to be used in applying for these grants. These forms are available at most institutional offices of sponsored research or from the Office of Grants Inquiries, Room No. 1040, 6701 Rockledge Drive, Division of Research Grants, National Institutes of Health, Bethesda, MD 20892. Phone: (301) 594-7248.

The RFA label available in the PHS 398 (rev. 9/91) application form must be affixed to the bottom of the face page of the application. 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. In addition, the RFA title and number must be typed on line 2a of the face page of the application form and the YES box must be marked.

Submit a signed, typewritten original of the application, including the Checklist, and three signed, photocopies, in one package to:

Division of Research Grants
National Institutes of Health
Room 1040
6701 Rockledge Drive
Bethesda, MD 20892
(Express Mail zip code is 20817)

At the time of submission, two additional copies of the application must also be sent to:

Ms. Linda Engel
Office of Scientific Review
National Human Genome Research Institute
Building 38A, Room 604, MSC 6050
38 Library Drive
Bethesda, MD 20892-6050
E-mail: engell@odder.nhgri.nih.gov

Applications must be received by August 4, 1995. If an application is received after that date, it will be returned to the applicant without review. The Division of Research Grants (DRG) will not accept any application in response to this announcement that is essentially the same as one currently pending initial review, unless the applicant withdraws the pending application. The DRG will not accept any application that is essentially the same as one already 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.

Review Considerations

Upon receipt, applications will be reviewed for completeness by DRG and for responsiveness to the RFA by the NHGRI program staff. Incomplete applications will be returned to the applicant without further consideration. If the application is not responsive to the RFA, NHGRI staff will contact the applicant to determine whether to return the application to the applicant or submit it for review in competition with unsolicited applications at the next review cycle.

Those applications that are complete and responsive will be evaluated in accordance with the criteria stated below for scientific/technical merit by an appropriate peer review group convened by the NHGRI. Site visits will not be performed as part of the initial review and applicant interviews will only be conducted in exceptional cases. Therefore, applicants must present a complete and well-justified written proposal. As part of the initial merit review, all applications will receive a written critique and may undergo a process in which only those applications deemed to have the highest scientific merit will be discussed and assigned a priority score. All applications will receive a second level of review by the National Advisory Council for Human Genome Research.

Review Criteria

• Scientific and technical merit of the proposed research to meet the objectives of this RFA, including:
  • novelty of the strategies and methods proposed.
  • exportability of the strategies and technologies under investigation.
  • quality of the plan describing how the genome will be sequenced if the strategies and technologies are not exportable.
  • plan for incorporating new technologies (e.g., a new base-calling instrument) at reasonable cost.
• Significance and originality of the research and methodological approaches.
• Feasibility of the research and adequacy of the experimental design.
• Likelihood that the pilot project will be able to scale to a successful system for sequencing the entire human genome.
• Qualifications and research experience of the Principal Investigator and staff, particularly, but not exclusively, in the area of the proposed research.
• Quality of integration of the proposed solutions to critical large-scale sequencing issues (upstream to base-calling to downstream).
• Quality of the management plan.
• Availability of the facilities, resources and technology necessary to perform the research, and the level of institutional commitment.
• Appropriateness of the proposed budget and time-line in relation to the proposed research.

Additional factors to be considered in the evaluation of competing renewal applications will be:

• Prior demonstrated success in increasing throughput, decreasing cost, and maintaining accuracy in DNA sequencing.
• Timeliness with which data have been placed in the public domain.

Award Criteria

The earliest anticipated date of award is April 1, 1996. Proposals submitted in response to this RFA and RFA HG-95-04 will compete for the same pool of funds. Factors that will be used to make award decisions are as follows:

• Quality of the proposed project as determined by peer review.
• Promise of the proposed program to contribute to the goals of RFAs HG-95-04 and HG-95-05, and to the balance between further technology development and pilot sequence production in the NHGRI sequencing program.
• Overall contribution of the pilot project to knowledge and experience required to sequence the human genome in its entirety.
• Selection of region(s) for study that will present the array of problems likely to be encountered in sequencing the entire human genome.
• Nature and extent of the plans for placing DNA sequence data in the public domain and disseminating information on technological developments in a timely manner.
• Availability of funds.

Inquiries

Written and telephone inquiries concerning this RFA are encouraged. The opportunity to clarify any issues or questions from potential applicants is welcome.

Direct inquiries regarding programmatic issues to:

Jane L. Peterson, Ph.D. or
Jeffery A. Schloss, Ph.D.
Mammalian Genomics Branch
National Human Genome Research Institute
38 Library Drive
Building 38A, Room 610, MSC 6050
Bethesda, MD 20892-6050
Phone: (301) 496-7531
FAX: (301) 480-2770
E-mail: petersoj@odder.nhgri.nih.gov
E-mail: schlossj@odder.nhgri.nih.gov

Direct inquiries regarding fiscal matters to:

Ms. Jean Cahill
Grants Management Officer
National Human Genome Research Institute
38 Library Drive
Building 38A, Room 613, MSC 6050
Bethesda, MD 20892-6050
Phone: (301) 402-0733
E-mail: cahillj@odder.nhgri.nih.gov

Authority and Regulations

This program is described in the Catalog of Federal Domestic Assistance No. 93.172. Awards are made under authorization of the Public Health Service Act, Title IV, Part A (Public Law 78-410, as amended by Public Law 99-158, 42 USC 241 and 285) and administered under PHS grants policies and Federal Regulations 42 CFR 52 and 45 CFR Part 74. This program is not subject to the intergovernmental review requirements of Executive Order 12372 or Health Systems Agency review.

The Public Health Service (PHS) strongly encourages all grant recipients to provide a smoke-free workplace and promote the non-use of all tobacco products. This is consistent with the PHS mission to protect and advance the physical and mental health of the American people.

Last Reviewed: February 25, 2012