Part I Overview Information

Department of Health and Human Services

Participating Organizations
National Institutes of Health (NIH), (http://www.nih.gov)

Components of Participating Organizations
National Human Genome Research Institute (NHGRI), (http://www.genome.gov)
National Cancer Institute (NCI), (http://www.nci.nih.gov)
National Center for Research Resources (NCRR), (http://www.ncrr.nih.gov)
National Eye Institute (NEI), (http://www.nei.nih.gov)
National Heart, Lung, and Blood Institute (NHLBI), (http://www.nhlbi.nih.gov/)
National Institute on Aging (NIA), (http://www.nia.nih.gov)
National Institute on Alcohol Abuse and Alcoholism (NIAAA), (http://www.niaaa.nih.gov)
National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), (http://www.niams.nih.gov)
National Institute of Child Health and Human Development (NICHD), (http://www.nichd.nih.gov)
National Institute on Drug Abuse (NIDA), (http://www.nida.nih.gov)
National Institute of Deafness and Other Communication Disorders (NIDCD), (http://www.nidcd.nih.gov)
National Institute of Dental and Craniofacial Research (NIDCR), (http://www.nidcr.nih.gov)
National Institute of Environmental Health Sciences (NIEHS), (http://www.niehs.nih.gov)
National Institute of Mental Health (NIMH), (http://www.nimh.nih.gov)
National Institute of Neurological Disorder and Stroke (NINDS), (http://www.ninds.nih.gov)

Title: Completion of a Comprehensive Mouse Knockout Resource

Announcement Type
New

Update: The following updates relating to this announcement have been issued:

Request For Applications (RFA) Number: RFA-HG-05-007

Catalog of Federal Domestic Assistance Number(s)
93.172, 93.396, 93.389, 93.867, 93.837, 93.838, 93.839, 93.233, 93.866, 93.273, 93.846, 93.865, 93.279, 93.173, 93.121, 93.114, 93.242, 93.853

Key Dates:
Release Date: September 8, 2005
Letters of Intent Receipt Date(s): October 20, 2005
Application Receipt Dates(s): November 22, 2005
Peer Review Date(s): January - March, 2006
Council Review Date(s): May 2006
Earliest Anticipated Start Date: July 1, 2006
Additional Information To Be Available Date (Url Activation Date):
Expiration Date: November 23, 2005

Applicant Information Meeting:
October 6, 2005, 2-4 p.m.
NIH main Campus, Bldg 50
1st Floor Conference Center
National Institutes of Health (NIH)
9000 Rockville Pike
Bethesda, Maryland 20892

Due Dates for E.O. 12372
Not Applicable

Additional Overview Content

Executive Summary

Table of Contents

Part I Overview Information

Part II Full Text of Announcement

  Section I. Funding Opportunity Description
   1. Research Objectives

  Section II. Award Information
   1. Mechanism(s) of Support
   2. Funds Available

  Section III. Eligibility Information
   1. Eligible Applicants
     A. Eligible Institutions
     B. Eligible Individuals
   2.Cost Sharing or Matching
   3. Other - Special Eligibility Criteria

  Section IV. Application and Submission Information
   1. Address to Request Application Information
   2. Content and Form of Application Submission
   3. Submission Dates and Times
     A. Receipt and Review and Anticipated Start Dates
       1. Letter of Intent
     B. Sending an Application to the NIH
     C. Application Processing
   4. Intergovernmental Review
   5. Funding Restrictions
   6. Other Submission Requirements

 Section V. Application Review Information
   1. Criteria
   2. Review and Selection Process
     A. Additional Review Criteria
     B. Additional Review Considerations
     C. Sharing Research Data
     D. Sharing Research Resources
   3. Anticipated Announcement and Award Dates

  Section VI. Award Administration Information
   1. Award Notices
   2. Administrative and National Policy Requirements
   3. Reporting

  Section VII. Agency Contact(s)
   1. Scientific/Research Contact(s)
   2. Peer Review Contact(s)
   3. Financial/ Grants Management Contact(s)

  Section VIII. Other Information - Required Federal Citations

Part II - Full Text of Announcement
Section I. Funding Opportunity Description

1. Research Objectives

The purpose of this RFA is to solicit applications for research projects to initiate a trans-NIH program for the production of a comprehensive resource of mouse mutants in which every gene in the mouse genome has been knocked out by a null mutation marked with a reporter system of high utility. The ideal resource would be one in which all of the mutations are carried on a uniform background in strain C57BL/6, which is the strain most widely utilized by mouse researchers. But the NIH recognizes that, at present, there are certain technical problems, primarily related to low efficiency, with the use of C57BL/6 as the background strain for this type of high-throughput project. Therefore, the primary focus of this solicitation will be on construction of the mutations, and a secondary focus will be on the choice of mouse stain. However, applications that propose approaches to the cost-efficient generation of the mutations directly in strain C57BL/6 will be given preference for funding.

This RFA is being issued to further the value of the mouse as a powerful and important tool in the study of human disease. For many years, mouse mutants with phenotypes that mimic human traits have served as critical research tools in understanding the genetics underlying mammalian biology. The importance of the mouse as a model organism was indicated by the inclusion of a goal for the construction of genetic and physical maps of the mouse genome in the initial plan for the Human Genome Project (HGP). In fact, the HGP was actually able to accomplish significantly more than generating such maps of the mouse genome, and a high quality, finished sequence of the mouse genome (strain C57BL/6) will be completed by the end of 2005. Another major genomic resource for mouse research has been developed by the Mammalian Gene Collection (MGC) project (http://mgc.nci.nih.gov/), which as of July 2005 included 15,325 full-ORF (open reading frame) cDNA clones, representing 11,501 individual mouse genes.  The goal of the MGC mouse cDNA program is to produce, by 2007, at least one full-ORF cDNA clone for each of the ~18,000 currently well-defined mouse genes.

To complement the mouse genome sequence and full-length cDNA collection, a defined genetic resource that can be used to elucidate gene function is needed. To this end, the attendees at an international meeting convened in the fall of 2003 strongly supported the establishment of a focused, large-scale international effort to produce a publicly available, comprehensive collection of mouse knockout strains, i.e. a library of mice containing a null mutation in every gene in the mouse genome (Austin, C.P, et al. Nature 36, 921-924 (2004). The meeting attendees also recommended a phased production approach, beginning with the construction of a resource of ES cells comprising a comprehensive collection of null, ideally conditional, alleles. This was to be followed by the construction of mice from the ES cells and then phenotyping the mice with an increasingly sophisticated set of tests: Tier 1, or basic phenotyping, was to be done centrally on nearly all of the mice created by the project; and Tier 2, microarray and transcriptome based phenotyping, was to be carried out on a subset of these mice. Subsequent specialized phenotyping and further in depth analyses on specific mice would then be supported by individual labs.

There has subsequently been a significant set of international efforts to further define and deliver the proposed resource. In March 2005, the NIH held a workshop to update the concept and assess the status of the field (http://www.genome.gov/15014549). At that meeting, information was presented about the number of existing mouse knockouts (primarily null mutations); this information was based on data taken from the Mouse Genome Database (data curated from the published scientific literature) maintained by the Mammalian Genome Informatics (MGI) at Jackson Laboratories, gene trap sequence data submitted to the data base of genome survey sequencing (dbGSS) at the National Center for Biotechnology Information (NCBI), and a new inventory of available, but unreported, knockout mice. In summary, mutations, primarily nulls, have been constructed in approximately 10,000 unique mouse genes by either gene-trap or targeted knockout methods; although the response to the inventory request on unpublished mouse knockouts was good, it was not complete, so it is almost certain that this number is an underestimate of the number of unique mouse genes that have already been knocked out. However, most of these are still unavailable to the scientific public, and so cannot be considered as available to the proposed effort until they are deposited in public repositories.

Several international groups have been funded, or have planned, for efforts to create conditional mouse knockouts. For example, the European Conditional Mouse Mutagenesis Program (EUCOMM) has received funding to generate 20,000 conditional mutations (12,000 conditional gene-trap mutations and 8,000 conditional targeted mutations) in ES cells, all in strain 129. A complementary project is being considered in Canada. However, it was noted at the NIH workshop that, to date, the high throughput construction of conditional null mutant mice from mutated ES cells has not been validated. Furthermore, there have been a few reports that the procedures used to manipulate the conditional mutations in mice can introduce genetic artifacts. Therefore, the NIH workshop endorsed the recommendation of the 2003 meeting that a comprehensive collection of null mutants is an important tool for dissecting mammalian gene function and would be a critical complement to the conditional mutant resource being constructed elsewhere. Additionally, the NIH workshop endorsed several other points: (1) the preference of researchers for a resource fully based on the C57BL/6 strain, if technology were available to do that; (2) given that nearly 10,000 of the approximately 20-25,000 genes in the mouse genome have been knocked out (made null), isolation of mutations in a minimum of 10,000 remaining mouse genes is needed to complete the current resource; (3) given that of the estimated 10,000 genes that have already been knocked out, only 3 to 4,000 are represented in existing knockout mice currently residing in research laboratories around the world, an effort to collect and preserve as many as possible of these existing mutants as embryos is of high priority. Through this RFA and two companion RFAs (RFA-DA-06-009 and RFA-HG-05-008) the NIH is now establishing a Knockout Mouse Project (KOMP) to address the goals identified by the international research community over the past two years.

Given current knowledge and technology, it is possible that the first step toward creating a complete resource on a homogenous genetic background may have to be construction of the complete set of knockout mutations in different strain backgrounds. For example, to date, nearly 60% of the genes in the mouse genome have been knocked out using either gene trapping methods (http://www.igtc.ca) or gene targeting by homologous recombination, both of which, for technical reasons, have usually used strain 129 as the background. As gene trapping is not likely to be able to access all genes, one approach to completing a comprehensive mouse null mutant resource would involve the use of gene targeting methodology in ES cells to make null mutations in the remaining genes. Thus, one path toward a C57BL/6 resource might initially have to involve a heterogeneous resource of nulls in at least one other background. This would, unfortunately, require subsequent breeding to move the mutation collection to a C57BL/6 background, which would involve considerable additional expense and time.

To attain the goal of a fully C57BL/6-based null resource more efficiently, it would be desirable if the gene targeting work could be done in C57BL/6. There have been some reports of improved efficiency in the use of C57BL/6 ES cells for targeted mutagenesis. Thus, applications that propose high-throughput, cost-efficient gene targeting directly in C57BL/6 would be considered responsive to this RFA. In addition, a companion RFA (RFA-DA-06-009) is being issued to support research projects for the further development of the C57BL/6 ES cell system as a host for gene targeting. If this technology were to progress rapidly enough during the next three years, it is conceivable that any efforts funded under the present RFA-HG-05-007 would be asked to shift the gene targeting work to use a C57BL/6 ES cell system developed under RFA-DA-06-009.

Another conceivable approach to generating a C57BL/6-based resource would be to create a full set of new null mutants directly in that strain background. Such an approach would require new, efficient low-cost technologies, and there are reports that transposon-mediated mutagenesis technology may already be sufficiently specific, high throughput and inexpensive enough to produce such a resource, or at least a significant fraction of it, directly in mouse embryos (as opposed to ES cells). However, given the lack of general information about this approach, it is not clear what fraction of mouse genes could be expected to be satisfactorily mutated (i.e., carry a null mutation) by this approach. Furthermore, it would be desirable if the technology could create a null mutation that is marked with a reporter and is fully reversible, such that every gene could be returned to wild-type expression levels and patterns.

Any application that proposes a plan to generate a complete or nearly complete set of knockout mutations of the genes in the mouse genome in the C57BL/6 genetic background, or to make significant progress toward that ultimate goal through obtaining null mutations (in C57BL/6 or another genetic background if necessary) marked with a reporter in the 10,000 mouse genes for which such mutants have not yet been isolated will be considered to be responsive to this RFA. Applicants to this RFA should propose creative, highly efficient and cost-effective high-throughput methods to contribute to the goal of generating a C57BL/6 null mutant mouse resource. Applicants are not required to propose obtaining all 10,000 mutants, but must propose the generation of a significant portion (at least 25%) within five years. Approaches that will be considered include, but are not limited to, gene targeting in strain C57BL/6 ES cells, gene targeting in 129 ES cells, transposon-based approaches or other approaches, including gene trapping, to directly generate ES cells or mutant mice in the C57BL/6 background. All proposals, whether to work in the C57BL/6 background directly or to complete the genome-wide null mutant resource in a strain other than C57BL/6, must justify the strain to be used on the basis of scientific utility, throughput, and cost effectiveness. For any approach (gene targeting or insertional mutagenesis), the proposed plans must be based on realistic, documentable current capabilities. (see SPECIAL GUIDANCE FOR APPLICANTS and http://www.genome.gov/15515029 for information that may be useful for the applicant in describing and documenting past and planned activities), and may include a ramp-up period. Factors that will be considered in making funding decisions will include both the timetable and the cost of eventually constructing the C57BL/6-based resource.

Additional background and information on gene targeting.

This technology is well established as a high throughput technology in strain 129 and is one of the complementary technologies that might be used to complete the set of null mutations for the entire mouse genome. Success in gene targeting using strain C57BL/6 has been less robust, but recent reports suggest that improved methods have been, or are being, developed. The scope of this RFA includes efforts to utilize gene targeting in either strain to complete the set of null mutations. It is expected that the gene targeting approach is necessary to complement either the existing set of gene trap and gene targeted mutations or the set of genes that would be mutated by a transposon/gene trap-based approach in C57BL/6. In the proposal, the applicant should not specify the genes that will be targeted, as these will be chosen after funding and after further analysis of the existing knockout mutations or of those produced by any new technologies funded under this RFA.

Applications considered responsive to this RFA will include proposals to use gene-targeting methods to complete the null mutant resource and may be made in ES cells of either the C57BL/6 or 129 background. It is expected that an applicant who proposes to use C57BL/6 as the ES cell background will provide convincing data of the efficiency of utilizing that strain as compared to the 129 system. Applicants should note that RFA-DA-06-009, which calls for technology development to improve the efficiency of germline transmission using C57BL/6 ES cells, is being issued at the same time. A decision as to whether further development of the C57BL/6 ES cell system is needed will be made after the review of the applications received in response to the two RFAs (the present RFA and DA-06-009), and will be partially determined by whether any of the applications received in response to the present RFA to complete the null mutant resource in C57BL/6 are likely to be successful. Alternatively, if no effort utilizing C57BL/6 as the background for generating the resource is considered meritorious enough for funding in July 2006, it is hoped that improvements in the technology will be achieved under RFA-DA-06-009 within 2 to 3 years. If that were to happen, any awards funded under the present RFA will be asked to seriously consider shifting their efforts to produce the remainder of the resource with the newly improved C57BL/6 ES cell lines. Therefore, applicants who propose the initial use of 129 as the ES cell background should also address the possibility of converting to use of C57BL/6 ES cells if and when that technology becomes competitive.

As this RFA calls for proposals for the high-throughput, cost-effective production of null mutants, it will be important for the applicant to provide enough detail in the application to allow reviewers to adequately assess the merit of the proposal. The following paragraphs describe the information that the applicant should address in a gene targeting production pipeline.

Gene targeting production pipeline: Current high throughput approaches to generate targeted mouse mutants can be described according to the following components: (a) generation of the targeting construct using BAC recombineering, (b) electroporation of the targeting construct into ES cells and screening of the ES cells to identify clones in which proper integration of the construct has occurred, and (c) expansion and freezing of the mutant ES cell clones. The application should be organized so that each of these components is addressed clearly (see SPECIAL GUIDANCE FOR APPLICANTS at the end of this announcement for further details that may be useful in describing these components and for cost spreadsheets that can be used as a format and are available at http://www.genome.gov/15515029). The applicant may propose appropriate collaborations and/or subcontracts for the specific components, but must describe how they will integrate such efforts with their own program.

(a) Generation of the targeting construct using BAC recombineering. The applicant must describe the construction of a targeting vector library consisting of a null mutation marked with a maximally useful reporter for at least the number of unique genes proposed to be mutated. The targeting vector library must be made with genomic DNA from strain C57BL/6. However, while t he sequence of the C57BL/6 genome will be substantially complete by the time applications in response to this RFA will be due, annotation will not be sufficient for all genes by the time that funding could begin. Thus, the applicant should address the issue of generating the constructs for the entire set of genes being proposed over the course of the five-year program, as well as the projected throughput, production goals and explicit milestones, characteristics of the constructs, method(s) for probe generation, method(s) for confirming that the intended mutation has been generated, the expected success rate for targeting vector construction, other quality control measures, the timeline and all other pertinent factors

Constructs from the targeting vector library will be used for construction of null mutants whether the ES cells used are from the strain C57BL/6 or 129 background. Applicants proposing to use 129-derived ES cells must address how the constructs will be engineered to ensure high rates of recombination. Methods other than BAC recombineering will be considered, provided that they produce a high rate of homologous recombination.

Reporter system. The applicant should propose the use of a reporter system with as broad utility as possible, considering the variety of uses of reporter technology. Breadth of utility may be achieved by a single reporter, tandem reporters, or an exchangeable system, although applicants are not limited to these examples.

(b) Electroporation of the targeting construct into ES cells and screening of the ES cells to identify clones in which proper integration of the construct has occurred. The applicant should present sufficiently detailed plans for setting up and maintaining a production pipeline for the large-scale generation of mutant ES cells. The discussion should address the electroporation and colony-picking steps that will be used to generate the ES cells, the projected throughput , the production goals and explicit milestones , the method(s) for screening to determine if integration has occurred correctly, the characteristics and quality expected of the mutant ES cell line's potential to be transmitted through the germline in mice, a timeline, and all other pertinent factors. As mentioned above, it would be preferable to generate as much of this resource as possible in the C57BL/6 background. Applicants who propose to utilize C57BL/6 must include convincing data that a sufficiently high rate of homologous recombination and germline transmission can be achieved to justify the use of the C57BL/6 on a cost-benefit basis. The efficiency of the mutation being transmitted through the germline in a high throughput process should be a rate of at least 1 in 4 ES clones for each mutated gene. The proposal must also include a quality control plan that demonstrates that mice carrying and transmitting the null mutation can be produced by the large-scale process. This plan should include an estimate of the number of ES cell clones per gene that must be injected as part of the quality control process and the number or % of unique genes that need to be tested. As mentioned above, to be considered responsive to the RFA, an application must propose to produce at least 25% of the 10,000 unique mutant ES cells to be generated by the KOMP over the course of five years. The list of genes to be targeted will be provided and updated regularly during the course of the five years by a panel of individuals charged by NIH with prioritization of targets.

(c) Expansion and freezing of mutant ES cell clones. All reagents produced by this program will be made publicly available through designated NIH supported repositories. The applicant should describe the steps that will be taken to expand and freeze the mutant ES cells in compliance with the standards for international repositories, as well as the protocol for depositing them in an NIH-designated repository. The applicant should provide information that demonstrates either a track record of successfully completing these tasks on the scale that will be required for this RFA or the ability to successfully scale up to meet the requirements of this RFA.

Additional background on transposon mutagenesis and gene trapping.

It is estimated that ES cells derived from strain 129 have already been used to produce putative null gene trap mutations that represent nearly 60% of the mouse genes. However, it is widely thought that the productivity (in terms of generating mutations in previously unmutated genes) of the random gene-trap approach is diminishing and may have effectively reached a plateau, so that one or more other approaches will be needed to generate nulls in the remaining genes. As mentioned above, the EUCOMM is using targeted gene trap technology to create a conditional resource in mouse strain 129. Therefore, to avoid duplicating existing resources or efforts, this RFA does not address the generation of additional gene trap mutations in the 129 background. However, proposals based on efficient gene trapping in the C57BL/6 strain background, either in an ES cell line or directly in mouse germ cells/embryos, will be considered.

As for transposon-based mutagenesis, there have been recent reports of new high-throughput, low-cost methods that could potentially be used to produce a large fraction of the desired resource directly in C57BL/6 mouse embryos, obviating the need for ES cells entirely. Transposon insertion, as is the case with gene trap systems, has the potential to produce null, hypomorphic and allelic mutations. Given the newness of transposon-based technology, it is particularly important that the proposed approach be described in detail and that sufficient background information is provided regarding the robustness of the technology, including the percentage of mouse genes that can be expected to be mutated, the throughput, and the cost. Preference will be given to applications that produce a mouse embryo or sperm resource, as opposed to an ES cell resource.

Transposon or gene trap mutagenesis in a C57BL/6 production pipeline: Current high throughput approaches to generating mouse mutants utilizing transposons or gene traps can be broken down into the following components:(a) design and development of (i) the transposon or gene-trap insertion vectors, (ii) transposase transgenic(s) (if required), and (iii) the reporter system to be utilized; (b) methods for introducing the transposon or gene-trap vector into mouse embryos or ES cells; (c) analysis of the locus after integration to determine the location and copy number of the insertion; (d) ES cell expansion and/or mouse breeding to create and preserve the resource. The application should be organized so that each of these components is addressed clearly (see suggested guidelines for addressing these elements in SPECIAL GUIDANCE FOR APPLICANTS at the end of this announcement for further details and for cost spreadsheets that may be used to present past and future costs available at http://www.genome.gov/15515029). Applicants who propose collaborations and/or subcontracts for specific components should describe how they will integrate their efforts with their collaborators or subcontractors.

(a) Design and development of the transposon or gene trap system. Information about the type of transposon or gene trap that will be used to generate the resource should be provided, including a description and background information about the insertional element and a discussion of the strategies that will be taken to prevent transposon or gene trap replication and spontaneous, or self, excision. The applicant must describe the preferred reporter system and the anticipated number of genes expected to be mutated, the frequency with which mutations in previously non-mutated genes will be expected, and estimated overlap with current known targeted or gene trap mutations.

(b) Methods for introducing the transposon or gene-trap vector into mouse embryos or ES cells. Applicants proposing to use transposon-based systems to directly inactivate genes in mice must describe the types and number of founder mice for both the transposon donor and activating transposase, the breeding schema, the number of mice that will be needed, the efficiency of this process and the number of mutations per mouse line. Applicants proposing to use gene traps must address the methodology and efficiency of the process to be utilized in either C57BL/6 ES cells or, preferably, directly in mice.

(c) Analysis of the locus after integration to determine the location and copy number of the insertion. All discussions should include descriptions of the molecular biological analyses that will be performed to identify the gene that has been hit, the precise location of the insertion in the genome (either on cDNA or genomic sequence--analysis of the 5' and 3' insertion points of the mutated gene), the copy number of the inserted DNA and the expected rate of re-hitting genes. In addition, the types of genes that can or cannot be hit (e.g. expressed genes, telomeric regions, heterochromatin) should be discussed, and a comparison or estimate of overlap with current mouse and ES knockouts would be desirable. The long-term stability of the integrated sequence must also be addressed.

(d) ES cell expansion and/or mouse breeding to create and preserve the resource. All reagents will be made publicly available through designated NIH supported repositories. The applicant should describe the steps that will be taken to expand and freeze the mutant ES cells, sperm or embryos from the mutant C57BL/6 mice in compliance with the standards for international repositories, as well as the protocol for depositing them in an NIH-designated repository. The applicant should provide information that demonstrates either a track record of successfully completing these tasks on the scale that will be required for this RFA or the successful ability to scale up to meet the requirements of this RFA.

In addition to the above strategy-specific issues, there are a number of production pipeline issues that must be addressed by applications for all approaches:

Information Technology. The applicant should discuss all pertinent informatics issues. These include, but are not limited to, the informatics infrastructure of the production system, such as the basic IT infrastructure/system administration, the laboratory information management system, and the system for data handling and deposition, plus any informatics that will be used to provide a public interface for describing the status of all mutational efforts. In all cases, any needed software development should be described in detail.

Technology development. Incremental technology improvements will play an important role in increasing the efficiency and decreasing the cost of the high-throughput production of mouse knockouts. NIH encourages applicants to include plans for such technology development activities in their proposals. The plans for technology improvement should be well described and the cost of the proposed technology development should be justified in terms of reducing production costs. The cost of such technology development will be included in the overall production cost on a “per knockout” basis.

Quality control. The applicant should discuss any additional means that will be taken to ensure the quality of, or otherwise validate, the resources that will be generated, beyond those mentioned above. Examples of appropriate quality control procedures include those for identification of the null mutation, confirmation of the knockout, demonstration that no undesired alterations have occurred at the site of mutation, determination of the stability of the integration and the vector sequence copy number, determination of the ES cell germline potential, embryo or sperm cryopreservation, and testing the pathogen status of all biological reagents. Evidence of the effectiveness of the proposed quality control programs should be included.

Cost per gene knockout produced. The applicant should describe plans for determining and reducing the cost of generating gene targeting vectors and mutant ES cell lines or transposon insertions or gene traps in ES cells and/or mutant mice. All proposed costs and projected cost reductions should be given in terms of the total costs, i.e. the fully loaded costs (including overhead). The applicant may find the budget forms provided at http://www.genome.gov/15515029 to be useful. These sheets will calculate the costs per gene knocked out.

P.I. Effort. The effective management of a production project requires a significant commitment by the Principal Investigator (P.I.). The P.I. of a large-scale project funded under this RFA is expected to devote at least 20% effort to the project. Additionally, it will be helpful for the applicant to describe how he/she envisions managing the proposed project, and how that management will support achievement of the proposed goals and milestones. Useful elements of this description include the organization of the proposed production effort, its management structure, including integration of the separate components to form an efficient pipeline, key personnel, section leaders, and reporting relationships. Recruitment and training of personnel may also be discussed. The plan should also describe how the various components of the proposed production effort will be integrated, and how collaborations or subcontracts, if proposed, will be managed. It would be useful to discuss coordination of the awardee's activities with those of other international efforts to produce mouse knockouts.

Data and materials release. Applicants should be familiar with the NIH statements regarding sharing of resources developed with Federal funds (http://www.ott.nih.gov/policy/rt_guide_final.html). In the case of genomic data and materials, creative and innovative plans for widespread dissemination and access is needed in line with the aims of the RFA. With regard to the present solicitation, NHGRI and the other participating Institutes have identified the goal of the KOMP as the production of a “community materials” as described in the proceedings of the Meeting on Sharing Data from Large-Scale Biological Research Projects (http://www.wellcome.ac.uk/doc_wtd003208.html). Therefore, responses to this RFA should propose a specific and comprehensive plan for the rapid release of data and materials resulting from the knockout mouse production effort to the appropriate databases and repositories, respectively. The quality of this plan will be an important criterion in the award of the cooperative, and an appropriate plan for release of data and materials will be made a condition of the awards made as a result of this RFA.

In presenting the data release plan, the release of data to the project's public tracking website should be discussed and should include, but is not limited to: (A) for gene targeting -- information as to the genes that have been assigned to the project, when the effort to knock out each gene is scheduled to begin or actually began, when the construct was made and when the sequence of that construct was sent to dbGSS, data that confirm a knockout has been successfully made, information that the ES cell has been deposited in a public resource designated by NIH and its repository location and finally that a mouse has been made from the mutant ES cell line and its repository location (for the small number that will be made under this RFA as a quality control measure); (B) for transposon or gene trap mutagenesis -- confirmatory data that a gene has been hit by a transposon or gene trap vector, information that a mouse embryo or sperm has been made, information that the mouse embryo has been deposited in a public resource designated by NIH and its repository location.

In presenting the materials release plan, provision for community access should include, but not be limited to: (A) for gene targeting -- BAC targeting vectors, mutant ES cells, and any knockout mice, including frozen embryos and sperm samples, derived in the course of the supported work; (B) for transposon or gene trap mutagenesis – knockout mice, including embryos and sperm samples, and if applicable, mutant ES cells. In the case of mice, embryos and sperm samples, deposition to specific repositories identified by the KOMP program at the time of funding will be required.

Additionally, the applicant's data or materials release plan should address how software or technology improvements developed under this funding will be publicly released.

The release plans are expected to fully address how the end users of the ES cells, embryos, and other materials generated by the funded activity, in both the public and private sectors, will be fully enabled to share and use the materials, consistent with achieving the goals of this project. Section IV.6. “Other Submission Requirements” contains additional sections entitled “Plan for Sharing Research Data” and “Sharing Research Resources.” Only a single plan for the sharing of data and materials is needed and should address information presented in that section as well as the information given in this paragraph.

Intellectual Property.  If, in the course of constructing the desired mouse knockouts, the applicant proposes to use technology covered by third party patent claims, then the applicant must provide evidence that s/he will be able to freely practice the technology. The applicant must also demonstrate that s/he will be free to distribute the knockout ES cells, embryos and mice to the repositories and, ultimately, end-users without any restriction on the repositories' ability to transfer the materials to end-users or end-users' ability to use the materials for research purposes. This plan must include users in both the public and private sectors, although it is recognized that there may be different approaches to the issue of use in the two sectors. A uniform MTA such as the SLA (http://ott.od.nih.gov/NewPages/SimplLtrAgr.pdf)  or the UBMTA (http://ott.od.nih.gov/NewPages/ubmta.pdf) will be used for all repositories which receive resources made by this effort to ensure that the resources made by this initiative are available in a manner consistent with the goals of this RFA and with no additional reach through rights to inventions[/discoveries] made by the end users. (See additional information section for issues regarding the intellectual property plan that should be addressed). Applicants with insufficient plans to deal with the intellectual property will not be funded. Applicants are free to patent their discoveries so long as the ES cells, embryos and mice are made available for research purposes in a manner consistent with the goals of this RFA. 

Budget. The budget requested should be described clearly and be well justified. Applicants should submit the Detailed Budget for the Initial Budget Period (page 4 of PHS-398) and the Budget for Entire Proposed Period of Support (page 5 of PHS-398). Additionally, the applicant may find it helpful to submit budget spreadsheets that can be found at http://www.genome.gov/15515029. These sheets request information broken down by process steps relating to 1) funds spent and reagents generated as the result of past activities and 2) funds requested and reagents to be generated as part of this application.

Non-U.S. applicants. NIH can award grants to international applicants if the application represents a unique approach, resource or service that is not available in the U.S. Non-U.S. applicants should provide a detailed explanation of how their proposal meets this criterion of uniqueness. Additionally, resources generated outside the U.S. under this RFA must be imported to NIH-designated, U.S. repositories for use by the U.S. research community. A plan for doing so must be described, with particular attention to pathogen screening, use of approved reagents and U.S. importation restrictions.

Specific instructions on how to respond to these production considerations are detailed below in the section SPECIAL GUIDANCE FOR APPLICANTS.

In summary, applicants for awards under this RFA:

See Section VIII, Other Information - Required Federal Citations, for policies related to this announcement.

Section II. Award Information

1. Mechanism(s) of Support

This funding opportunity will use the cooperative agreement award mechanism(s).

As an applicant, you will be solely responsible for planning, directing, and executing the proposed project.

The NIH U01 is a cooperative agreement award mechanism. In the cooperative agreement mechanism, the Principal Investigator retains the primary responsibility and dominant role for planning, directing, and executing the proposed project, with NIH staff being substantially involved as a partner with the Principal Investigator, as described under the Section VI. 2. Administrative Requirements, "Cooperative Agreement Terms and Conditions of Award." Plans for continuation of this program beyond this current funding opportunity are not definite.

2. Funds Available

The participating IC(s) NHGRI, NCI, NCRR, NHLBI, NEI, NIA, NIAAA, NIAMS, NICHD, NIDA, NIEHS, NIDCD, NIDCR, NIMH, and NINDS intend to commit up to $50 million in new grants in response to this RFA. An applicant may request a project period of up to five years and a budget for direct costs up to five million dollars per year.

Because the nature and scope of the proposed research will vary from application to application, it is anticipated that the size and duration of each award will also vary. Although the financial plans of the IC(s) provide support for this program, awards pursuant to this funding opportunity are contingent upon the availability of funds and the receipt of a sufficient number of meritorious applications.

Facilities and administrative costs requested by consortium participants are not included in the direct cost limitation, see NOT-OD-05-004.

Section III. Eligibility Information

1. Eligible Applicants

1.A. Eligible Institutions

You may submit (an) application(s) if your organization has any of the following characteristics:

1.B. Eligible Individuals

Any individual with the skills, knowledge, and resources necessary to carry out the proposed research is invited to work with their 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.

2. Cost Sharing or Matching

Cost sharing is not required.

The most current Grants Policy Statement can be found at: http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm#matching_or_cost_sharing.

3. Other-Special Eligibility Criteria

Applicants for this RFA must have a proven track record of producing at least 100 mutant (targeted, gene trapped or transposon mutated) ES cells or mice. Experience must support the proposed production approach and goals. Documentation of this production track record must be included.

Section IV. Application and Submission Information

1. Address to Request Application Information

The PHS 398 application instructions are available at http://grants.nih.gov/grants/funding/phs398/phs398.html in an interactive format. Applicants must use the currently approved version of the PHS 398. For further assistance contact Grants Info, Telephone (301) 435-0714, Email: GrantsInfo@nih.gov.

Telecommunications for the hearing impaired: TTY 301-451-5936.

2. Content and Form of Application Submission

Applications must be prepared using the most current PHS 398 research grant application instructions and forms. Applications must have a Dun & Bradstreet (D&B) Data Universal Numbering System (DUNS) number as the universal identifier when applying for Federal grants or cooperative agreements. The D&B number can be obtained by calling (866) 705-5711 or through the web site at http://www.dnb.com/us/. The D&B number should be entered on line 11 of the face page of the PHS 398 form.

The title and number of this funding opportunity must be typed on line 2 of the face page of the application form and the YES box must be checked.

Foreign Organizations

Several special provisions apply to applications submitted by foreign organizations:

Proposed research should provide a unique research opportunity not available in the U.S.

3. Submission Dates and Times
Applications must be received on or before the receipt date described below (Section IV.3.A). Submission times N/A.

3.A. Receipt, Review and Anticipated Start Dates

Letter of Intent Receipt Date: October 20, 2005
Application Receipt Date(s): November 22, 2005
Peer Review Date: January - March 2006
Council Review Date: May, 2006
Earliest Anticipated Start Date: July 1, 2006

Applicant Information Meeting: October 6, 2005, 2-4:00 p.m.
NIH main Campus, Bldg 50
1st Floor Conference Center
National Institutes of Health (NIH)
9000 Rockville Pike
Bethesda, Maryland 20892

3.A.1. Letter of Intent

Prospective applicants are asked to submit a letter of intent that includes the following information:

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

The letter of intent is to be sent by the date listed at the beginning of this document.

The letter of intent should be sent to:

Jane L. Peterson, Ph.D.
Division of Extramural Research
National Institute of Human Genome Research
5635 Fisher Lane
Suite 4076
Bethesda, MD 20892
Telephone: (301) 496-7531
FAX: (301) 480-2770
Email: jane_peterson@nih.gov

3.B. Sending an Application to the NIH

Applications must be prepared using the research grant applications found in the PHS 398 instructions for preparing a research grant application. Submit a signed, typewritten original of the application, including the checklist, and three signed photocopies in one package to:

Center for Scientific Review
National Institutes of Health
6701 Rockledge Drive, Room 1040, MSC 7710
Bethesda, MD 20892-7710 (U.S. Postal Service Express or regular mail)
Bethesda, MD 20817 (for express/courier service; non-USPS service)

Personal deliveries of applications are no longer permitted (see http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-040.html).

At the time of submission, two additional copies of the application and all copies of the appendix material must be sent to:

Rudy Pozzatti, Ph.D.
Office of Scientific Review
National Human Genome Research Institute
5635 Fisher Lane
Suite 4076
Bethesda, MD 20892
Telephone: (301) 496-7531
FAX: (301) 480-2770
Email: pozzattr@mail.nih.gov

Using the RFA Label: The RFA label available in the PHS 398 application instructions must be affixed to the bottom of the face page of the application. Type the RFA number on the label. 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 2 of the face page of the application form and the YES box must be marked. The RFA label is also available at: http://grants.nih.gov/grants/funding/phs398/labels.pdf.

3.C. Application Processing

Applications must be received on or before the application receipt date(s) described above (Section IV.3.A.). If an application is received after that date, it will be returned to the applicant without review. Upon receipt, applications will be evaluated for completeness by the CSR and responsiveness by the NHGRI. Incomplete and non-responsive applications will not be reviewed.

The NIH will not accept any application in response to this funding opportunity that is essentially the same as one currently pending initial review, unless the applicant withdraws the pending application. However, when a previously unfunded application, originally submitted as an investigator-initiated application, is to be submitted in response to a funding opportunity, it is to be prepared as a NEW application. That is, the application for the funding opportunity must not include an Introduction describing the changes and improvements made, and the text must not be marked to indicate the changes from the previous unfunded version of the application.

Although there is no immediate acknowledgement of the receipt of an application, applicants are generally notified of the review and funding assignment within eight (8) weeks.

4. Intergovernmental Review
This initiative is not subject to intergovernmental review.

5. Funding Restrictions

All NIH awards are subject to the terms and conditions, cost principles, and other considerations described in the NIH Grants Policy Statement. The Grants Policy Statement can be found at http://grants.nih.gov/grants/policy/policy.htm.

Pre-Award Costs are allowable. A grantee may, at its own risk and without NIH prior approval, incur obligations and expenditures to cover costs up to 90 days before the beginning date of the initial budget period of a new or competing continuation award if such costs: are necessary to conduct the project, and would be allowable under the grant, if awarded, without NIH prior approval. If specific expenditures would otherwise require prior approval, the grantee must obtain NIH approval before incurring the cost. NIH prior approval is required for any costs to be incurred more than 90 days before the beginning date of the initial budget period of a new or competing continuation award.

The incurrence of pre-award costs in anticipation of a competing or non-competing award imposes no obligation on NIH either to make the award or to increase the amount of the approved budget if an award is made for less than the amount anticipated and is inadequate to cover the pre-award costs incurred. NIH expects the grantee to be fully aware that pre-award costs result in borrowing against future support and that such borrowing must not impair the grantee's ability to accomplish the project objectives in the approved time frame or in any way adversely affect the conduct of the project. See NIH Grants Policy Statement http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm.

6. Other Submission Requirements

Special Guidance for Applicants

The NHGRI has conducted several competitions for large-scale projects and it has been our experience that there are specific information items and presentation formats that the reviewers have found to be critical for their ability to assess proposals for such efforts effectively. The following guidance summarizes that experience in the form of a format that the applicant may use to provide that information. If there is additional information, not addressed in this Guidance, that the applicant wishes to present, s/he is encouraged to provide it in a concise form, in addition to the information requested here. Following are specific instructions that may be used for writing the Progress Report and the Research Proposal for the approaches called for in this RFA: 6A) gene targeting and 6B) transposon mutagenesis and gene trap technologies.

6.A. Guidance for applications proposing gene targeting:

6.A.I. Report of track record. The report of track record section should adequately describe the applicant's past experience in production of targeting vectors and production of mutant ES cells or mice. The total length for this section must not exceed 15 pages; brief, concise summaries are encouraged. The report of track record should represent the applicant's past accomplishments, rather than future plans. In addition to presenting the information requested in this section, the applicant may also use the suggested format for a cost spreadsheet entitled “Report of Past Activities (gene targeting)” available at http://www.genome.gov/15515029. This suggested format may be used for the convenience of the applicant; its purpose is to facilitate a uniform summary of the information from applicants to ensure equitable review.

This report of track record should include the following:

6.A.I.1. Production of targeting vectors. The applicant should describe past and current efforts to construct libraries of targeting vectors, whether or not they were made by using BAC recombineering. If the applicant has had experience with BAC recombineering, the relevant information should be provided. The discussion should address vector design and construction, generation of probes, and validation steps to demonstrate that a knockout was made successfully. The applicant should also describe the throughput rate, quality, and cost, and should include, but not be limited to, the following information:

a. Throughput and quality rate:
i. The number of targeting vectors made in the most recent six months of activity either by BAC recombineering or with smaller clones. Describe the process used, based on tasks performed and individuals' efforts. For example, was the process organized by tasks or did each individual perform multiple steps?
ii. The generation of probes for assessing whether or not a knockout was made. Was the screening PCR based? What was the monthly success rate of vector and probe generation during the most recent six month period?
iii. The total current total monthly production in the applicant's laboratory or center. This number should be based on an average of at least the last six months of targeting vector construction and should include the number of attempted constructs, the number of successful constructs, and the number of FTE or equivalents needed. What were the main reasons for failures?
iv. Any other metrics that the applicant has found to be useful in evaluating and managing targeting vector and probe production.

6.A.I.2. Mutant ES cell production. The applicant should describe efforts over at least the most recent six months of activity to generate mutant ES cells by gene targeting methods. The strain background of the ES cells (129, C57BL/6, or other) should be clearly identified. The discussion should address the steps of electroporation, screening to ensure that integration has occurred, quality control efforts, growth and freezing of the mutant ES cells for storage. The applicant should describe the rate of throughput, quality (e.g., pathogen screening and germline transmission rate), and cost, and should include, but not be limited to, the following:

a. Throughput rate and quality:
i. The number of targeted ES cells made in the most recent six months of activity;
ii. Steps taken to ensure that homologous recombination has occurred. What is the copy number of the insert in each mutant? What is the current success rate and how has it changed over the course of the past year?
iii. The current monthly production of mutant ES cells in the applicant's laboratory or center. This number should be based on an average of the most recent six months of activity and should include the number of attempted gene targets.
iv. Procedures for expanding and freezing mutant cells for storage and distribution. Quality control measures to ensure proper freezing and storage conditions. v. The steps (including a cost estimate) currently utilized to produce mice from a limited number of ES cells as a quality control measure.
vi. Any other internal metrics that the applicant has found to be useful in evaluating and managing the production of targeted ES cell mutants.

6.A.I.3. Technology Development. The applicant should address any experience that s/he has had in developing and improving technology for targeting vector construction and production and for production of targeted ES cell mutants. The discussion should describe, in quantitative terms, the effect that such technology improvements have had in process improvement and decreased production costs.

6.A.I.4. Prior experience in attaining milestones. The applicant should discuss his/her experience in defining and meeting useful milestones and budgets for a biological production effort.

6.A.II. The Research Proposal. This section (a maximum of 50 pages) comprises the applicant's description for a production project to generate the set of BAC targeting vectors that will be used for the proposed number of ES cell mutants to be generated in the requested period of time (2,500-10,000 over five years). The organization suggested below for this section of the application is based on the NIH staff's current understanding of the steps in these processes. The applicant is free to propose an alternative strategy but, in so doing, must address all of the issues raised below.

6.A.II.1. Targeting vector production. The applicant should present a clear plan, including concrete milestones, for (1) achieving production of a sufficient number of targeting vectors to knock out the number of unique genes proposed in the application (2,500 – 10,000), and (2) increasing the efficiency of targeting vector production. All phases of the production process (vector design, construction, generation of probes and validation steps to demonstrate that a knockout has been made) must be addressed, as well as:

i. the overall projected throughput of the proposed center and how it will be attained;
iii. potential bottlenecks or other problems that can be anticipated, as well as proposed solutions;
iv. timelines and quantitative milestones where appropriate;

6.A.II.2. Mutant ES cell production. The applicant should present a clear plan, including concrete milestones, for (1) achieving production of (a minimum of 2,500 and a maximum of 10,000) ES clones each containing a null mutation marked with a highly versatile reporter for each of the mouse genes (the applicant should not identify the genes to be knocked out, as that list will be determined by the KOMP's Steering Committee and the KOMP Project Team), and (2) increasing the efficiency of production over the five-year time frame of this initiative. All phases of the production pipeline (electroporation, screening to ensure that integration has occurred, other characterization of cells that may be carried out as a quality control step, growing up and freezing cells for storage) should be addressed, as well as:

i. the overall projected throughput of the proposed center and how it will be attained;
ii. potential bottlenecks or other problems that can be anticipated as well proposed solutions;
iii. timelines and quantitative milestones where appropriate;

6.A.II.3. Informatics. All production data and materials should be linked to the gene as the reference point. The informatics issues and requirements associated with both the targeting vector and mutant ES cell production should be discussed in a manner such that all of the data will be integrated and linked to information on the gene of interest. I t is anticipated that developing the gene list to be targeted will be an ongoing iterative process. The applicant should address how the genes assigned for targeting will be identified and defined. The rationale for the targeting strategy should also be explained, e.g. choosing a generic approach of mutating exon 1 vs. selecting a key exon in each gene. The successful grantee will be expected to transfer all relevant data to the Data Coordination Center, which is to be funded under the companion RFA-HG-05-008. The applicant should propose how a plan to transfer data to that center will be developed and suggest elements of that plan if possible. This data exchange format should contain elements to describe data related to all steps in the process of generating knockout mutants and be an explicitly defined, parsable format.

6.A.II.4. Technology development. The Research Plan should include a separate section describing plans for technology development efforts to improve the efficiency of the production pipeline for making mutant ES clones by gene targeting during the proposed project.

6.A.III. Budget Request. The budget requested must be described clearly and be well justified. Applicants should submit the Detailed Budget for the Initial Budget Period (page 4 of PHS-398) and the Budget for Entire Proposed Period of Support (page 5 of PHS-398). Additionally, the applicant may use the suggested format cost spreadsheet entitled “Projected Costs (gene targeting)” available at http://www.genome.gov/15515029. These sheets format information in a way that allows analysis of the funds requested as related to the materials (cost per knockout mouse) to be generated as part of this application. The spread sheets are provided for the convenience of the applicant and will be used by the review committee to assess the applicant's proposed plans regarding resource production and costs. Other formats that provide this information may be used.

6B. Guidance for applications proposing transposon mutagenesis or gene trapping in C57BL/6 ES cells:

6.B.I. Report of track record. The reports of track record section should adequately describe the applicant's past experience in production of transposon or gene traps and production of mutant ES cells or mice. The total length for this section must not exceed 15 pages. Brief, concise summaries are encouraged. In addition to presenting the information requested in this section, the applicant should also complete the cost spreadsheet entitled “Report of Past Activities (transposon mutagenesis or gene trapping)” available at http://www.genome.gov/15515029. This report should be based on the applicant's past accomplishments, rather than on future plans, and include the following:

6.B.I.1. Transposon or gene trap production. The applicant should describe past and current efforts to construct gene mutations using transposons or gene traps in ES cells or mice. The discussion must should address vector design, construction, generation of probes and validation steps to demonstrate that a knockout has been made with a stable, single-copy insertion. Additionally, the applicant should describe the throughput rate, quality, and cost, and should include, but not be limited to, the following:

a. Throughput rate and quality:
i. The number of transposon or gene trap insertions, made in either ES cells or mice in the most recent six months of activity. Describe the process in terms of the separate tasks that comprise the overall process. For example, is the process organized into separate tasks for each individual staff member or does each individual perform multiple steps?
ii. The generation of probes for assessing whether or not a knockout has been made. Is the screening PCR-based? Is any sequencing performed to confirm the recombination? Are both 5' and 3' insertion points analyzed? What is the current success rate of vector and probe generation?
iii. The total current monthly production in the applicant's laboratory or center. This number should be based on an average of at least the last six months of transposon or gene trap mutational events, screening and confirmation and should include number of attempted events and the number of FTE or equivalents needed What are the main reasons for failures?
iv. Other internal metrics that the applicant has found to be useful in evaluating and managing the high throughput production of transposon or gene trap mutations.

6.B.I.2. Mutant ES cell or mouse production. The applicant should describe past and current efforts to generate mutant ES cells or mice during the most recent six months of activity. The background strain must be identified and the results of any efforts to work in the C57BL/6 should be specified. The discussion must address electroporation or microinjection or breeding schema, screening to ensure that integration has occurred, other characterizations of cells or sperm or mice that may be carried out as quality control steps, expansion and freezing of cells, sperm or embryos for storage. The applicant should describe the throughput rate, quality control measures (e.g. pathogen testing and germline or reproductive ability), and cost, and should include, but not be limited to, the following:

a. Throughput rate and quality:
i. The number of transposon or gene trap-mutated ES clones or mice made in the most recent six months of activity, with a breakdown of the mouse strain(s) used in the experiments.
ii. The screening steps employed to ensure that a null mutation has been generated and an analysis of the copy number of the inserted sequence. What is the current success rate and how has it changed over the course of the past year?
iii. The total monthly production of mutant ES cells or mice in the applicant's laboratory or center for the past six months. This number should include the number of attempted events, e.g. number of ES cells or mice screened and the number of identified insertions into known genes or ESTs.
iv. The steps the laboratory takes to expand and freeze down mutant cells, sperm and/or embryos for storage and distribution, as well as the quality control measures that are used to monitor stability of the mutation, proper freezing and storage conditions.
v. The steps (including a cost estimate) currently utilized to produce mice from a limited number of ES cells, sperm and/or embryos as a quality control measure.
vi. Any other internal metrics that the applicant has found to be useful in evaluating and managing progress in knockout mutant production.

6.B.I.3. Technology Development. The progress report should describe any relevant experience the center has in developing and improving transposon or gene-trap mutagenesis and the production of mutant mice or ES cells. The discussion should include discussion of the quantitative effect that such technology development has had in decreasing the costs and improving efficiency of the applicant's production efforts.

6.B.I.4. Prior experience in attaining milestones. The applicant should discuss experience in defining and meeting useful milestones and budgets for a biological project.

6.B.II. The Research Proposal. This section (a maximum of 50 pages) comprises the applicant's proposal for a production project to generate, directly in the C57BL/6 genetic background, either a transposon-based mutation resource or a gene trap-based mutation resource for the entire genome, or as many genes as are practical and cost effective in five years. The organization suggested for this section of the application is based on the NIH staff's current understanding of these processes. The applicant is free to propose an alternative strategy, but in so doing, must address all of the issues raised.

6.B.II.1. Transposon or gene trap production. The applicant must present a clear plan, including concrete milestones, for achieving production of mutations in a large number of the genes in the mouse genome using highly efficient transposon or gene trap vector systems. All phases of the production process should be addressed, including vector design (if further development is required), construction of mutations, generation of probes, and validation steps to demonstrate that a single copy, stable knockout with a versatile reporter system has been made. Specifically, the applicant should address:

i. the overall projected throughput of the proposed project and how it will be attained;
ii. potential bottlenecks or other problems that can be anticipated, as well as proposed solutions;
iii. timelines and, where appropriate, quantitative milestones;

6.B.II.2. Mutant ES cell or mouse production. The applicant should present a clear plan, including concrete milestones, for producing a resource of mutant C57BL/–based ES cells, sperm or embryos. The resource should consist of a null mutation marked with a highly versatile reporter in each gene The production plan should include a component designed to increase the efficiency of production over the five-year project period. The plan should address all components of the production pipeline (electroporation, microinjection and/or mouse breeding, screening to ensure that integration has occurred, other characterization of cells or mice that may be carried out as a quality control step, growing up and freezing cells, sperm or embryos for storage) including,

i. the overall projected throughput of the proposed project and how it will be attained;
ii. potential bottlenecks or other problems that can be anticipated, as well as proposed solutions;
iii. timelines and, where appropriate, quantitative milestones;

6.B.II.3. Informatics. All production data and materials should be linked to the gene as the reference point. Thus, the informatics issues and requirements-associated analysis and documentation associated with both the transposon or gene trap insertions and ES cell, mouse, sperm, and/or embryo production should be discussed so that all of the data is integrated and linked to information on the gene of interest. The applicant should address how the mutated genes will be identified, defined and assessed for their potential as a null mutation. The successful grantee will be required to transfer data to the Data Coordination Center, which is to be funded under the companion RFA-HG-05-008. The applicant should propose how a plan to transfer data to that center will be developed and suggest elements of that plan if possible. This data exchange format should contain elements to describe data related to all steps in the process of generating knockout mutants and be an explicitly defined, parsable format.

6.B.II.4. Technology development. The Research Plan should include a separate section describing any plans for technology development to improve the throughput and reduce the cost of making the mutant ES cells and/or mice, sperm or embryos during the project period.

6.B.III. Budget Request. The budget requested should be described clearly and be well justified. Applicants should submit the Detailed Budget for the Initial Budget Period (page 4 of PHS-398) and the Budget for Entire Proposed Period of Support (page 5 of PHS-398). Additionally, the applicant may use the suggested format cost spreadsheet entitled “Projected Costs (transposon mutagenesis and gene trapping)” available at http://www.genome.gov/15515029. These spread sheets format information in a way that allows analysis of the funds requested as related to the materials (cost per knockout mouse) to be generated as part of this application. The spread sheets are provided for the convenience of the applicant and will be used by the review committee to assess the applicant's proposed plans regarding resource production and costs. Other formats that provide this information may be used.

Plan for Sharing Research Data

All applications must include a plan for sharing research data. The standard NIH data sharing policy is available at http://grants.nih.gov/grants/policy/data_sharing. All investigators responding to this funding opportunity should include a description of how final research data will be shared, or explain why data sharing is not possible. However, rapid release of the data would be of benefit to the scientific user community because of the scope of this community resource project as described in this RFA and because of the national and scientific investment that the NIH will make in KOMP. Accordingly, applicants should not feel constrained by the standard approach to data sharing but should display and promote innovative methods for achieving the maximum use of the KOMP resource.

The reasonableness of the data sharing plan or the rationale for not sharing research data will be assessed by the reviewers. However, reviewers will not factor the proposed data sharing plan into the determination of scientific merit or the priority score. The adequacy of the resources sharing plan and any related data sharing plans will be considered by Program staff of the funding organization when making recommendations about funding applications. Section I. “Research Objectives” contains a section entitled “Data and Materials Release” that addresses the issues that can be used in a data sharing plan for a KOMP component.

Sharing Research Resources

NIH policy requires that grant awardee recipients make unique research resources readily available for research purposes to qualified individuals within the scientific community after publication (NIH Grants Policy Statement http://grants.nih.gov/archive/archive/grants/policy/nihgps_2003/index.htm and http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm#_Toc54600131). Investigators responding to this funding opportunity should include a plan for sharing research resources addressing how unique research resources will be shared or explain why sharing is not possible. However, as indicated in the previous section with respect to the data sharing plan, applicants should not feel constrained to propose a standard plan for sharing materials, given the scope of KOMP as defined by the RFA and the NIH's investment in this project. Widespread dissemination and access to the materials generated through this program to the public and private research sectors are an aim of this RFA and will require innovative methods for achieving the maximum use of the resource to be produced under this project.

The adequacy of the resources sharing plan and any related data sharing plans will be considered by Program staff of the funding organization when making recommendations about funding applications. The effectiveness of the resource sharing will be evaluated as part of the administrative review of each non-competing Grant Progress Report (PHS 2590, http://grants.nih.gov/grants/funding/2590/2590.htm). See Section VI.3. Reporting.

Section V. Application Review Information

1. Criteria

The following will be considered in making funding decisions:

2. Review and Selection Process

Applications that are complete and responsive to the RFA will be evaluated for scientific and technical merit by an appropriate peer review group convened by NHGRI in accordance with the review criteria stated below.

As part of the initial merit review, all applications will:

The goals of NIH supported research are to advance our understanding of biological systems, to improve the control of disease, and to enhance health. In their written critiques, reviewers will be asked to comment on each of the following criteria in order to judge the likelihood that the proposed research will have a substantial impact on the pursuit of these goals. Each of these criteria will be addressed and considered in assigning the overall score, weighting them as appropriate for each application. Note that an application does not need to be strong in all categories to be judged likely to have major scientific impact and thus deserve a high priority score. For example, an investigator may propose to carry out important work that by its nature is not innovative but is essential to move a field forward.

Significance: Does this study address an important problem? If the aims of the application are achieved, how will scientific knowledge or clinical practice be advanced? What will be the effect of these studies on the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field?

Approach: Are the conceptual or clinical framework, design, methods, and analyses adequately developed, well integrated, well reasoned, and appropriate to the aims of the project? Does the applicant acknowledge potential problem areas and consider alternative tactics?

Innovation: Is the project original and innovative? For example: Does the project challenge existing paradigms or clinical practice; address an innovative hypothesis or critical barrier to progress in the field? Does the project develop or employ novel concepts, approaches, methodologies, tools, or technologies for this area?

Investigators: Are the investigators appropriately trained and well suited to carry out this work? Is the work proposed appropriate to the experience level of the principal investigator and other researchers? Does the investigative team bring complementary and integrated expertise to the project (if applicable)?

Environment: Does the scientific environment in which the work will be done contribute to the probability of success? Do the proposed studies benefit from unique features of the scientific environment, or subject populations, or employ useful collaborative arrangements? Is there evidence of institutional support?

2.A. Additional Review Criteria:

Additional Review Criteria: In addition to the above criteria, applications received in response to RFA-HG-05-007 will also be reviewed with respect to the following:

In addition to the above criteria, the following items will continue to be considered in the determination of scientific merit and the priority score:

Care and Use of Vertebrate Animals in Research: If vertebrate animals are to be used in the project, the five items described under Section F of the PHS Form 398 research grant application instructions will be assessed.

Biohazards: If materials or procedures are proposed that are potentially hazardous to research personnel and/or the environment, determine if the proposed protection is adequate.

2.B. Additional Review Considerations

Budget: The reasonableness of the proposed budget and the requested period of support in relation to the proposed research. The priority score will not be affected by the evaluation of the budget.

2.C. Plan for Sharing Research Data

All applications must include a plan for sharing research data. The standard NIH data sharing policy is available at http://grants.nih.gov/grants/policy/data_sharing. All investigators responding to this funding opportunity should include a description of how final research data will be shared, or explain why data sharing is not possible. However, rapid release of the data would be of benefit to the scientific user community because of the scope of this community resource project as described in this RFA and because of the national and scientific investment that the NIH will make in KOMP. Accordingly, applicants should not feel constrained by the standard approach to data sharing but should display and promote innovative methods for achieving the maximum use of the KOMP resource.

The reasonableness of the data sharing plan or the rationale for not sharing research data will be assessed by the reviewers. However, reviewers will not factor the proposed data sharing plan into the determination of scientific merit or the priority score. The adequacy of the resources sharing plan and any related data sharing plans will be considered by Program staff of the funding organization when making recommendations about funding applications. Section I. “Research Objectives” contains a section entitled “Data and Materials Release” that addresses the issues that can be used in a data sharing plan for a KOMP component.

2.D. Sharing Research Resources

NIH policy requires that grant awardee recipients make unique research resources readily available for research purposes to qualified individuals within the scientific community after publication (NIH Grants Policy Statement http://grants.nih.gov/archive/archive/grants/policy/nihgps_2003/index.htm and http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm#_Toc54600131). Investigators responding to this funding opportunity should include a plan for sharing research resources addressing how unique research resources will be shared or explain why sharing is not possible. However, as indicated in the previous section with respect to the data sharing plan, applicants should not feel constrained to propose a standard plan for sharing materials, given the scope of KOMP as defined by the RFA and the NIH's investment in this project. Widespread dissemination and access to the materials generated through this program to the public and private research sectors are an aim of this RFA and will require innovative methods for achieving the maximum use of the resource to be produced under this project.

The adequacy of the resources sharing plan and any related data sharing plans will be considered by Program staff of the funding organization when making recommendations about funding applications. The effectiveness of the resource sharing will be evaluated as part of the administrative review of each non-competing Grant Progress Report (PHS 2590, http://grants.nih.gov/grants/funding/2590/2590.htm). See Section VI.3. Reporting.

3. Anticipated Announcement and Award Dates
Not applicable

Section VI. Award Administration Information

1. Award Notices

After the peer review of the application is completed, the Principal Investigator will also receive a written critique called a Summary Statement.

If the application is under consideration for funding, NIH will request "just-in-time" information from the applicant. For details, applicants may refer to the NIH Grants Policy Statement Part II: Terms and Conditions of NIH Grant Awards, Subpart A: General (http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm).

A formal notification in the form of a Notice of Grant Award (NGA) will be provided to the applicant organization. The NGA signed by the grants management officer is the authorizing document. Once all administrative and programmatic issues have been resolved, the Notice of Grant Award will be generated via email notification from the awarding component to the grantee business official (designated in item 14 on the Application Face Page). If a grantee is not email enabled, a hard copy of the NGA will be mailed to the business official.

Selection of an application for award is not an authorization to begin performance. Any costs incurred before receipt of the NGA are at the recipient's risk. These costs may be reimbursed only to the extent considered allowable pre-award costs. See Also Section IV.5. Funding Restrictions.

2. Administrative and National Policy Requirements

NIH policy requires that awards to foreign institutions be made only for unique resources or contributions to research. Therefore, the applicant must provide justification as to the unique contribution an international site will provide for the application (see Section IV.2 above).

All NIH grant and cooperative agreement awards include the NIH Grants Policy Statement as part of the notice of grant award. For these terms of award, see the NIH Grants Policy Statement Part II: Terms and Conditions of NIH Grant Awards, Subpart A: General (http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm) and Part II Terms and Conditions of NIH Grant Awards, Subpart B: Terms and Conditions for Specific Types of Grants, Grantees, and Activities (http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm).

The following Terms and Conditions will be incorporated into the award statement and will be provided to the Principal Investigator as well as to the appropriate institutional official, at the time of award.

Terms and Condition for HG-05-007

2.A. Cooperative Agreement Terms and Conditions of Award

The following special terms of award are in addition to, and not in lieu of, otherwise applicable OMB administrative guidelines, HHS grant administration regulations at 45 CFR Parts 74 and 92 (Part 92 is applicable when State and local Governments are eligible to apply), and other HHS, PHS, and NIH grant administration policies.

The administrative and funding instrument used for this program will be the cooperative agreement (U01), an "assistance" mechanism (rather than an "acquisition" mechanism), in which substantial NIH programmatic involvement with the awardee is anticipated during the performance of the activities. Under the cooperative agreement, the NIH purpose is to support and stimulate the recipient's activities by involvement in and otherwise working jointly with the award recipient in a partnership role; it is not to assume direction, prime responsibility, or a dominant role in the activities. Consistent with this concept, the dominant role and prime responsibility resides with the awardee for the project as a whole, although specific tasks and activities may be shared between the awardee and the NIH as defined below.

The KOMP Research Network will involve four distinct activities (generation of the knockout mouse resource, a data coordination center, further development of the C57BL/6 ES cell system, and KOMP repositories); funding of these activities will be solicited by a set of set of four RFAs (HG-05-007 (the current RFA), HG-05-008, DA-06-009, and an as-yet unpublished RFA for the KOMP repositories that will be published by NCRR). All components of the KOMP program will be funded by cooperative agreements and a single Steering Committee (section 2.A.3) and a single Panel of Scientific Consultants (section 2.A.4) will serve for all of the KOMP activities. The Terms and Conditions described below are specific for this RFA (HG-05-007), but have been coordinated and made consistent with those described in the other RFAs soliciting components of the KOMP Research Network.

2.A.1. Principal Investigator Rights and Responsibilities

The P.I. will have the primary responsibility for defining the details for the gene knockout production project within the guidelines of RFA HG-05-007 and for performing the scientific activities.  The P.I. will agree to collaboration with the other members of the KOMP Research Network and to accept close coordination, cooperation, and participation of NIH staff and advisors in those aspects of scientific and technical management of the project as described under 2.A.2. NIH Responsibilities

The P.I.will:

The awardee will retain custody of and have primary rights to the data and software developed under these awards, subject to Government rights of access consistent with current HHS, PHS, and NIH policies.

2.A.2. NIH Responsibilities

NIH Project Scientists will have substantial programmatic involvement that is above and beyond the normal stewardship role in awards, as described below. For the KOMP Research Network, a Project Scientist will be appointed from each of the Institutes that is responsible for the participating cooperative agreements, that is, NHGRI (this RFA and RFA HG-05-008), NIDA (RFA DA-06-009) and NCRR (NIH-funded, KOMP repositories).

For RFA-HG-05-007 (this RFA), the NHGRI Project Scientist will have substantial scientific/programmatic involvement during the conduct of this activity through technical assistance, advice and coordination. However, the role of the NHGRI Project Scientist will be to facilitate and not to direct the activities. It is anticipated that decisions in all collaborative activities will be reached by consensus of the KOMP Steering Committee, of which the PI is a member, and that the NHGRI Project Scientist will participate in this process. The NHGRI Project Scientist shall participate as a member of the Steering Committee and will have one vote.

The Project Scientist will:

2.A.3. Collaborative Responsibilities

The Steering Committee will serve as the main governing board of the KOMP Research Network. The Steering Committee membership will include the P.I. of each awarded cooperative agreement and the NIH Project Scientist of each of the four components of the KOMP Research Network. Additional members may be added by action of the Steering Committee. Members of the KOMP Working Group may attend the Steering Committee meetings. Government employees outside of KOMP Working Group members may also attend, if their expertise is required for specific discussions.

The Steering Committee will:

Each full member will have one vote; the total votes of the NIH Project Scientist-members of the Steering Committee will constitute a minority of the votes. Awardee members of the Steering Committee will be required to accept and implement policies approved by the Steering Committee.

2.A.4. Panel of Scientific Consultants

The Panel of Scientific Consultants (PSC) will be responsible for reviewing and evaluating the progress of the members of the KOMP Research Network toward meeting their individual and collective goals. The PSC will provide recommendations to the KOMP Working Group, the Directors of NHGRI, NIDA and NCRR, as well as the Directors of the all other participating institutes, about continued support of the components of the KOMP Research Network. The Panel will be composed of four to six senior scientists with relevant expertise who are not P.I.s of a cooperative agreement involved in the KOMP Research Network. The Panel of Scientific Consultants will be appointed by the Directors of NHGRI, NIDA, and NCRR, with concurrence from the Directors of all other participating Institutes. The membership of the Panel of Scientific Consultants may be enlarged permanently, or on an ad hoc basis, as needed.

The Panel of Scientific Consultants will meet at least once a year and by conference call 2 to 3 times per year. During part of this meeting, there will be a joint meeting with the Steering Committee to allow the PSC members to interact directly with the awardees. Annually, the PSC will make recommendations to the NIH regarding progress of the KOMP Research Network and present advice about changes, if any, which may be necessary in the KOMP Research Network program to the Directors of NHGRI, NIDA and NCRR and the Directors of the other participating institutes.

2.A.5. KOMP Working Group

The KOMP Working Group consists of program staff from the each of the NIH institutes supporting the KOMP. The purpose of the KOMP Working Group will be to disseminate information about the progress of the KOMP Research Network to the participating institutes and to provide a forum for the participating institutes to discuss issues related to KOMP. The KOMP Working Group members will report to the Director of their respective IC. The KOMP Working Group will be chaired by the NHGRI Project Scientist for the knockout mouse resource component of the KOMP.

2.A.6. Arbitration Process

Any disagreement that may arise on scientific/programmatic matters (within the scope of the award), between award recipients and the NHGRI may be brought to arbitration. An Arbitration Panel will be composed of (i) a designee of the Steering Committee chosen without the NHGRI staff voting, (ii) one NHGRI designee, and (iii) a third designee with relevant expertise who is chosen by the other two (in the case of an individual disagreement, the first member may be chosen by the individual awardee). The Arbitration Panel will help resolve both scientific and programmatic issues that develop during the course of work and that restrict progress. This special arbitration procedure in no way affects the awardee's right to appeal an adverse action that is otherwise appealable in accordance with NIH regulations 42 CFR Part 50, Subpart D and HHS regulation at 45 CFR Part 16.

2.A.7. Yearly Milestones

Each awardee will be asked to define a set of yearly milestones at the time of the award and to update these milestones annually at the anniversary date. These will be made a condition of the award. In accord with the procedures described above, NHGRI may withhold or reduce funds for a project that substantially fails to meet its milestones or to maintain the state of the art in the field.

3. Reporting

Awardees will be required to submit the PHS Non-Competing Grant Progress Report, Form 2590 annually (http://grants.nih.gov/grants/funding/2590/2590.htm) and financial statements as required in the NIH Grants Policy Statement. Awardees will be required to submit periodic (at least every six months) progress reports in a standard format, as agreed upon by the Steering Committee and the Scientific Advisory Panel.

Section VII. Agency Contacts

We encourage your inquiries concerning this funding opportunity and welcome the opportunity to answer questions from potential applicants. Inquiries may fall into three areas: scientific/research, peer review, and financial or grants management issues:

1. Scientific/Research Contacts:

Jane L. Peterson, Ph.D.; Mark W. Moore, Ph.D.
Division of Extramural Research
National Institute of Human Genome Researach
5635 Fisher Lane
Suite 4076
Bethesda, MD 20892
Telephone: (301) 496-7531
FAX: (301) 480-2770
Email: jane_petersoon@nih.gov; mmoore3@mail.nih.gov

2. Peer Review Contacts:

Rudy Pozzatti, Ph.D.
Office of Scientific Review
National Human Genome Research Institute
5635 Fisher Lane
Suite 4076
Bethesda, MD 20892
Telephone: (301) 496-7531
FAX: (301) 435-1580
Email: pozzattr@mail.nih.gov

3. Financial or Grants Management Contacts:

Cheryl Chick.
Grants Management Officer
Grants Administration Branch
5635 Fisher Lane
Suite 4076
Bethesda, MD 20892
Telephone: (301) 496-7531
FAX: (301) 402-1951
Email: chickc@mail.nih.gov

Section VIII. Other Information

Required Federal Citations

Use of Animals in Research:
Recipients of PHS support for activities involving live, vertebrate animals must comply with PHS Policy on Humane Care and Use of Laboratory Animals (http://grants.nih.gov/grants/olaw/references/PHSPolicyLabAnimals.pdf) as mandated by the Health Research Extension Act of 1985 (http://grants.nih.gov/grants/olaw/references/hrea1985.htm), and the USDA Animal Welfare Regulations (http://www.nal.usda.gov/awic/legislat/usdaleg1.htm) as applicable.

Access to Research Data through the Freedom of Information Act:
The Office of Management and Budget (OMB) Circular A-110 has been revised to provide access to research data through the Freedom of Information Act (FOIA) under some circumstances. Data that are (1) first produced in a project that is supported in whole or in part with Federal funds and (2) cited publicly and officially by a Federal agency in support of an action that has the force and effect of law (i.e., a regulation) may be accessed through FOIA. It is important for applicants to understand the basic scope of this amendment. NIH has provided guidance at http://grants.nih.gov/grants/policy/a110/a110_guidance_dec1999.htm. Applicants may wish to place data collected under this funding opportunity in a public archive, which can provide protections for the data and manage the distribution for an indefinite period of time. If so, the application should include a description of the archiving plan in the study design and include information about this in the budget justification section of the application. In addition, applicants should think about how to structure informed consent statements and other human subjects procedures given the potential for wider use of data collected under this award.

URLs in NIH Grant Applications or Appendices:
All applications and proposals for NIH funding must be self-contained within specified page limitations. Unless otherwise specified in an NIH solicitation, Internet addresses (URLs) should not be used to provide information necessary to the review because reviewers are under no obligation to view the Internet sites. Furthermore, we caution reviewers that their anonymity may be compromised when they directly access an Internet site.

Healthy People 2010:
The Public Health Service (PHS) is committed to achieving the health promotion and disease prevention objectives of "Healthy People 2010," a PHS-led national activity for setting priority areas. This PA is related to one or more of the priority areas. Potential applicants may obtain a copy of "Healthy People 2010" at http://www.health.gov/healthypeople.

Authority and Regulations:
This program is described in the Catalog of Federal Domestic Assistance at http://www.cfda.gov/ and is not subject to the intergovernmental review requirements of Executive Order 12372 or Health Systems Agency review. Awards are made under the authorization of Sections 301 and 405 of the Public Health Service Act as amended (42 USC 241 and 284) and under Federal Regulations 42 CFR 52 and 45 CFR Parts 74 and 92. All awards are subject to the terms and conditions, cost principles, and other considerations described in the NIH Grants Policy Statement. The NIH Grants Policy Statement can be found at http://grants.nih.gov/grants/policy/policy.htm.

The PHS strongly encourages all grant recipients to provide a smoke-free workplace and discourage the use of all tobacco products. In addition, Public Law 103-227, the Pro-Children Act of 1994, prohibits smoking in certain facilities (or in some cases, any portion of a facility) in which regular or routine education, library, day care, health care, or early childhood development services are provided to children. This is consistent with the PHS mission to protect and advance the physical and mental health of the American people.


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