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
This Funding Opportunity Announcement (FOA) is developed as a Common Fund initiative (http://commonfund.nih.gov/) through the NIH Office of the NIH Director, Office of Strategic Coordination (http://dpcpsi.nih.gov/osc/). This FOA will be administered by the National Center for Research Resources (NCRR)  (http://www.ncrr.nih.gov/).on behalf of the NIH (http://www.nih.gov/). Other participating Institutes include:
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)
Eunice Kennedy Shriver 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:   Knockout Mouse Production and Cryopreservation (U42)

Announcement Type

New

Update: The following update relating to this announcement has been issued:

Request For Applications (RFA) Number:  RFA-RM-10-013

Catalog of Federal Domestic Assistance Number(s)
93.310, 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 10, 2010
Letters of Intent Receipt Date(s): September 15, 2010
Application Receipt Dates(s):November 10, 2010
Peer Review Date(s): February, 2011
Council Review Date(s): May, 2011
Earliest Anticipated Start Date: July, 2011
Additional Information To Be Available Date (Url Activation Date): N/A
Expiration Date:  November 11, 2010

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, Review and Anticipated Start Dates
         1. Letter of Intent
    B. Sending an Application to the NIH
    C. Application Processing
   D.  Application Assignment
4. Intergovernmental Review
5. Funding Restrictions
6. Other Submission Requirements

Section V. Application Review Information
1. Criteria
2. Review and Selection Process
3. Anticipated Announcement and Award Dates

Section VI. Award Administration Information
1. Award Notices
2. Administrative and National Policy Requirements
     A. Cooperative Agreement Terms and Conditions of Award
         1. Principal Investigator Rights and Responsibilities
         2. NIH Responsibilities
         3. Collaborative Responsibilities
         4. Dispute Resolution Process
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

PURPOSE: The purpose of this FOA, is to solicit applications for research projects to make maximum progress toward the goal of converting the International Knockout Mouse Consortium (IKMC) ES cell resource into mice, performing preliminary phenotyping, and cryopreserving germplasm of those mice (which will be phenotyped by grantees funded through an FOA being published in parallel). This is part of an overall pilot effort aimed at developing a widely available resource of well-characterized mutant mice that can be used by the scientific community to elucidate functional information for each protein-coding gene in the mammalian genome. Depending upon the success of this pilot, the program will be scaled up during an additional 5 years to complete the phenotyping of a total of 8,500 knockout strains. The mouse is the ideal mammalian system in which to produce a functional genomics resource because of the long history and depth of understanding of mouse genetics, the sophistication of ES cell technology in the mouse system, and the low cost of working with mice in comparison to other mammals.

BACKGROUND: The mouse has long been an important mammalian model system for the study of gene function in human health and disease. Mouse mutants with phenotypes that mimic human traits have served as critical research tools in understanding the genetics underlying mammalian biology. Equally important, mouse mutants have been the tools used to begin to understand gene function and pathways as the field has moved from gene identification to mammalian functional genomics. Because of its importance to human biology, mapping and sequencing the genome of mouse strain C57BL/6 was carried out as part of the Human Genome Project. Another major genomic resource for mouse research was developed by the Mammalian Gene Collection (MGC) project (http://mgc.nci.nih.gov/), which as of December 2009 included 27,285 full-ORF (open reading frame) cDNA clones representing 17,701 individual 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, a proposal was made in the fall of 2003 to establish a focused, large-scale international effort to produce a publicly available, comprehensive collection of mouse knockout mutants, i.e., a library containing a null mutation in every gene in the mouse genome (Austin, C.P., et al. Nature 36, 921-924 (2004)). The meeting attendees recommended that this be accomplished in a phased production approach, beginning with the construction of a resource of ES cells comprising a comprehensive collection of null and conditional alleles. This would 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, would be done on nearly all of the mice created by the project. Tier 2, microarray and transcriptome based phenotyping, would be carried out on a subset of these mice. Subsequent specialized phenotyping and further in depth analyses on specific mice would then be pursued as part of individual research programs.

There followed a number of international efforts that further defined the proposed knockout mouse resource. Following a March 2005 workshop which endorsed the concept (http://www.genome.gov/15014549), the NIH launched the Knockout Mouse Program (KOMP) to generate knockout (null) mutations in 8,500 genes in C57BL/6 knockout mice lines by deleting all or most of the exons in target genes (Valenzuela, D.M., et al., Nature Biotechnology 6, 652-659 (2003)) or knockout-first conditional ready alleles (Testa, G., et al., Genesis 38, 151-158 (2004)). As of the end of June 2010, KOMP had produced knockouts of about 5,500 genes and is on target to complete the goal of producing 8,500 knockout mutant ES cell lines by the end of 2011. In parallel, the European Conditional Mouse Mutagenesis Program (EuCOMM) and the North American Conditional Mouse Mutagenesis Program (NorCOMM) are on track to complete their goals of producing an additional 9,000 knockout mice by the end of 2011. The three programs will thus produce a comprehensive resource of mutant mouse ES cell lines. They have coordinated their efforts through the formation of the International Knockout Mouse Consortium (IKMC).

As part of KOMP, the NIH established a repository to archive, maintain, and distribute high quality ES cell clones, as well as live mouse lines, frozen embryos and sperm, and vectors (http://www.komp.org). As part of its quality control procedures, KOMP is generating live mice from a fraction of the ES cells as they are generated. The original goal was 500 and current efforts are exceeding that goal. To date, 413 lines of mice have been generated and, at current production rates, about 850 strains will be produced by the end of 2011.

Thus, the first phase of the proposed resource is on schedule to be completed by 2011, and attention has now turned toward implementation of the second phase. Over the past year, there have been a number of discussions, and planning a potential mouse phenotyping effort has begun. The NIH held a KOMP Phenotyping Conference in Bethesda, MD in October 2009, at which a group of researchers representing diverse scientific backgrounds expressed their unanimous enthusiasm and support for a proposed effort to conduct high-throughput and comprehensive phenotyping of the resource being produced by the members of the IKMC (meeting report available at http://www.komp.org). The meeting attendees were supportive of a proposed strategy to first convert ES cells into mice at one or more high-throughput facilities that can also efficiently conduct highly informative preliminary analyses (e.g., LacZ expression, stage of embryonic lethality, fecundity), followed by performance of a defined set of standard broad-based phenotype tests at KOMP phenotyping facilities. The phenotyping data would be rapidly and freely released to the public as they are generated, with the mice being archived for distribution to the research community. The meeting participants stressed that any U.S. phenotyping effort must be coordinated with comparable efforts elsewhere (similar discussions and plans are being made in Europe, Canada, and Asia).The standard phenotyping tests, analyses, and examinations that are included in the resource effort should be chosen primarily on the basis of their reliability, power, and likelihood to reveal disease and human clinical relevance. These recommendations were highly similar to those that have come from other efforts to solicit input from the US national research community.

The first large-scale phenotyping effort was funded by the European Commission (EC) in 2008. The European Mouse Disease Clinic (EUMODIC, http://www.eumodic.org/) program is comprised of 4 mouse phenotyping centers,  whose goals are to provide phenotype information on 500 EUCOMM, NorCOMM and KOMP knockout mouse lines by 2011, using a common phenotyping protocol developed by the European Mouse Phenotyping Resource of Standardized Screens (EMPReSS, http://empress.har.mrc.ac.uk/) developed by the European Union Mouse Research for Public Health and Industrial Applications (EUMORPHIA) Program. This data is made accessible through a separately funded database, EUROPHENOME (http://www.europhenome.org/). It is expected that the NIH will ask successful applicants to this RFA to coordinate their efforts with the EUMODIC programs and the currently-forming International Mouse Phenotyping Consortium (IMPC), to select knockout lines to be phenotyped, harmonize phenotyping platforms, and make use of prior know-how and experience (http://commonfund.nih.gov/KOMP2/ipmc-policies.asp).

RESEARCH OBJECTIVE: The KOMP phenotyping program (KOMP2) will consist of several components. This FOA solicits a mouse production capability of not less than 830 strains and up to 2500 strains over five years. One companion FOA (RFA-RM-10-011) calls for applications to propose a broad-based phenotyping program, and another companion FOA (RFA-RM-10-012) calls for proposals to provide the bioinformatics support for the entire KOMP2 program. Applicants may apply for more than one component by simultaneously applying to more than one of the FOAs in coordinated applications, or by collaboration or subcontracting approaches. For any approach, the proposed plans must be based on realistic, documentable current capabilities and may include a ramp-up period. The KOMP2 program is envisioned as a five year pilot, which if successful, will be followed by 5 years of ramped up production with some additional funds.  Therefore, critical to the programs funded by all of the FOAs listed above, will be plans to improve the technology and decrease costs over the 5 years of the pilot phase.

ES Cell Handling: The KOMP2 program will involve one to three mouse production centers with a total capability of converting 500 ES cell knockout lines per year to mouse strains, for a total of 2500 over five years. Applicants should describe their past and current abilities to handle hundreds of ES cell lines per year for expansion, cryopreservation and archiving, as a demonstration of their ES cell capabilities. The proposal should describe the steps that will be used to handle the ES cells obtained from the IKMC, the projected throughput, the production goals and explicit milestones, the characteristics and quality expected of the mutant ES cell lines, the ES lines' potential to be transmitted through the germline in mice, and all other pertinent factors. As mentioned above, it would be preferable to demonstrate as much experience as possible in the C57BL/6 background. However, since the technology to produce mice from ES cells in a high throughput manner is more well-established for mouse strain 129, proposals from applicants that can demonstrate extensive experience with ES cells of either the C57BL/6 or 129 backgrounds will be considered to be responsive to the FOA.

Mouse Production from Targeted ES cells: The applicant must present sufficiently detailed plans for setting up and maintaining a production pipeline for the large-scale generation of mouse lines from mutant ES cells obtained from the IKMC repositories (costs detailed at www.komp.org and www.eummcr.org). The specific ES cell lines to be turned into mice will be initially provided and updated regularly during the course of the five year project by NIH.

Germplasm Cryopreservation: The KOMP2 program includes the cryopreservation of mouse strains after demonstration of successful germline transmission of targeted knockout mutations. All mouse strains produced by this program will be made publicly available as rapidly as possible, without a hold-back period, through designated repositories (www.komp.org, or www.emmanet.org).

Neo Cassette and Critical Exon Removal:  The strategies used to generate the KOMP knockout mutations lead to the retention of a Neo cassette in the genome of the derived ES cells. It will be necessary to remove the Neo cassette from mice prior to phenotyping to avoid effects of the heterologous promoter used to drive the Neo gene.

Mouse Breeding: Following Cre excision, heterozygous null mice will be bred to determine if the homozygous mice are viable and fertile. This plan should include mating of homozygous male and female mice to proven breeders in order to test fertility, as well as determination of embryonic or perinatal lethality of the mutant allele being tested.

Lac Z expression profiling: All IMKC mice contain a LacZ reporter inserted under the control of the endogenous promoter of the mutated gene. Each application for a production center must provide detailed plans to perform or outsource the analysis of multi-tissues LacZ expression. The data and scanned images will be uploaded to a mouse phenotyping database to be determined.

Plan for measuring embryonic lethals: It is expected that a number of the knockout mutations will result in embryonic lethality. Applications must propose a method to determine if death occurs before or after embryonic day 12.

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. It is vital that the production data and phenotypic data be provided in a format that can be easily uploaded to external databases. It is anticipated that the data uploads will occur on at least a bi-monthly basis, and include sufficient tracking information to assure that project goals are being met. This data set will include, at a minimum:

ES lines imported, ES lines thawed, ES lines injected and/or aggregated, QC of 5% of ES lines, chimeras born per line, % chimeras in each line, re-injected lines (with different clones), chimeras breeding per line, germline results on each line, data on breeding lines set up with Cre Deleter lines, offspring born in each line crossed with Cre deleter lines, data confirming correct excision events with Cre recombinase, mice bred to homozygosity, results of homozygosity breeding for viability and fertility, mice in LacZ analysis, data from LacZ analysis, materials shipped to phenotyping centers, and materials shipped to repositories. Additional required data elements may be added, as needed. In all cases, any necessary software development should be described in detail.

Technology development. Incremental technology improvements always play an important role in increasing the efficiency and decreasing the cost of high-throughput production processes, and in the initial characterization of the production products. As noted above, it is critical that the successful grantee improve the mouse production process sufficiently so that continuation of the pilot program beyond the first five years at a moderately higher funding level will be possible.  Therefore plans for technology development activities in the proposal are important to the overall success of the program. The plans for technology improvement should be well described, and the cost of any proposed technology development should be justified in terms of the technology’s effect in 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 means that will be taken to determine and 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 targeted allele, 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 copy number of the vector sequence , determination of the ES cell germline potential, embryo or sperm cryopreservation, and testing the pathogen status of all biological reagents. The applicant should briefly discuss their proposed animal husbandry conditions, and their experience in producing standardized mice to be phenotyped.  Evidence of the effectiveness of the proposed quality control programs should be included.

Costs per gene knockout strain produced. The applicant should describe plans for determining and reducing the cost of generating knockout 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).  These costs will be reported by the applicant on a quarterly basis and tracked by the NIH.

In summary, applicants for awards under this FOA should:

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

Section II. Award Information


1. Mechanism of Support

This funding opportunity will use the U42 award mechanism(s).

This FOA uses “Just-in-Time” information concepts. It also uses non-modular budget formats described in the PHS 398 application instructions (see http://grants.nih.gov/grants/funding/phs398/phs398.html). 

This funding opportunity will use a cooperative agreement award mechanism. In the cooperative agreement mechanism, the Project Director/Principal Investigator (PD/PI) 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". The KOMP2 project may be continued for an additional five year period, depending on the results of a program review in the 3rd or 4th year of the initial project, but new FOAs will be issued rather than accept applications for a renewal of this FOA.

2. Funds Available

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.

NIH grants policies as described in the NIH Grants Policy Statement will apply to the applications submitted and awards made in response to this FOA.

Section III. Eligibility Information


1. Eligible Applicants

1.A. Eligible Institutions

The following organizations/institutions are eligible to apply:

Foreign institutions are not eligible to apply in response to this FOA;  however, subcontractual arrangements with foreign institutions are allowed. 

1.B. Eligible Individuals

Any individual with the skills, knowledge, and resources necessary to carry out the proposed research as the PD/PI is invited to work with his/her institution to develop an application for support. Individuals from underrepresented racial and ethnic groups as well as individuals with disabilities are always encouraged to apply for NIH program support.

More than one PD/PI, or multiple PDs/PIs, may be designated on the application for projects that require a “team science” approach and therefore clearly do not fit the single-PD/PI model. Additional information on the implementation plans, policies and procedures to formally allow more than one PD/PI on individual research projects is available at http://grants.nih.gov/grants/multi_pi. All PDs/PIs must be registered in the NIH eRA Commons prior to the submission of the application (see http://grants.nih.gov/grants/ElectronicReceipt/preparing.htm for instructions).

The decision of whether to apply for a grant with a single PD/PI or multiple PDs/PIs is the responsibility of the investigators and applicant organizations, and should be determined by the scientific goals of the project. Applications for grants with multiple PDs/PIs will require additional information, as outlined in the instructions below. When considering multiple PDs/PIs, please be aware that the structure and governance of the PD/PI leadership team as well as the knowledge, skills and experience of the individual PDs/PIs will be factored into the assessment of the overall scientific merit of the application.  Multiple PDs/PIs on a project share the authority and responsibility for leading and directing the project, intellectually and logistically. Each PD/PI is responsible and accountable to the grantee organization, or, as appropriate, to a collaborating organization, for the proper conduct of the project or program, including the submission of required reports. For further information on multiple PDs/PIs, please see http://grants.nih.gov/grants/multi_pi.

Principal Investigator (P.I.) Effort. The effective management of a production project requires a significant commitment by the P.I. The P.I. of a large-scale project funded under this FOA is expected to devote at least 2.4 (CY) person months 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.

2. Cost Sharing or Matching

This program does not require cost sharing as defined in the current NIH Grants Policy Statement.

3. Other-Special Eligibility Criteria

Number of Applications. Applicants may submit more than one application, provided they are scientifically distinct.

Resubmissions. Resubmission applications are not permitted in response to this FOA.

Renewals. Renewal applications are not permitted in response to this FOA.

Section IV. Application and Submission Information


1. Address to Request Application Information

The current 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 GrantsInfo, Telephone (301) 435-0714, Email: GrantsInfo@nih.gov.

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

2. Content and Form of Application Submission

Prepare all applications using the PHS 398 application forms and in accordance with the PHS 398 Application Guide (http://grants.nih.gov/grants/funding/phs398/phs398.html).

Applications must have a 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 in item (box) 2 only of the face page of the application form and the YES box must be checked.

Foreign Organizations (Non-domestic (non-U.S.) Entity)

Non-domestic (non-U.S.) entities (Foreign Organizations) are not eligible to serve as primary applicants for this FOA. However, foreign components may submit a research project or subcontract within a domestic application, under this FOA.

NIH policies concerning grants to foreign (non-U.S.) organizations can be found in the NIH Grants Policy Statement at: http://grants.nih.gov/grants/policy/nihgps_2003/NIHGPS_Part12.htm#_Toc54600260.

Applications from foreign organizations must:

In addition, for applications from foreign organizations:

Proposed research should provide special opportunities for furthering research programs through the use of unusual talent, resources, populations, or environmental conditions in other countries that are not readily available in the United States or that augment existing U.S. resources.

Applications with Multiple PDs/PIs

When multiple PD/PIs are proposed, use the Face Page-Continued page to provide items 3a – 3h for all PD/PIs. NIH requires one PD/PI be designated as the “contact PD/PI” for all communications between the PD/PIs and the agency. The contact PD/PI must meet all eligibility requirements for PD/PI status in the same way as other PD/PIs, but has no special roles or responsibilities within the project team beyond those mentioned above. The contact PD/PI may be changed during the project period. The contact PD/PI should be listed in block 3 of Form Page 1 (the Face Page), with all additional PD/PIs listed on Form Page 1-Continued. When inserting the name of the PD/PI in the header of each application page, use the name of the “Contact PD/PI, et. al.” The contact PD/PI must be from the applicant organization if PD/PIs are from more than one institution.

All individuals designated as PD/PI must be registered in the eRA Commons and must be assigned the PD/PI role in that system (other roles such as SO or IAR will not give the PD/PI the appropriate access to the application records). Each PD/PI must include their respective eRA Commons ID in the eRA Commons User Name field.

Multiple PD/PI Leadership Plan: For applications designating multiple PDs/PIs, the section of the Research Plan entitled, “Multiple PD/PI Leadership Plan”, must be included. A rationale for choosing a multiple PD/PI approach should be described. The governance and organizational structure of the leadership team and the research project should be described, and should include communication plans, process for making decisions on scientific direction, and procedures for resolving conflicts. The roles and administrative, technical, and scientific responsibilities for the project or program should be delineated for the PDs/PIs and other collaborators. 

If budget allocation is planned, the distribution of resources to specific components of the project or the individual PDs/PIs should be delineated in the Leadership Plan. In the event of an award, the requested allocations may be reflected in a footnote on the Notice of Award (NoA).

Additional information is available in the PHS 398 grant application instructions.

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(s): September 15, 2010
Application Receipt Date(s): November 10, 2010
Peer Review Date(s): February, 2011
Council Review Date(s): May, 2011
Earliest Anticipated Start Date(s): July, 2011

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 in Section IV.3.A.

The letter of intent should be sent to:

Raymond R. O'Neill, Ph.D.
Division of Comparative Medicine
National Center for Research Resources
6701 Democracy Blvd.
Bethesda, MD 20892
Telephone: (301) 435-0749
FAX: (301) 480-3819
Email: oneillr@mail.nih.gov

3.B. Sending an Application to the NIH

Applications must be prepared using the forms 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:

Ken Nakamura
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: nakamurak@mail.nih.gov

3.C. Application Processing

Applications must be received on or before the application receipt date described above (Section IV.3.A.). If an application is received after that date, the application may be delayed in the review process or not reviewed.  Upon receipt, applications will be evaluated for completeness by the CSR and for responsiveness by the reviewing Institute. Incomplete and/or 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.

Information on the status of an application should be checked by the Principal Investigator in the eRA Commons at: https://commons.era.nih.gov/commons/.

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 NIH Grants Policy Statement.

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 award if such costs: 1) are necessary to conduct the project, and 2) 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 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/grants/policy/nihgps_2003/NIHGPS_Part6.htm.)

6. Other Submission Requirements

A Special Guidance for Applicants.

The NHGRI and NCRR (two of the NIH Institutes supporting this FOA) have conducted several competitions for large-scale projects and have noted 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 Report of Track Record and the Research Proposal for the approaches called for in this RFA.

6. Guidance for applications proposing mouse production:

6.I. Report of track record. The report of track record section should adequately describe the applicant's past experience in production of mice from ES cells; brief, concise summaries are encouraged. The report of track record should represent the applicant's past accomplishments, rather than future plans and should include the following:

6.I.1. Production and distribution of knockout mice. The applicant should describe past and current efforts to construct and distribute knockout mice from ES cells. The description should include discussion of the throughput rate, quality, and cost, and should include, but not be limited to, the following information:

a. Throughput and quality:

i. The number of mice made in the most recent six months of activity, either by blastocyst or morula injection or by aggregation. Describe the process(es) used, including tasks performed and individuals' efforts. For example, was the process organized by task or did each individual perform multiple steps?

ii. Any use of probes for assessing whether or not a knockout was transmitted through the germline. Was the screening PCR-based? What was the monthly success rate of germline transmission 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 mouse production and should include the number of attempted injections/aggregations, the number of successful injections/aggregations, and the number of FTE or equivalents needed. What were the main reasons for any failures?

iv. Any other metrics that the applicant has found to be useful in evaluating and managing the production of knockout mice from ES cells.

v. The total number of knockout mice distributed to other institutions in the past six months.

6.I.2. Mutant mouse cryopreservation. The applicant should describe efforts over at least the most recent six months of activity to cryopreserve mouse germplasm. The strain background of the mice (129, C57BL/6, or other) should be clearly identified. The discussion should address the steps of breeding and crypopreservation, quality control, and re-animation. The applicant should describe the rate of throughput, quality (e.g., re-animation rate), and cost, and should include, but not be limited to, the following:

a. Throughput and quality:

i. The number of strains cryopreserved per month in the most recent six months of activity;

ii. The form of germplasm cryopreserved, i.e., embryos or sperm;

iii. Steps taken to ensure that cryopreservation was successful. What is the current success rate and how has it changed over the course of the past year?

iv. Any other internal metrics that the applicant has found to be useful in evaluating and managing the production of cryopreserved germplasm.

6.I.3. Technology Development. The applicant should address any experience that s/he has had in developing and improving technology for mouse production, distribution and cryopreservation. The discussion should describe, in quantitative terms, the effect that such technology improvements have had in process improvement and decreased production costs.

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

6.II. The Research Proposal. This section comprises the applicant's description for a production project to generate strains of live mice from knockout ES cells (830 - 2500 over five years), characterize, and cryopreserve them. 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 organization or strategy but, in so doing, must address all of the issues raised below.

6.II.1. Knockout mouse production and distribution. The applicant should present a clear plan, including concrete milestones, for (1) achieving production of a sufficient number of chimeric founder mice in order to characterize and cryopreserve 830 - 2500 knockout mouse strains over five years, and (2) increasing the efficiency of chimeric mouse production. The techniques employed are expected to include, but are not limited to, ES microinjection (either morula or blastocysts) and aggregation chimeras, and are at the discretion of the applicant. The application should present both a cost analysis for generating lines with the techniques employed and a detailed assessment of past and current success rates. The applicant’s projected production rates and costs (including the purchase of mutant ES cell lines from the repositories) should be justified in detail. Information on how the applicant has improved the process and reduced costs in the past and plans for future improvements should be included.All phases of the production process must be addressed, as well as:

i. the overall projected throughput and how it will be attained;

ii. potential bottlenecks or other problems that can be anticipated, as well as proposed solutions;

iii. timelines and quantitative milestones where appropriate;

iv. QC method(s) for screening to confirm the correct genotype of ES cell lines and mice

Neo Cassette and Critical Exon Removal. The applicant should describe in sufficient detail the Cre lines and their genetic backgrounds that will be used to remove the expression cassette. Alternatively, the applicant may propose and justify a plan to remove the Neo selection cassette by transfection of ES cells with a Cre-expressing plasmid. A detailed molecular analysis should be described to ensure the integrity of the alleles following Cre deletion. Cryopreservation of germplasm, but not necessarily embryos, should also be performed.

i. the overall projected throughput and how it will be attained;

ii. potential bottlenecks or other problems that can be anticipated, as well as proposed solutions;

iii. timelines and quantitative milestones where appropriate;

iv. QC method(s) for screening to confirm the correct genotype of ES cell lines or mice

6.II.2. Fecundity testing. The applicant should provide a clear plan to test the fecundity of the derived knockout mouse strains. The applicant should describe breeding schemes, number of offspring that will need to be observed, and his/her ability to perform (or outsource) genotyping of at least 250 mutant mouse lines per year. The applicant should also describe the available space that will be used for the breeding of the necessary mouse lines and the duration for which this space will be available for the project funded under this FOA. The applicant should describe an efficient plan to export either live mice or germplasm to Phenotyping Centers funded under the companion FOA (RFA-RM-10-011). In cases where the animals die before weaning or are deemed too sick for phenotyping, the applicant should describe a plan to provide heterozygous mice or germplasm to the phenotyping centers. It is expected that a number of the knockout mutations will result in embryonic lethality. Applications must propose a method to determine if death occurs before or after embryonic day 12. All phases of the production process must be addressed, as well as:

i. the overall projected throughput and how it will be attained;

ii. potential bottlenecks or other problems that can be anticipated, as well as proposed solutions;

iii. timelines and quantitative milestones where appropriate;

6.II.3. LacZ staining. The applicant should provide a clear plan to collect and section tissues from adult male and female mice and then stain sections to detect LacZ expression. The rationale for tissue selection should be presented. In addition the applicant should discuss a plan to perform wholemount staining of embryos. Rationale should be presented for the age of the embryo to be observed and for the particular techniques that will be employed. The plan to image the stained sections and wholemounts, annotate, and organize the data should be presented. All phases of the production process must be addressed, as well as:

i. the overall projected throughput and how it will be attained;

ii. potential bottlenecks or other problems that can be anticipated, as well as proposed solutions;

iii. timelines and quantitative milestones where appropriate;

6.II.4. Cryopreservation of mouse germplasm. The applicant should present a clear plan, including concrete milestones, for (1) cryopreservation of germplasm for the 830 - 2500 mouse strains produced, and (2) increasing the efficiency of production over the five-year time frame of this initiative. All phases of the production pipeline (natural matings or in vitro fertilization, sperm harvesting, freezing) and quality control steps (reanimation, pathogen testing) should be addressed, as well as:

i. the overall projected throughput and how it will be attained;

ii. potential bottlenecks or other problems that can be anticipated, as well as proposed solutions;

iii. timelines and quantitative milestones where appropriate;

6.II.5. Informatics. All production data and materials should be linked to the gene as the reference point. The informatics issues and requirements associated with mutant mouse 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. It is anticipated that developing the gene list to be produced will be an ongoing iterative process done in conjunction with NIH staff, other participants in the KOMP phenotyping program, and the Panel of Scientific Consultants (see below). The successful grantee will be expected to transfer all relevant data to a database to be determined. The applicant should propose how a plan to transfer data 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, machine readable format.

6.II.6. 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 mice during the proposed project through innovation rather then simple improvements in process control.

6.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)

Awardees must agree to the "Cooperative Agreement Terms and Conditions of Award" in Section VI.2.A "Award Administration Information".

PHS398 Research Plan Sections

All application instructions outlined in the PHS398 Application Instructions are to be followed, with the following additional requirements:

Budget

This FOA uses non-modular budget formats described in the PHS 398 application instructions (see http://grants.nih.gov/grants/funding/phs398/phs398.html). 

All foreign applicants must complete and submit budget requests using the Research & Related Budget component found in the application package for this FOA. See NOT-OD-06-096.

Appendix Materials

All paper PHS 398 applications submitted must provide appendix material on CDs only.  Include five identical CDs in the same package with the application. See http://grants.nih.gov/grants/guide/notice-files/NOT-OD-08-031.html.

Do not use the Appendix to circumvent the page limitations.  An application that does not observe the required page limitations may be delayed in the review process.

Resource Sharing Plan(s)

NIH considers the sharing of unique research resources developed through NIH-sponsored research an important means to enhance the value of, and advance research. When resources have been developed with NIH funds and the associated research findings published or provided to NIH, it is important that they be made readily available for research purposes to qualified individuals within the scientific community. If the final data/resources are not amenable to sharing, this  should be explained in Resource Sharing section of the application. See http://grants.nih.gov/grants/policy/data_sharing/data_sharing_faqs.htm.

(a) Data Sharing Plan: Investigators seeking $500,000 or more in direct costs in any year are expected to include a brief 1-paragraph description of how final research data will be shared, or explain why data-sharing is not possible. Applicants are encouraged to discuss data-sharing plans with their NIH program contact. See Data-Sharing Policy or http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-032.html.

(b) Sharing Model Organisms: Regardless of the amount requested, all applications where the development of model organisms is anticipated are expected to include a description of a specific plan for sharing and distributing unique model organisms and related resources, or state appropriate reasons why such sharing is restricted or not possible. See Sharing Model Organisms Policy, and NIH Guide NOT-OD-04-042.

(c) Genome-Wide Association Studies (GWAS): Regardless of the amount requested, applicants seeking funding for a genome-wide association study are expected to provide a plan for submission of GWAS data to the NIH-designated GWAS data repository, or provide an appropriate explanation why submission to the repository is not possible.  A genome-wide association study is defined as any study of genetic variation across the entire genome that is designed to identify genetic associations with observable traits (such as blood pressure or weight) or the presence or absence of a disease or condition.  For further information see Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies, NIH Guide NOT-OD-07-088, and http://grants.nih.gov/grants/gwas/.

All applications are expected to 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 FOA and because of the national and scientific investment that the NIH will make in KOMP2. 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 KOMP2 resource.

Data release. Applicants should be familiar with the NIH statements regarding sharing of resources developed with Federal funds (http://grants.nih.gov/grants/intell-property_64FR72090.pdf). In the case of phenotypic data, plans for the dissemination and access of the data to a centralized database 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 KOMP2 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 resulting from the knockout mouse production and phenotyping effort to the appropriate databases. None of the funds of this project are intended to support the creation of a publically accessible database for each phenotyping center, as it is envisioned that a single separately funded database will provide public access to all phenotyping data. 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 website should be discussed and should include, but is not limited to: information as to the genes that have been assigned to the project, when the effort to study the mice is scheduled to begin or actually began, data that confirm a knockout mouse has been successfully made, date that data were collected and shipped to a central phenotyping database, and other pertinent data.

Additionally, the applicant's data release plan should address how software or technology improvements developed under this funding will be publicly released. It is highly likely that software solutions and LIMS system development would benefit the other IMPC phenotyping centers as well as other investigators.

The release plans are expected to fully address how the end users of the mice, embryos, data, 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.

The reviewers will assess the reasonableness of the data sharing plan or the rationale for not sharing research data. Program staff of the funding organization, when making recommendations about funding applications, will consider the adequacy of the resources sharing plan and any related data sharing plans. 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 KOMP2 component.

Sharing Research Resources

NIH policy expects 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/grants/policy/nihgps_2003/index.htm and http://grants.nih.gov/grants/policy/nihgps_2003/NIHGPS_Part7.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 KOMP2 as defined by the FOA 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 FOA and will require innovative methods for achieving the maximum use of the resource to be produced under this project.

Program staff of the funding organization, when making recommendations about funding applications, will consider the adequacy of the resources sharing plan and any related data sharing plans. 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.

Material Transfer. A uniform MTA such as the Simple Letter Agreement (SLA), Material Transfer Agreement for the Transfer of Organisms (MTA-TO) 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. Although NIH Policy strongly discourages the patenting of research resources, applicants are free to patent their discoveries so long as the ES cells, embryos, mice, and data are made available for research purposes in a manner consistent with the NIH Data Sharing Policy, other NIh sharing policies (see http://sharing.nih.gov), and the goals of this FOA. Applicants will not be separate distribution centers or develop public websites, unless agreed to by the current repositories and the NIH Program Officer.

Authorization and Consent

(a) The Government authorizes and consents to all use and manufacture of any invention described in and covered by a United States patent in the performance of this Cooperative Agreement at all tiers.

Notice and Assistance Regarding Patent and Copyright Infringement.

(a) The Grantee shall report to the Program Director, promptly and in reasonable written detail, each notice or claim of patent or copyright infringement based on the performance of this Cooperative Agreement of which the Grantee has knowledge.

(b) In the event of any claim or suit against the Government on account of any alleged patent or copyright infringement arising out of the performance of this Cooperative Agreement or out of the use of any supplies furnished or work or services performed under this Cooperative Agreement, the Grantee shall furnish to the Government, when requested by the Program Director, all evidence and information in possession of the Grantee pertaining to such suit or claim. Such evidence and information shall be furnished at the expense of the Government except where the Grantee has agreed to indemnify the Government.

(c) The Grantee agrees to include, and require inclusion of, this clause in all sub-awards and subcontracts at any tier for supplies or services (including construction and architect-engineer sub-awards and subcontracts and those for material, supplies, models, samples, or design or testing services). 

Awardees must agree to the "Cooperative Agreement Terms and Conditions of Award" in Section VI.2.A.

Section V. Application Review Information


1. Criteria

Only the review criteria described below will be considered in the review process.

2. Review and Selection Process

Review Process

Applications that are complete and responsive to the FOA will be evaluated for scientific and technical merit by an appropriate peer review group convened by NHGRI and in accordance with NIH peer review procedures (http://grants1.nih.gov/grants/peer/), using the review criteria stated below.

As part of the scientific peer review, all applications will:

The mission of the NIH is to support science in pursuit of knowledge about the biology and behavior of living systems and to apply that knowledge to extend healthy life and reduce the burdens of illness and disability.  As part of this mission, applications submitted to the NIH for grants or cooperative agreements to support biomedical and behavioral research are evaluated for scientific and technical merit through the NIH peer review system. 

Overall Impact

Reviewers will provide an overall impact/priority score to reflect their assessment of the likelihood for the project to exert a sustained, powerful influence on the research field(s) involved, in consideration of the following five scored review criteria, and additional review criteria (as applicable for the project proposed). 

Scored Review Criteria

Reviewers will consider each of the five review criteria below in the determination of scientific and technical merit, and give a separate score for each.  An application does not need to be strong in all categories to be judged likely to have major scientific impact.  For example, a project that by its nature is not innovative may be essential to advance a field.

Significance.  Does the project address an important problem or a critical barrier to progress in the field?  If the aims of the project are achieved, how will scientific knowledge, technical capability, and/or clinical practice be improved?  How will successful completion of the aims change the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field?

Investigator(s).  Are the PD/PIs, collaborators, and other researchers well suited to the project?  If Early Stage Investigators or New Investigators, or in the early stages of independent careers, do they have appropriate experience and training?  If established, have they demonstrated an ongoing record of accomplishments that have advanced their field(s)?  If the project is collaborative or multi-PD/PI, do the investigators have complementary and integrated expertise; are their leadership approach, governance and organizational structure appropriate for the project?

Innovation.  Does the application challenge and seek to shift current research or clinical practice paradigms by utilizing novel theoretical concepts, approaches or methodologies, instrumentation, or interventions?  Are the concepts, approaches or methodologies, instrumentation, or interventions novel to one field of research or novel in a broad sense?  Is a refinement, improvement, or new application of theoretical concepts, approaches or methodologies, instrumentation, or interventions proposed?

Approach.  Are the overall strategy, methodology, and analyses well-reasoned and appropriate to accomplish the specific aims of the project?  Are potential problems, alternative strategies, and benchmarks for success presented?   If the project is in the early stages of development, will the strategy establish feasibility and will particularly risky aspects be managed?
If the project involves clinical research, are the plans for 1) protection of human subjects from research risks, and 2) inclusion of minorities and members of both sexes/genders, as well as the inclusion of children, justified in terms of the scientific goals and research strategy proposed?

Environment.  Will the scientific environment in which the work will be done contribute to the probability of success?  Are the institutional support, equipment and other physical resources available to the investigators adequate for the project proposed?  Will the project benefit from unique features of the scientific environment, subject populations, or collaborative arrangements? 

Additional Review Criteria

As applicable for the project proposed, reviewers will consider the following additional items in the determination of scientific and technical merit, but will not give separate scores for these items.

Protections for Human Subjects.  For research that involves human subjects but does not involve one of the six categories of research that are exempt under 45 CFR Part 46, the committee will evaluate the justification for involvement of human subjects and the proposed protections from research risk relating to their participation according to the following five review criteria: 1) risk to subjects, 2) adequacy of protection against risks, 3) potential benefits to the subjects and others, 4) importance of the knowledge to be gained, and 5) data and safety monitoring for clinical trials.

For research that involves human subjects  and meets the criteria for one or more of the six categories of research that are exempt under 45 CFR Part 46, the committee will evaluate: 1) the justification for the exemption, 2) human subjects involvement and characteristics, and 3) sources of materials.

Inclusion of Women, Minorities, and Children.  When the proposed project involves clinical research, the committee will evaluate the proposed plans for inclusion of minorities and members of both genders, as well as the inclusion of children.

Vertebrate Animals.  The committee will evaluate the involvement of live vertebrate animals as part of the scientific assessment according to the following five points: 1) proposed use of the animals, and species, strains, ages, sex, and numbers to be used; 2) justifications for the use of animals and for the appropriateness of the species and numbers proposed; 3) adequacy of veterinary care; 4) procedures for limiting discomfort, distress, pain and injury to that which is unavoidable in the conduct of scientifically sound research including the use of analgesic, anesthetic, and tranquilizing drugs and/or comfortable restraining devices; and 5) methods of euthanasia and reason for selection if not consistent with the AVMA Guidelines on Euthanasia. For additional information, see http://grants.nih.gov/grants/olaw/VASchecklist.pdf.

Biohazards.  Reviewers will assess whether materials or procedures proposed are potentially hazardous to research personnel and/or the environment, and if needed, determine whether adequate protection is proposed.

Resubmission Applications.  Resubmissions are not applicable to this FOA.

Renewal Applications.  Renewals are not applicable to this FOA.

Revision Applications. Revisions are not applicable to this FOA.

Additional Review Considerations

As applicable for the project proposed, reviewers will address each of the following items, but will not give scores for these items and should not consider them in providing an overall impact/priority score.

Applications from Foreign Organizations.  Foreign institutions are not eligible to apply in response to this FOA;  however, subcontractual arrangements with foreign institutions are allowed. 

Select Agents Research. Reviewers will assess the information provided in this section of the application, including 1) the Select Agent(s) to be used in the proposed research, 2) the registration status of all entities where Select Agent(s) will be used, 3) the procedures that will be used to monitor possession use and transfer of Select Agent(s), and 4) plans for appropriate biosafety, biocontainment, and security of the Select Agent(s).

Resource Sharing Plans.  Reviewers will comment on whether the following Resource Sharing Plans, or the rationale for not sharing the following types of resources, are reasonable:  1) Data Sharing Plan (http://grants.nih/gov/grants/policy/data_sharing/data_sharing_guidance.htm); 2) Sharing Model Organisms (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-04-042.html); and 3) Genome Wide Association Studies (GWAS) (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-07-088.html).

Budget and Period Support.  Reviewers will consider whether the budget and the requested period of support are fully justified and reasonable in relation to the proposed research.

Selection Process

The following will be considered in making funding decisions:

NIH considers the following in evaluating Center grant applications:

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 PD/PI will be able to access his or her Summary Statement (written critique) via the eRA Commons.

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.

A formal notification in the form of a Notice of Award (NoA) will be provided to the applicant organization. The NoA signed by the grants management officer is the authorizing document. Once all administrative and programmatic issues have been resolved, the NoA will be generated via email notification from the awarding component to the grantee business official.

Selection of an application for award is not an authorization to begin performance. Any costs incurred before receipt of the NoA 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

All NIH grant and cooperative agreement awards include the NIH Grants Policy Statement as part of the NoA. 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/grants/policy/nihgps_2003/NIHGPS_Part4.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/grants/policy/nihgps_2003/NIHGPS_part9.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.

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 an "assistance" mechanism (rather than an "acquisition" mechanism), in which substantial NIH programmatic involvement with the awardees is anticipated during the performance of the activities. Under the cooperative agreement, the NIH purpose is to support and stimulate the recipients' activities by involvement in and otherwise working jointly with the award recipients 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 awardees for the project as a whole, although specific tasks and activities may be shared among the awardees and the NIH as defined below.

2. A.1. Principal Investigator Rights and Responsibilities

The Principal Investigator will have the primary responsibility for defining the details for the gene knockout production project within the guidelines of RFA-RM-10-013 and for performing the scientific activities. The P.I. will agree to collaboration with the other members of the KOMP2 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:

Awardees 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
 
An NIH Project Scientist  will have substantial programmatic involvement that is above and beyond the normal stewardship role in awards, as described below.
For the KOMP2 Research Network, a Project Scientist will be appointed from each of the Institutes that is responsible for the participating cooperative agreements, that is, NCRR and NHGRI.

For RFA-RM-10-013 (this RFA), the NCRR 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 NCRR 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 KOMP2 Steering Committee, of which the PI is a member, and that the NCRR Project Scientist will participate in this process. The NCRR 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 KOMP2 Research Network will involve three distinct activities (generation of the knockout mouse resource, a data coordination center, and KOMP2 phenotyping centers); funding of these activities will be solicited by a set of set of three RFAs (RM-10-013 (the current RFA), RFA-RM-10-012, RFA-RM-10-011). All components of the KOMP2 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 KOMP2 activities. The Terms and Conditions described below are specific for this RFA (RM-10-013), but have been coordinated and made consistent with those described in the other FOAs soliciting components of the KOMP2 Research Network.

The Steering Committee will serve as the main governing board of the KOMP2 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 components of the KOMP2 Research Network. Additional members may be added by action of the Steering Committee. Members of the KOMP2 Working Group may attend the Steering Committee meetings. Government employees outside of KOMP2 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.

Panel of Scientific Consultants:

This program will be coordinated with and be a member of the IMPC. Because that program is in its formative stage, the degree of interactions of the KOMP2 Steering committee with the IMPC and the nature of IMPC input into the oversight of the KOMP2 is not yet known. The advisory structure may include:     

A Panel of Scientific Consultants (PSC) will be responsible for reviewing and evaluating the progress of the members of the KOMP2 Research Network toward meeting their individual and collective goals. The PSC will provide recommendations to the KOMP2 Working Group, the Directors of NHGRI, NCRR, and DPCPSI as well as the Directors of the all other participating institutes, about continued support of the components of the KOMP2 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 KOMP2 Research Network. The Panel of Scientific Consultants will be appointed by the Directors of NHGRI, NCRR, and DPCPSI 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 KOMP2 Research Network and present advice about changes, if any, which may be necessary in the KOMP2 Research Network program to the Directors of NHGRI, NCRR and DPCPSI and the Directors of the other participating institutes.

The KOMP2 Working Group consists of program staff from the each of the NIH institutes supporting the KOMP2. The purpose of the KOMP2 Working Group will be to disseminate information about the progress of the KOMP2 Research Network to the participating institutes and to provide a forum for the participating institutes to discuss issues related to KOMP2. The KOMP2 Working Group members will report to the Director of their respective IC. The KOMP2 Working Group will be chaired by the NHGRI Project Scientist for the knockout mouse phenotyping component of the KOMP2.

2.A.4. Dispute Resolution Process

Any disagreements that may arise in scientific or programmatic matters (within the scope of the award) between award recipients and the NIH may be brought to Dispute Resolution. A Dispute Resolution Panel composed of three members will be convened. It will have three members: a designee of the Steering Committee chosen without NIH staff voting, one NIH designee, and a third designee with expertise in the relevant area who is chosen by the other two; in the case of individual disagreement, the first member may be chosen by the individual awardee. This special dispute resolution procedure does not alter the awardee's right to appeal an adverse action that is otherwise appealable in accordance with PHS regulations 42 CFR Part 50, Subpart D and HHS regulations 45 CFR Part 16.

3. Reporting

Awardees will be required to submit the Non-Competing Continuation Grant Progress Report (PHS 2590) annually and financial statements as required in the NIH Grants Policy Statement.

Each awardee will be asked to define a set of monthly 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, NCRR 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.

A final progress report, invention statement, and Financial Status Report are required when an award is relinquished when a recipient changes institutions or when an award is terminated.

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:

Raymond R. O'Neill, Ph.D.
Division of Comparative Medicine
National Center for Research Resources
6701 Democracy Blvd.
Bethesda, MD 20892
Telephone: (301) 435-0749
FAX: (301) 480-3819
Email: oneillr@mail.nih.gov

2. Peer Review Contacts:

Ken Nakamura
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: nakamurak@mail.nih.gov

3. Financial or Grants Management Contacts:

Ruthann Rand
Grants Management Specialist
NIH/NCRR
6701 Democracy Boulevard
Room 1051
Bethesda, MD  20892-4874
(use 20817 for express mail)
Phone:  (301) 451-4238
Fax:      (301) 480-3777
E-mail: randrudy@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.

Human Subjects Protection:
Federal regulations (45CFR46) require that applications and proposals involving human subjects must be evaluated with reference to the risks to the subjects, the adequacy of protection against these risks, the potential benefits of the research to the subjects and others, and the importance of the knowledge gained or to be gained (http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.htm).

Data and Safety Monitoring Plan:
Data and safety monitoring is required for all types of clinical trials, including physiologic toxicity and dose-finding studies (phase I); efficacy studies (Phase II); efficacy, effectiveness and comparative trials (Phase III). Monitoring should be commensurate with risk. The establishment of data and safety monitoring boards (DSMBs) is required for multi-site clinical trials involving interventions that entail potential risks to the participants (NIH Policy for Data and Safety Monitoring, NIH Guide for Grants and Contracts, http://grants.nih.gov/grants/guide/notice-files/not98-084.html).

Sharing Research Data:
Investigators submitting an NIH application seeking $500,000 or more in direct costs in any single year are expected to include a plan for data sharing or state why this is not possible (http://grants.nih.gov/grants/policy/data_sharing).

Investigators should seek guidance from their institutions, on issues related to institutional policies and local IRB rules, as well as local, State and Federal laws and regulations, including the Privacy Rule.

Policy for Genome-Wide Association Studies (GWAS):
NIH is interested in advancing genome-wide association studies (GWAS) to identify common genetic factors that influence health and disease through a centralized GWAS data repository. For the purposes of this policy, a genome-wide association study is defined as any study of genetic variation across the entire human genome that is designed to identify genetic associations with observable traits (such as blood pressure or weight), or the presence or absence of a disease or condition. All applications, regardless of the amount requested, proposing a genome-wide association study are expected to provide a plan for submission of GWAS data to the NIH-designated GWAS data repository, or provide an appropriate explanation why submission to the repository is not possible. Data repository management (submission and access) is governed by the Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies, NIH Guide NOT-OD-07-088. For additional information, see http://grants.nih.gov/grants/gwas/.

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.

Sharing of Model Organisms:
NIH is committed to support efforts that encourage sharing of important research resources including the sharing of model organisms for biomedical research (see http://grants.nih.gov/grants/policy/model_organism/index.htm). At the same time the NIH recognizes the rights of grantees and contractors to elect and retain title to subject inventions developed with Federal funding pursuant to the Bayh Dole Act (see the NIH Grants Policy Statement http://grants.nih.gov/grants/policy/nihgps_2003/index.htm). All investigators submitting an NIH application or contract proposal, beginning with the October 1, 2004 receipt date, are expected to include in the application/proposal a description of a specific plan for sharing and distributing unique model organism research resources generated using NIH funding or state why such sharing is restricted or not possible. This will permit other researchers to benefit from the resources developed with public funding. The inclusion of a model organism sharing plan is not subject to a cost threshold in any year and is expected to be included in all applications where the development of model organisms is anticipated.

Inclusion of Women And Minorities in Clinical Research:
It is the policy of the NIH that women and members of minority groups and their sub-populations must be included in all NIH-supported clinical research projects unless a clear and compelling justification is provided indicating that inclusion is inappropriate with respect to the health of the subjects or the purpose of the research. This policy results from the NIH Revitalization Act of 1993 (Section 492B of Public Law 103-43). All investigators proposing clinical research should read the "NIH Guidelines for Inclusion of Women and Minorities as Subjects in Clinical Research (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-02-001.html); a complete copy of the updated Guidelines is available at http://grants.nih.gov/grants/funding/women_min/guidelines_amended_10_2001.htm. The amended policy incorporates: the use of an NIH definition of clinical research; updated racial and ethnic categories in compliance with the new OMB standards; clarification of language governing NIH-defined Phase III clinical trials consistent with the new PHS Form 398; and updated roles and responsibilities of NIH staff and the extramural community. The policy continues to require for all NIH-defined Phase III clinical trials that: a) all applications or proposals and/or protocols must provide a description of plans to conduct analyses, as appropriate, to address differences by sex/gender and/or racial/ethnic groups, including subgroups if applicable; and b) investigators must report annual accrual and progress in conducting analyses, as appropriate, by sex/gender and/or racial/ethnic group differences.

Inclusion of Children as Participants in Clinical Research:
The NIH maintains a policy that children (i.e., individuals under the age of 21) must be included in all clinical research, conducted or supported by the NIH, unless there are scientific and ethical reasons not to include them.

All investigators proposing research involving human subjects should read the "NIH Policy and Guidelines" on the inclusion of children as participants in research involving human subjects (http://grants.nih.gov/grants/funding/children/children.htm).

Required Education on the Protection of Human Subject Participants:
NIH policy requires education on the protection of human subject participants for all investigators submitting NIH applications for research involving human subjects and individuals designated as key personnel. The policy is available at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-00-039.html.

Human Embryonic Stem Cells (hESC):
Criteria for federal funding of research on hESCs can be found at http://stemcells.nih.gov/index.asp and at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-09-116.html. Only research using hESC lines that are registered in the NIH Human Embryonic Stem Cell Registry will be eligible for Federal funding (http://escr.nih.gov). It is the responsibility of the applicant to provide in the project description and elsewhere in the application as appropriate, the official NIH identifier(s) for the hESC line(s) to be used in the proposed research.

NIH Public Access Policy Requirement:
In accordance with the NIH Public Access Policy (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-08-033.html) investigators must submit or have submitted for them their final, peer-reviewed manuscripts that arise from NIH funds and are accepted for publication as of April 7, 2008 to PubMed Central (http://www.pubmedcentral.nih.gov/), to be made publicly available no later than 12 months after publication. As of May 27, 2008, investigators must include the PubMed Central reference number when citing an article in NIH applications, proposals, and progress reports that fall under the policy, and was authored or co-authored by the investigator or arose from the investigator’s NIH award.  For more information, see the Public Access webpage at http://publicaccess.nih.gov/.

Standards for Privacy of Individually Identifiable Health Information:
The Department of Health and Human Services (DHHS) issued final modification to the "Standards for Privacy of Individually Identifiable Health Information", the "Privacy Rule", on August 14, 2002. The Privacy Rule is a federal regulation under the Health Insurance Portability and Accountability Act (HIPAA) of 1996 that governs the protection of individually identifiable health information, and is administered and enforced by the DHHS Office for Civil Rights (OCR).

Decisions about applicability and implementation of the Privacy Rule reside with the researcher and his/her institution. The OCR website (http://www.hhs.gov/ocr/) provides information on the Privacy Rule, including a complete Regulation Text and a set of decision tools on "Am I a covered entity?" Information on the impact of the HIPAA Privacy Rule on NIH processes involving the review, funding, and progress monitoring of grants, cooperative agreements, and research contracts can be found at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-025.html.

URLs in NIH Grant Applications or Appendices:
All applications and proposals for NIH funding must be self-contained within specified page limitations. For publications listed in the appendix and/or Progress report, internet addresses (URLs) must be used for publicly accessible on-line journal articles.  Unless otherwise specified in this solicitation, Internet addresses (URLs) should not be used to provide any other information necessary for 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 FOA 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. 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.

Loan Repayment Programs:
NIH encourages applications for educational loan repayment from qualified health professionals who have made a commitment to pursue a research career involving clinical, pediatric, contraception, infertility, and health disparities related areas. The LRP is an important component of NIH's efforts to recruit and retain the next generation of researchers by providing the means for developing a research career unfettered by the burden of student loan debt. Note that an NIH grant is not required for eligibility and concurrent career award and LRP applications are encouraged. The periods of career award and LRP award may overlap providing the LRP recipient with the required commitment of time and effort, as LRP awardees must commit at least 50% of their time (at least 20 hours per week based on a 40 hour week) for two years to the research. For further information, please see: http://www.lrp.nih.gov.


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