Part I Overview Information


Department of Health and Human Services

Issuing Organization
National Human Genome Research Institute (NHGRI), (http://www.genome.gov)

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

Components of Participating Organizations
National Human Genome Research Institute (NHGRI), (http://www.genome.gov)

Title: A Data Coordination Center for the Model Organism ENCODE Project (modENCODE) [U41]
 
Announcement Type
New

Request For Applications (RFA) Number: RFA-HG-06-007

Catalog of Federal Domestic Assistance Number(s)
93.172

Key Dates
Release Date: March 10, 2006
Letters of Intent Receipt Date(s): June 21, 2006
Application Submission Dates(s): July 21, 2006
Peer Review Date(s): November 2006
Council Review Date(s):  February 12-13, 2007
Earliest Anticipated Start Date: March 1, 2007
Additional Information To Be Available Date (Url Activation Date): Not applicable
Expiration Date: July 22, 2006

Due Dates for E.O. 12372
Not Applicable

Additional Overview Content

Executive Summary 

Table of Contents


Part I Overview Information

Part II Full Text of Announcement

Section I. Funding Opportunity Description
  1. Research Objectives

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

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

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

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

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

The purpose of this RFA is to solicit applications for a Biotechnology Resource Cooperative Agreement (U41) award to develop and implement a Data Coordination Center (DCC) as part of the ENCODE (Encyclopedia of DNA Elements) Project for model organisms (modENCODE). The modENCODE Project will establish a Research Consortium that will conduct experiments to identify all of the sequence-based functional elements in the Caenorhabditis elegans and/or Drosophila melanogaster genomes.  Both computational and experimental approaches will be critical components of these efforts and a separate RFA, HG-06-006, “Identification of all functional elements in selected model organism genomes” is being issued to support the modENCODE Project.  The Research Consortium will be separate from, but affiliated with, the ENCODE Consortium that is directed toward the human genome and is currently working on a pilot project focused on locating all of the sequence-based functional elements in a selected 1% of that genome.  The DCC will be funded primarily to develop, house, and maintain databases to track, store, and provide access to the data generated as part of the modENCODE Project.  In addition, the DCC will import data from related projects that are relevant to the goals of the modENCODE Project.

With the availability of a complete, high quality genomic sequence of an organism, one of the next major challenges for genome biology is to generate a comprehensive catalog of all of the sequence-based functional elements encoded in that DNA.  Toward this end, in 2003, the NHGRI launched the Encyclopedia of DNA Elements (ENCODE) Project (http://www.genome.gov/ENCODE), the long-term goal of which is to identify all of the sequence-based functional elements in the human genome.  This project began with a pilot phase in which a defined 1% (30 Mb) of the human genome sequence is being analyzed.  The ENCODE Project also included a technology development effort, with the purpose of expanding the repertoire of high-throughput methods available for the identification of sequence-based functional elements.  While significant knowledge will be developed by the ENCODE pilot project, studying the human genome imposes some serious limitations.  One is the difficulty of validating the biological relevance of the elements discovered, as many of the necessary experiments cannot be done with humans.  Also, because the ENCODE pilot addresses only 1% of the human genome, it is also limited in its ability to test the efficacy of technologies that can only be applied on a genome-wide basis. 

These limitations would not pertain to an effort to identify all of the sequence-based functional elements in the genome of certain model organisms, specifically those with a genome that is small enough to allow most current technologies to be applied and which can be used in experimental studies.  At present, there are some modestly sized research projects that are focused on identifying functional elements in the genomes of a few of the best-studied non-vertebrate model organisms.  For example, an effort is underway to identify and clone representative full-length cDNAs for every gene in D. melanogaster, and genomes of related Drosophila species are being sequenced to identify sequence elements conserved during evolution.  While such efforts are proceeding rapidly, NHGRI has concluded that there would be significant benefit to a coordinated effort that encourages multiple groups to work together to address the entire genome of an important model organism.  Having such a comprehensive data set on the functional elements in a well-studied model organism would help provide important insights into the biology of the organism under study as well as other organisms, including the human.  It would also stimulate new and more effective methods for storing, displaying, and analyzing genome-wide data. 

With the issuance of the two modENCODE RFAs, HG-06-006 and HG-06-007, NHGRI announces its intention to initiate a model organism ENCODE Project (modENCODE) to find all of the functional sequence-based elements in the entire genome of either or both of the very widely used multicellular model organisms with finished genome sequences, Caenorhabditis elegans and Drosophila melanogaster.  Because of the nature of these two organisms as laboratory systems, the scope of modENCODE will be somewhat broader than that of the ENCODE.  modENCODE will address the entire genome of the target organism(s).  It will also make use of the experimental opportunities offered by the model system(s) not only to allow discovery, but also to promote further understanding of functional elements in ways that would not be possible with the human or even other mammalian systems.  Applicants for the companion RFA HG-06-006 may propose to work on either or both organisms.  Based in large measure on the efforts proposed and on the determination of the scientific quality by peer review of the proposals, NHGRI will decide whether the modENCODE Project will include one or both organisms.  In making this decision, NHGRI will also consider:  1) the possibility that an effort including both organisms could achieve synergies that would not be obtained if only one were pursued, 2) the potential lost opportunities in choosing one organism and not both, and 3) whether the available funds will be sufficient to do a credible job on analyzing both organisms or whether the biomedical research enterprise would be best served by a more detailed analysis of one of them.

The modENCODE Project will be run as a Research Consortium that will be open to all academic, government, and private sector scientists interested in participating in an open process to facilitate the comprehensive annotation of these model organism genomes.  It is expected that groups with funding from other sources will be able to participate in the modENCODE Project and, therefore, funding through this initiative is not a prerequisite for participation in this Consortium. Awardees funded through this RFA will also participate in the Research Consortium. 

The modENCODE Project will need to manage both primary data from multiple experimental methods and data that result from processing the primary data with a variety of computational methods to identify the functional elements in the genome.  This RFA solicits applications to support a Data Coordination Center (DCC) for the modENCODE Project.  Following the model established by the ENCODE pilot project, primary data will be stored in available public databases such as the Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) or ArrayExpress at the European Bioinformatics Institute (EBI), while processed data that identify potential functional elements will be linked to the genome sequence and stored at the DCC.  A DCC will be required to support the tracking and management of data from the modENCODE Consortium.  The DCC will also be required to identify and import data from research projects outside of the modENCODE Consortium that are generating data related to the goals of the Consortium. 

The applicant should describe plans for a DCC that is capable of working with data from all of the members of the modENCODE Consortium who will be generating data for functional elements in C. elegans and/or D. melanogaster. The DCC will compile and track data being generated by different modENCODE research projects and will implement quality assurance methods to ensure that data meet the relevant data standards.  The DCC should be prepared to work with data from the range of different experimental and computational projects that are expected to be funded through the companion RFA HG-06-006 “Identification of all functional elements in selected model organism genomes”.  For example, the experimental and computational data being generated in the human ENCODE pilot project include data from comparative sequencing, promoter reporter assays, microarray chip hybridization assays from a variety of different experimental approaches, and assays to identify DNase hypersensitive sites.  (The project descriptions at http://www.genome.gov/12513391 provide a complete listing of experimental approaches in the current ENCODE pilot project). It is expected that the data types that will be generated by modENCODE will be as broad, if not broader than in the current human ENCODE pilot project. The DCC should be able to provide links to primary data in public repositories, to the location of any identified sequence element in the corresponding reference model organism genome sequence, to metadata describing the experimental methods including any informatics methods, and as appropriate, to information in relevant Model Organism Databases (MODs) i.e., FlyBase or Wormbase.  Since the companion RFA HG-06-006 is open to proposals on both C. elegans and D. melanogaster, the DCC should be able to work with data from both model organisms or, if only one model organism is selected for modENCODE, data from the selected model organism.

The DCC should provide multiple mechanisms for delivering data about functional elements in the model organism, including a genome browser view of the functional elements identified by the modENCODE Consortium, links to a description of the data including any metadata associated with an experiment, and a method of freely downloading large datasets from the DCC so that users can acquire and analyze all or large parts of the data.  This resource should provide the data in formats that will facilitate additional analysis by members of the Consortium and by the broader scientific community.  The application should include information on how efficient and unencumbered access to the DCC will be maintained. The efforts of the DCC should be focused on collecting, tracking, and distributing relevant information for the modENCODE Project, and should not duplicate the informatics efforts of other projects such as MODs that have been funded to describe the characteristics or functions of the corresponding model organism genes.  However, it will be important for the DCC to have close interactions with the corresponding MODs to facilitate the transfer of information to these informatics resources. 

The DCC funded by this RFA is expected to be a stable resource that will gather data from the modENCODE Consortium and other related genomic projects and integrate those data with genome sequence. The DCC should use robust data management tools capable of handling all of the modENCODE data that will be stored in the DCC. Where possible, the applicant should use existing software modules for the DCC, such as those produced by the Generic Model Organism Database project (http:\\www.gmod.org). The DCC is expected to be able to work with the other funded projects of the modENCODE Consortium to establish the exact types and formats of data that will be transferred to the DCC along with developing procedures to track the quality of incoming data. As the identity of these projects will not be known at the time that the applications for the DCC in response to this RFA are due, the applicant should provide a general plan that addresses many types of data related to functional sequence elements, for example the data currently being produced by the ENCODE pilot project.  For all of the data in the DCC, the sources of the data should be identified and links back to these sources should be provided. 

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 NIH U41 Biotechnology Resource Cooperative Agreement award mechanism.  In the cooperative agreement mechanism, the Principal Investigator retains the primary responsibility and dominant role for planning, directing, and executing their components of the modENCODE Project, with NIH staff being substantially involved as a partner with the Principal Investigators, as described under the Section VI. 2. Administrative Requirements, Cooperative Agreement Terms and Conditions of Award". This RFA is a one-time solicitation.  At the current time, NHGRI anticipates that this will be a three-year project unless circumstances warrant a continuation of this effort.

2. Funds Available

The NHGRI intends to commit approximately $1.5 million dollars in FY 2007 to fund 1 new cooperative agreement in response to this RFA.  An applicant may request a project period of up to 3 years.  Although the financial plans of NHGRI provide support for this program, awards pursuant to this RFA are contingent upon the availability of funds and the receipt of a sufficient number of meritorious applications.   The earliest anticipated award date is March 1, 2007.

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

Section III. Eligibility Information


1. Eligible Applicants

1.A. Eligible Institutions

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

1.B. Eligible Individuals

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

2. Cost Sharing or Matching

No cost sharing or matching is required for applications submitted in response to this RFA.

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

3. Other-Special Eligibility Criteria

Applicants for this RFA must have a proven track record of establishing and maintaining databases that contain data similar to that which will be generated by the modENCODE Consortium.   Documentation of this track record must be included in the application.

Section IV. Application and Submission Information


1. Address to Request Application Information

The PHS 398 application instructions are available at http://grants.nih.gov/grants/funding/phs398/phs398.html in an interactive format. Applicants must use the currently approved version of the PHS 398. For further assistance contact 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

Applications must be prepared using the most current PHS 398 research grant application instructions and forms. 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 on line 2 of the face page of the application form and the YES box must be checked.

Foreign Organizations

Several special provisions apply to applications submitted by foreign organizations:

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

3. Submission Dates and Times

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

3.A. Receipt, Review and Anticipated Start Dates

Letter of Intent Receipt Date: June 21, 2006
Application Submission Date(s): July 21, 2006
Peer Review Date: November 2006
Council Review Date: February 12-13, 2007
Earliest Anticipated Start Date: March 1, 2007

3.A.1. Letter of Intent

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

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

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

The letter of intent should be sent to:

Peter Good, PhD
Program Director, Genome Informatics
Division of Extramural Research
National Human Genome Research Institute
5635 Fishers Lane, Ste. 4076, MSC 9305
Rockville, MD 20852 (courier/overnight service)
Bethesda, MD 20892-9306 (regular mail)
Telephone: (301) 496-7531
FAX: (301) 480-2770
Email: goodp@mail.nih.gov
 
3.B. Sending an Application to the NIH

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

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

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

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

Ken Nakamura, PhD
Scientific Review Branch
National Human Genome Research Institute
5635 Fishers Lane, Ste. 4076, MSC 9306
Rockville, MD 20852 (courier/overnight service)
Bethesda, MD 20892-9306 (regular mail)
Telephone: (301) 402-0838
FAX:  (301) 435-1580    
Email:  ken_nakamura@nih.gov


Using the RFA Label: The RFA label available in the PHS 398 application instructions must be affixed to the bottom of the face page of the application. Type the RFA number on the label. Failure to use this label could result in delayed processing of the application such that it may not reach the review committee in time for review. In addition, the RFA title and number must be typed on line 2 of the face page of the application form and the YES box must be marked. The RFA label is also available at: http://grants.nih.gov/grants/funding/phs398/labels.pdf.

3.C. Application Processing

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

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

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

4. Intergovernmental Review

This initiative is not subject to intergovernmental review.

5. Funding Restrictions

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

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

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

6. Other Submission Requirements
Not Applicable

Plan for Sharing Research Data
 
The NHGRI is committed to the principle of rapid data release to the scientific community.  This principle was initially implemented during the Human Genome Project and has been recognized as leading to one of the most effective ways of promoting the use of the human genome sequence to advance scientific knowledge.  At a meeting in Ft. Lauderdale, FL that was co-sponsored by the Wellcome Trust and NHGRI in January 2003, the concept of rapid data release by genomic sequence data producers was reaffirmed, and the attendees strongly recommended applying the practice to other types of data produced by “community resource projects”.  The attendees recognized, however, that different issues, particularly with respect to data validation, would be involved in the development of appropriate release practices for different types of data.  Since they also recognized that sustaining the practice of rapid, prepublication data release by community resources requires that the interests of all involved - including the data producers, data users, and funding agencies - be addressed, they emphasized the need to develop a tripartite system of responsibility. The meeting report from the Ft. Lauderdale meeting can be found on the Wellcome Trust website at: http://www.wellcome.ac.uk/doc_wtd003208.html

The NHGRI has identified the modENCODE Project as a community resource project.  As such, the modENCODE Project aims to function openly by making all data available to the scientific community in a timely manner.   It is expected that the modENCODE Consortium will establish a common data release policy and that all participants will agree to abide by that policy.  The human ENCODE Consortium established a data release policy that the NHGRI deems appropriate for the modENCODE Project as well (see http://www.genome.gov/12513440).  Applicants should provide specific plans for data release in the application. 

Sharing Research Resources

NIH policy requires that grant awardee recipients make unique research resources readily available for research purposes to qualified individuals within the scientific community after publication (NIH Grants Policy Statement http://grants.nih.gov/archive/archive/grants/policy/nihgps_2003/index.htm and http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm#_Toc54600131). Investigators responding to this funding opportunity should include a plan for sharing research resources addressing how unique research resources will be shared or explain why sharing is not possible.

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

As the modENCODE Project is a community resource project, NHGRI expects that not only data, but also resources generated during the course of the program should be made rapidly available to the research community and that sharing plans should follow the same principles and spirit as the rapid data release policy.  Applicants should provide specific plans for resource sharing and distribution in the application.

Section V. Application Review Information


1. Criteria
 
The following will be considered in making funding decisions:

2. Review and Selection Process

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

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

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

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

Approach: Are the conceptual or clinical framework, design, methods, and analyses adequately developed, well integrated, well reasoned, and appropriate to the aims of the project? Does the applicant acknowledge potential problem areas and consider alternative tactics? Does the applicant intend to maintain databases for data on the entire genome of the proposed model organism(s)?

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

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

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

2.A. Additional Review Criteria:

In addition to the above criteria, applications received in response to RFA-HG-06-007 will also be reviewed with respect to the following:

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

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

2.B. Additional Review Considerations

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

2.C. Sharing Research Data

Data Sharing Plan: The reasonableness of the data sharing plan or the rationale for not sharing research data will be assessed by the reviewers. However, reviewers will not factor the proposed data sharing plan into the determination of scientific merit or the priority score. The presence of a data sharing plan will be part of the terms and conditions of the award. The funding organization will be responsible for monitoring the data sharing policy.

The NHGRI has identified the modENCODE Project is a community resource project (see Section IV.6).  As such, the modENCODE Project aims to function openly by making all data available to the scientific community in a timely manner prior to publication.   It is expected that the modENCODE Consortium will establish a common data release policy and that all participants will agree to abide by that policy.  The human ENCODE Consortium established a data release policy that the NHGRI deems would be appropriate for the modENCODE Project as well (see http://www.genome.gov/12513440).  The applicant should provide specific plans for data release in the application and indicate his/her willingness to abide by the data release policy that will eventually be adopted by the modENCODE Consortium.

Program staff will be responsible for the administrative review of the plan for sharing data. The adequacy of the data sharing plan will be considered by program staff of the funding organization when making recommendations about funding applications. Program staff may negotiate modifications of the data sharing plan with the awardee before recommending funding of an application. The final negotiated version of the data sharing plan will become a condition of the award of the cooperative agreement. The effectiveness of the data sharing will be evaluated as part of the administrative review of each non-competing Grant Progress Report (PHS 2590). See Section VI.3. Reporting.

2.D. Sharing Research Resources

 NIH policy requires that grant awardee recipients make unique research resources readily available for research purposes to qualified individuals within the scientific community after publication (See the NIH Grants Policy Statement http://grants.nih.gov/archive/grants/policy/nihgps/part_ii_5.htm#availofrr and http://www.ott.nih.gov/policy/rt_guide_final.html). Investigators responding to this funding opportunity should include a sharing research resources plan addressing how unique research resources will be shared or explain why sharing is not possible.

Program staff will be responsible for the administrative review of the plan for sharing research resources.

The adequacy of the resources sharing plan will be considered by Program staff of the funding organization when making recommendations about funding applications. Program staff may negotiate modifications of the data and resource sharing plans with the awardee before recommending funding of an application. The final version of the data and resource sharing plans negotiated by both will become a condition of the award of the grant. The effectiveness of the resource sharing will be evaluated as part of the administrative review of each non-competing Grant Progress Report (PHS 2590). See Section VI.3. Reporting.

3. Anticipated Announcement and Award Dates
Not Applicable

Section VI. Award Administration Information


1. Award Notices

After the peer review of the application is completed, the Principal Investigator will 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 (http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm).

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 (designated in item 12 on the Application Face Page). If a grantee is not email enabled, a hard copy of the NoA will be mailed to the business official.

Selection of an application for award is not an authorization to begin performance. Any costs incurred before receipt of the 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
 
There will be terms and conditions on the awards pertaining to data policy and resources release policy (where applicable) that have agreed upon by the applicant and the program staff.

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/archive/grants/policy/nihgps_2003/index.htm) and Part II Terms and Conditions of NIH Grant Awards, Subpart B: Terms and Conditions for Specific Types of Grants, Grantees, and Activities (http://grants.nih.gov/archive/grants/policy/nihgps_2003/index.htm).

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

2.A. Cooperative Agreement Terms and Conditions of Award

The following terms and conditions will be incorporated into the award statement of each cooperative agreement awarded under RFA HG-06-007 and will be provided to the Principal Investigators and the appropriate institutional officials at the time 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 instruments used for this program will be the NIH U41 Biotechnology Resource Cooperative Agreement award mechanism. The cooperative agreement is an "assistance" mechanism (rather than an "acquisition" mechanism), in which substantial NIH scientific and programmatic involvement with the awardee is anticipated during the performance of the activity.  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 reside 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 project within the guidelines of RFA-HG-06-007 and for performing the scientific activities.  The P.I. will agree to accept close coordination, cooperation, and participation of NIH staff in those aspects of scientific and technical management of the project as described under "NIH Responsibilities".

The P.I. of a modENCODE Project component 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

The NIH Project Scientist is a scientist of the NHGRI extramural staff who will have substantial scientific and programmatic involvement during the conduct of this activity through technical assistance, advice, and coordination.  However, the role of NIH staff will be to facilitate and not to direct the activities.  It is anticipated that decisions in all activities will be reached by consensus of the mECC and that NIH staff will be given the opportunity to offer input to this process.  One NHGRI Project Scientist will participate as a member of the mECC and will have one vote.  The Project Scientist will have the following substantial involvement:

Additionally, an NHGRI program director will be responsible for the normal scientific and programmatic stewardship of the award and will be named in the NoA.  The NHGRI program director may also serve as the NHGRI Project Scientist.

2.A.3. Collaborative Responsibilities

The mECC will serve as the main governing board of the modENCODE Consortium established under this RFA.   It is anticipated that additional coordination mechanisms will be set up with other U.S. and international groups that may join this effort.   The mECC membership will include one NIH Project Scientist and the P.I. from each awarded cooperative agreement from both RFAs HG-06-006 and HG-06-007.  The mECC may add additional members.  Other government staff may attend the mECC meetings, if their expertise is required for specific discussions. 

The mECC will be responsible for coordinating the activities being conducted by the modENCODE Consortium.  To address particular issues, the mECC may establish working groups as needed, which will include representatives from the Research Consortium and the NHGRI and possibly other experts.  Such groups might include ones to: 1) develop a list of common reagents needed for the modENCODE Project; 2) address data management issues; 3) analyze modENCODE data; 4) develop quality standards and methods to assess data quality; and 5) handle communication issues and develop principles for reporting findings. 

Awardee members of the Steering Committee will be required to accept and implement policies approved by the Steering Committee.

A Scientific Advisory Panel (SAP) will be established by the NHGRI to evaluate the progress of the modENCODE Research Consortium. The SAP will provide recommendations to the Director, NHGRI about the progress and scientific direction of all components of the program.  The SAP will be composed of six to eight senior scientists with relevant expertise, although the membership may be enlarged permanently or on an ad hoc basis as needed. 

The SAP will meet at least twice a year; some meetings may be conducted by telephone conference.  At least once a year, there will be a joint meeting with the mECC to allow the members of the both the SAP and the mECC to interact directly with each other.  Twice a year the SAP will make recommendations regarding progress of the modENCODE Research Consortium and present advice to the Director of NHGRI about changes, if any, which may be necessary in the modENCODE Research Consortium program.

2.A.4. Arbitration 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 arbitration. An Arbitration Panel composed of three members will be convened: a designee of the mECC 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 arbitration procedure in no way affects 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 electronically quarterly reports that describe the data entering the DCC and subsequent progress in tracking, storing, and displaying the data.  Additional reporting on cost will also be required.

Awardees will be required to submit the PHS Non-Competing Grant Progress Report, Form 2590 annually (http://grants.nih.gov/grants/funding/2590/2590.htm) and financial statements as required in the NIH Grants Policy Statement.

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:

Peter Good, PhD
Program Director
Division of Extramural Research
National Human Genome Research Institute
5635 Fishers Lane, Ste. 4076, MSC 9305
Rockville, MD 20852 (courier/overnight service)
Bethesda, MD 20892-9306 (regular mail)
Telephone: (301) 496-7531
FAX: (301) 480-2770
Email: goodp@mail.nih.gov

2. Peer Review Contacts:

Ken Nakamura, PhD
Scientific Review Branch
National Human Genome Research Institute
5635 Fishers Lane, Ste. 4076, MSC 9306
Rockville, MD 20852 (courier/overnight service)
Bethesda, MD 20892-9306 (regular mail)
Telephone: (301) 402-0838
FAX:  (301) 435-1580    
Email:  ken_nakamura@nih.gov


3. Financial or Grants Management Contacts:

Cheryl Chick
Grants Management Officer
Division of Extramural Research
National Human Genome Research Institute
5635 Fishers Lane, Ste. 4076, MSC 9306
Rockville, MD 20852 (courier/overnight service)
Bethesda, MD 20892-9306 (regular mail)
Telephone: (301) 435-7858
FAX: ( 301) 402-1951
Email: ChickC@mail.nih.gov

Section VIII. Other Information


Required Federal Citations

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. Reviewers will consider the data sharing plan but will not factor the plan into the determination of the scientific merit or the priority score.

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/archive/archive/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.

NIH Public Access Policy:
NIH-funded investigators are requested to submit to the NIH manuscript submission (NIHMS) system (http://www.nihms.nih.gov) at PubMed Central (PMC) an electronic version of the author's final manuscript upon acceptance for publication, resulting from research supported in whole or in part with direct costs from NIH. The author's final manuscript is defined as the final version accepted for journal publication, and includes all modifications from the publishing peer review process.

NIH is requesting that authors submit manuscripts resulting from 1) currently funded NIH research projects or 2) previously supported NIH research projects if they are accepted for publication on or after May 2, 2005. The NIH Public Access Policy applies to all research grant and career development award mechanisms, cooperative agreements, contracts, Institutional and Individual Ruth L. Kirschstein National Research Service Awards, as well as NIH intramural research studies. The Policy applies to peer-reviewed, original research publications that have been supported in whole or in part with direct costs from NIH, but it does not apply to book chapters, editorials, reviews, or conference proceedings. Publications resulting from non-NIH-supported research projects should not be submitted.

For more information about the Policy or the submission process please visit the NIH Public Access Policy Web site at http://publicaccess.nih.gov/ and view the Policy or other Resources and Tools including the Authors' Manual (http://publicaccess.nih.gov/publicaccess_Manual.htm).

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

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

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

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

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.


Weekly TOC for this Announcement
NIH Funding Opportunities and Notices


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