Participating Organization(s)	National Institutes of Health (NIH)
Components of Participating Organizations	National Human Genome Research Institute (NHGRI)
Funding Opportunity Title	Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data (U01)
Activity Code	U01 Research Project Cooperative Agreements
Announcement Type	New
Related Notices	November 16, 2011 - See Notice NOT-HG-12-002. The purpose of this Notice is to inform interested applicants from eligible institutions that NHGRI is changing the receipt date.
Funding Opportunity Announcement (FOA) Number	RFA-HG-11-025
Companion FOA	RFA-HG-11-024, U54 Specialized Center- Cooperative Agreements RFA-HG-11-026, U41 Biotechnology Resource Cooperative Agreements
Number of Applications	See Section III. 3. Additional Information on Eligibility
Catalog of Federal Domestic Assistance (CFDA) Number(s)	93.172
FOA Purpose	The Encyclopedia of DNA Elements (ENCODE) and modENCODE Projects have, since their inception, cataloged a significant fraction of the functional elements in the human and well-studied model organism genomes, respectively. These catalogs are increasingly being used by the research community to expand on basic biological knowledge and to interpret the results of disease-mapping studies. The purpose of this FOA is to solicit applications from researchers outside of the umbrella of the ENCODE Projects to support analysis activities on the ENCODE data. These activities might include developing new methods to improve on analysis and interpretation of ENCODE data, combining ENCODE data with related functional genomic data from other projects to derive new biological insights, or using the ENCODE data to improve on the analysis of disease mapping studies to identify causal variants.

Posted Date	October 4, 2011
Open Date (Earliest Submission Date)	November 6, 2011
Letter of Intent Due Date	November 6, 2011
Application Due Date(s)	(New Date December 21, 2011 per NOT-HG-12-002), Original Date December 6, 2011, by 5:00 PM local time of applicant organization.
AIDS Application Due Date(s)	Not Applicable
Scientific Merit Review	March, 2012
Advisory Council Review	May, 2012
Earliest Start Date(s)	July, 2012
Expiration Date	(New Expiration Date December 22, 2011 per NOT-HG-12-002), Original Date December 7, 2011
Due Dates for E.O. 12372	Not Applicable

Required Application Instructions

It is critical that applicants follow the instructions in the SF 424 (R&R) Application Guide except where instructed to do otherwise (in this FOA or in a Notice from the NIH Guide for Grants and Contracts). Conformance to all requirements (both in the Application Guide and the FOA) is required and strictly enforced. Applicants must read and follow all application instructions in the Application Guide as well as any program-specific instructions noted in Section IV. When the program-specific instructions deviate from those in the Application Guide, follow the program-specific instructions. Applications that do not comply with these instructions may be delayed or not accepted for review.

Part 1. Overview Information
Part 2. Full Text of the Announcement
Section I. Funding Opportunity Description
Section II. Award Information
Section III. Eligibility Information
Section IV. Application and Submission Information
Section V. Application Review Information
Section VI. Award Administration Information
Section VII. Agency Contacts
Section VIII. Other Information

The Encyclopedia of DNA Elements (ENCODE) and modENCODE Projects have, since their inception, cataloged a significant fraction of the functional elements in the human and well-studied model organism genomes, respectively. These catalogs are increasingly being used by the research community to expand on basic biological knowledge and to interpret the results of disease-mapping studies. The purpose of this FOA is to solicit applications from researchers outside of the umbrella of the ENCODE Projects to support analysis activities on the ENCODE data. These activities might include developing new methods to improve on analysis and interpretation of ENCODE data, combining ENCODE data with related functional genomic data from other projects to derive new biological insights, or using the ENCODE data to improve on the analysis of disease mapping studies to identify causal variants.

This FOA will use the U01 Research Project Cooperative Agreement mechanism. It is being issued in conjunction with two other FOAs: RFA-HG-11-024, Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Model Organisms and RFA-HG-11-026, Data Analysis and Coordination Centers for the Encyclopedia of DNA Elements (ENCODE) Project .

The long-term goal of the Encyclopedia of DNA Elements (ENCODE) Project has been to identify comprehensively all of the sequence-based functional elements in the human genome. The modENCODE Project is a parallel effort to annotate the genomes of worm (C. elegans) and fly (D. melanogaster) comprehensively. In addition, with funds from the American Recovery and Reinvestment Act (ARRA) of 2009, a small, two-year effort was supported to generate comparable data from the mouse (M. musculus) to facilitate the annotation of the human genome. For the purpose of this solicitation, these efforts will collectively be referred to as the ENCODE projects. These projects have been designated as community resource projects by NHGRI to accelerate access to and use of the data by the entire scientific community. Accordingly, pre-publication data is released rapidly to public databases. For more information about the ENCODE projects, see: http://www.genome.gov/ENCODE.

Functional elements that have been elucidated in the ENCODE projects include transcribed sequences, transcriptional control elements (including enhancers, promoters, and insulators), chromatin features, and regulatory elements acting at the RNA level post-transcriptionally (including those that may regulate splicing, translation, and stability). Using a variety of high-throughput methods, such as RNA-seq, ChIP-seq, RIP-seq, and DNase-seq, these functional elements have been identified by mapping different types of marks, including transcription factor binding sites, histone modifications, various measures of chromatin structure, sites where RNA-binding proteins bind, and different classes of transcribed sequences. These growing catalogs of functional elements are directly adding to our general understanding of genome structure and function, and also are enabling targeted research projects to examine the role of these elements in the regulation of genes of interest and in specific biological processes. As genetic and epigenetic variation at these elements is undoubtedly responsible for some observed phenotypes, comprehensive identification of functional elements is also expected to enhance our understanding of human health and disease.

Currently, several different levels of data analysis are being conducted within the ENCODE Projects. Each data production center has an analysis pipeline to process the primary data, to use particular data types to identify one or more specific classes of functional elements, and to identify any biological insights from these data. The data producers also process the data to prepare them for submission to a Data Coordination Center (DCC). There are two DCCs, one for ENCODE (http://www.encodeproject.org) and one for modENCODE (http://www.modencode.org), that are responsible for developing, housing, and maintaining databases to track, store, and provide access to the ENCODE and modENCODE data, respectively. Finally, each consortium has an Analysis Working Group (AWG) that is responsible for integrative analyses of all data sets from the respective projects. Supporting each AWG is a Data Analysis Center (DAC) that coordinates the high-level analytical activities and provides computational support for these analyses.

Each of the ENCODE Projects has functioned as a research consortium that brings the participants together in a highly collaborative and synergistic effort. For the last four years, the ENCODE Projects have focused on the comprehensive analysis of a limited set of common cell types, mainly cell lines, along with a survey of functional elements in other cell types. Analyses that have integrated the datasets within and across a variety of cell types for a given organism have amplified the amount of useful information that has been derived from the data (See: Nature 447:799-816, 2007; Science 330:1775-1787, 2010; Science 330:1787-1797, 2010; PLoS Biol 9:e1001046, 2011). The use of multiple cell types and multiple assays is, in fact, key to obtaining a comprehensive description of the functional elements in these genomes, as there is no one cell type or type of assay that can be used to identify all functional elements.

Despite these advances, current limitations in technology and available resources are barriers to the application of all assays to all cell types of interest. By the conclusion of the current ENCODE production period, these projects will have interrogated only a fraction of the cells and tissues needed for a comprehensive catalog of functional elements. Generation of truly comprehensive catalogs will require revolutionary new technologies to dramatically reduce the cost and increase the sensitivity of finding functional elements, and applications to develop such technologies were recently solicited through three FOAs: RFA-HG-11-013; RFA-HG-11-014 and RFA-HG-11-015.

The NHGRI plans to extend the ENCODE effort with a new set of FOAs. For data production, the companion FOA RFA-HG-11-024 solicits applications for focused projects to conduct high-throughput data-generation efforts that will significantly extend towards completion the current catalogs of sequence-based functional elements in the human, mouse (M. musculus), as well as possibly the fly (D. melanogaster) and worm (C. elegans) genomes. A second companion FOA, RFA-HG-11-026, solicits applications for projects to establish an ENCODE Data Coordination and Analysis Center (EDCAC). This EDCAC will support the activities currently being performed by the ENCODE and modENCODE DCCs and DACs. With this FOA, RFA-HG-11-025 Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data , NHGRI solicits applications to support additional analyses of the ENCODE data.

Applicants for this FOA should propose research projects to develop and apply innovative and advanced statistical, mathematical, and computational methods to analyze the data from the ENCODE Project with the goal of improving and interpreting the catalogs of functional elements in the human genome and the genomes of selected model organisms. The projects should focus on analysis activities that use the ENCODE data, either to improve the quality of the data, or to use them to gain additional insights into the biology of genomes and to inform studies of disease or other phenotypes. Applicants are encouraged to integrate the ENCODE data with other high-quality functional genomic datasets and with data from ongoing disease-mapping studies. However, any proposed disease-specific analyses must serve as models for other disease-related studies and should not be focused exclusively on the use of ENCODE data to study a particular disease.

Examples of research topics for this FOA include, but are not limited to:

• Development of statistical methods to assess the quality of data generated by the ENCODE Project;
• Definition of a minimum set of elements/marks needed to identify a unique molecular signature of a cell type to optimize the data generation from ENCODE and related projects;
• Development of methods to provide new derived datasets based on the ENCODE data, such as identifying functional elements in repetitive regions of the genome;
• Development of tools to use the ENCODE Project data in the formulation and testing of new predictions in both clinical and basic research;
• Integration of different ENCODE Project datasets with other functional genomic datasets, including but not limited to data from the NIH Common Fund Epigenomics (http://commonfund.nih.gov/epigenomics/) and GTEx (http://commonfund.nih.gov/GTEx/) Projects, to identify the biological roles of the identified functional elements;
• Use of ENCODE data to annotate variants in the genome, such as GWAS variants (http://www.genome.gov/26525384) to functionally annotate putative casual variants; and
• Use of ENCODE data to infer the transcriptional regulatory network within different cell types.

A proposed research project should, if necessary, include the development of software needed for the analysis, and should include documentation that would allow others to use that software. For the same reason, software developed by awardees should be modular and robust, so that it can work as a stand-alone package. If appropriate, the EDCAC may incorporate any new software developed as a consequence of this FOA into a uniform analysis pipeline for use by the entire Consortium. To facilitate such incorporation into any analysis pipelines at the EDCAC, software development should, to the extent possible, use standard formats for data input and output. Such standard formats will preferably be ones that already are in use by the Consortium; if new standard formats are needed, they should be developed in close collaboration with the ENCODE AWG.

Applicants may propose experimental work to test predictions that are generated as a result of the proposed computational analyses. However, this experimental component is not required and should not be a major focus of the application.

This solicitation is open to all investigators, both those who are currently participating in the ENCODE and modENCODE Projects and those who are not. The awardees funded through this FOA and the concurrent FOAs, RFA-HG-11-024 Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Model Organisms (U54), and FOA RFA-HG-11-026, Data Analysis and Coordination Centers for the Encyclopedia of DNA Elements (ENCODE)(U41) Project, will be members of the ENCODE Consortium. However, the ENCODE Consortium will continue to be open to all academic, government and private sector scientists willing to participate in an open process to facilitate the comprehensive annotation of the human genome. Groups with funding from other sources will be able to participate in the ENCODE Project provided they meet the criteria for participation (see http://www.genome.gov/12513439). Therefore, funding through these ENCODE FOAs is not a prerequisite for participation in the ENCODE Consortium.

Awardees funded in response to this FOA are welcome to participate as members of the ENCODE AWG, which will be responsible for organizing the integrative analyses of the ENCODE data and other consortium-wide analysis activities such as developing and implementing a uniform analysis pipeline for different data types. In contrast to the EDCAC funded in response to the companion FOA RFA-HG-11-026, awardees will not be directly responsible for supporting the activities of the AWG. However, all members of the ENCODE AWG are expected to share information about analysis activities to leverage possible overlap with either the informatics activities of each production center or the other activities of the EDCAC.

The NHGRI has designated the ENCODE Project as a community resource project and ENCODE Consortium members, including awardees from this FOA, will be expected to abide by the ENCODE data policy (http://www.genome.gov/27528022). Currently, this policy addresses only the release and use of primary data and analyses used to discover functional elements in the genome. NHGRI will revisit the current data release policy with awardees of this FOA and update it to include integrative analyses to ensure that the goals of the ENCODE Project and the interests of NHGRI along with those of the data producers and analysts continue to be met (see Section IV.2.

Funding Instrument	Cooperative Agreement
Application Types Allowed	New The OER Glossary and the SF 424 (R&R) Application Guide provide details on these application types.
Funds Available and Anticipated Number of Awards	NHGRI intends to commit $3 million in total costs in FY 2012 and to make 5-8 awards.
Award Budget	Application budgets are not limited, but need to reflect actual needs of the proposed project.
Award Project Period	The total project period for an application submitted in response to this RFA may not exceed three years.

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.

Higher Education Institutions

• Public/State Controlled Institutions of Higher Education
• Private Institutions of Higher Education

The following types of Higher Education Institutions are always encouraged to apply for NIH support as Public or Private Institutions of Higher Education:

• Hispanic-serving Institutions
• Historically Black Colleges and Universities (HBCUs)
• Tribally Controlled Colleges and Universities (TCCUs)
• Alaska Native and Native Hawaiian Serving Institutions

Nonprofits Other Than Institutions of Higher Education

• Nonprofits with 501(c)(3) IRS Status (Other than Institutions of Higher Education)
• Nonprofits without 501(c)(3) IRS Status (Other than Institutions of Higher Education)

For-Profit Organizations

• Small Businesses
• For-Profit Organizations (Other than Small Businesses)

Governments

• State Governments
• County Governments
• City or Township Governments
• Special District Governments
• Indian/Native American Tribal Governments (Federally Recognized)
• Indian/Native American Tribal Governments (Other than Federally Recognized)
• Eligible Agencies of the Federal Government
• U.S. Territory or Possession

Other

• Independent School Districts
• Public Housing Authorities/Indian Housing Authorities
• Native American Tribal Organizations (other than Federally recognized tribal governments)
• Faith-based or Community-based Organizations
• Regional Organizations

Non-domestic (non-U.S.) Entities (Foreign Institutions) are eligible to apply.
Non-domestic (non-U.S.) components of U.S. Organizations are eligible to apply.

Foreign components, as defined in the NIH Grants Policy Statement, are allowed.

Applicant organizations must complete the following registrations as described in the SF 424 (R&R) Application Guide to be eligible to apply for or receive an award. Applicants must have a valid Dun and Bradstreet Universal Numbering System (DUNS) number in order to begin each of the following registrations.

• Central Contractor Registration (CCR) must maintain an active registration, to be renewed at least annually
• Grants.gov
• eRA Commons

All Program Director(s)/Principal Investigator(s) (PD(s)/PI(s)) must also work with their institutional officials to register with the eRA Commons or ensure their existing eRA Commons account is affiliated with the eRA Commons account of the applicant organization.

All registrations must be completed by the application due date. Applicant organizations are strongly encouraged to start the registration process at least four (4) weeks prior to the application due date.

Any individual(s) with the skills, knowledge, and resources necessary to carry out the proposed research as the Program Director(s)/Principal Investigator(s) (PD(s)/PI(s)) is invited to work with his/her organization 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 support.

For institutions/organizations proposing multiple PD(s)/PI(s), visit the Multiple Program Director(s)/Principal Investigator(s) Policy and submission details in the Senior/Key Person Profile (Expanded) Component of the SF 424 (R&R) Application Guide.

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

Applicant organizations may submit more than one application, provided that each application is scientifically distinct.

NIH will not accept any application in response to this FOA that is essentially the same as one currently pending initial peer review unless the applicant withdraws the pending application.

Applicants must download the SF424 (R&R) application package associated with this funding opportunity using the Apply for Grant Electronically button in this FOA or following the directions provided at Grants.gov.

It is critical that applicants follow the instructions in the SF424 (R&R) Application Guide, except where instructed in this funding opportunity announcement to do otherwise. Conformance to the requirements in the Application Guide is required and strictly enforced. Applications that are out of compliance with these instructions may be delayed or not accepted for review.

For information on Application Submission and Receipt, visit Frequently Asked Questions Application Guide, Electronic Submission of Grant Applications.

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.

By the date listed in Part 1. Overview Information, prospective applicants are asked to submit a letter of intent that includes the following information:

• Descriptive title of proposed research
• Name, address, and telephone number of the PD(s)/PI(s)
• Names of other key personnel
• Participating institutions
• Number and title of this funding opportunity

The letter of intent should be sent to:

Peter Good, Ph.D.
Program Director, Genome Informatics
Division of Extramural Research
National Human Genome Research Institute (NHGRI)
5635 Fishers Lane, Ste. 4076, MSC 9305
Bethesda, MD 20892-9305 (U.S Postal Service Express or regular mail)
Rockville, MD 20852 (for express/courier service; non-USPS service)
Telephone: 301-496-7531
FAX: 301-480-2770
E-mail: [email protected]
Please transmit Letter of Intent by to: [email protected] by email.

The forms package associated with this FOA includes all applicable components, mandatory and optional. Please note that some components marked optional in the application package are required for submission of applications for this FOA. Follow all instructions in the SF424 (R&R) Application Guide to ensure you complete all appropriate optional components.

All page limitations described in the SF424 Application Guide and the Table of Page Limits must be followed.

All instructions in the SF424 (R&R) Application Guide must be followed, with the following additional instructions:

• Applicants should describe their expertise with analyses of functional genomic data such as the ENCODE data. They should describe how they would develop the analyses and the software to run the analyses. They should describe the input and output data types and formats.
• Applicants should describe the computing resources that are needed for the analyses and what resources they have available.
• The ENCODE Project has regular conference calls and meetings. Applicants should request funds over the three years to attend an annual meeting, usually in the Washington, D.C. area.

Resource Sharing Plan

Individuals are required to comply with the instructions for the Resource Sharing Plans (Data Sharing Plan, Sharing Model Organisms, and Genome Wide Association Studies (GWAS)) as provided in the SF424 (R&R) Application Guide, with the following modifications:

• Data Sharing: The NHGRI is committed to the principle of rapid data release to the scientific community from projects of broad community interest. This principle was initially implemented during the Human Genome Project and has been widely recognized by the community as leading to one of the most effective ways of promoting the use of the genome sequence data to advance scientific knowledge. The implementation of the concept of rapid, prepublication data release has evolved over time in response to the changing technological and scientific landscapes, as described in the report from a meeting held in Toronto in 2009 (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). Although the Toronto meeting report specifically did not use the earlier term community resource project, it did recommend that funding agencies should require rapid pre-publication data release for projects that generate data sets that have broad utility, are large in scale, are 'reference' in character and typically have community 'buy-in'.
• The ENCODE Project is one such project, and NHGRI will continue to consider it as a community resource project. The ENCODE and modENCODE Consortia established and currently operate under a common Data Release Policy (see http://www.genome.gov/27528022), which expects rapid pre-publication data release. The current policy allows a nine-month moratorium period on presentations and publications, during which time data users may freely use the ENCODE and modENCODE data to design and carry out their own research programs, but are asked not to submit publications or make public presentations that use the unpublished ENCODE/modENCODE data without prior consent. The purpose of this moratorium period has been to allow the data producers to have an opportunity to publish on their initial findings. At present, after the nine-month moratorium, all data are freely available to anyone to use in any manner in presentations and publications. Agreement to abide by that policy is a requirement for anyone to join one of the Consortia.
• NHGRI expects that the rapid data release principles of this policy will continue to be implemented during the next phase of the ENCODE Project. Applicants will be expected to propose a data release policy in their applications (see below) that addresses rapid data sharing with the community, consistent with achieving the goals of the project. However, NHGRI is concerned that the nine-month moratorium has not been achieving the goal of getting data to be used rapidly by the research community, and plans, at the start of the next phase of ENCODE, to raise for discussion amongst consortium members that there be no such moratorium. NHGRI’s rationale for such an approach is that while the utility of the ENCODE data is increasing, the data types themselves are no longer novel because of the maturation of both the ENCODE Project and the associated technologies. As a result, biological interpretation of the data, which is outside the scope of this initiative and which may take longer than nine months to complete, is increasingly being required for publication. A longer moratorium period to accommodate this would be inconsistent with the primary purpose of ENCODE to generate a high quality, comprehensive and broadly useful catalog of functional elements, and to make it available expeditiously to the research community. It is also NHGRI’s intent, going forward through this FOA, to fund fewer, more centralized, and higher throughput production centers that will not focus on specific biological studies beyond the minimum amount needed to validate the quality of the forthcoming data.
• Another issue that has arisen since the current ENCODE data release policy was developed is that of the pre-publication release of integrative data analyses from a community resource project. In situations where the analysis methods are stable and the Consortium thinks that the resultant analyses may be of value to the community, NHGRI believes that these analyses should also be rapidly released to the community prior to publication to further the advancement of research.
• Once the next phase of ENCODE begins, the ENCODE Consortium members will be asked to revisit the data release policy, consider the issues NHGRI has raised above and any other issues raised by the research community, and establish an updated data release policy as appropriate.
• Applicants should provide a specific proposal for release of production data in the application, and are encouraged to address the issue of the release of data analyses. The reasonableness of the proposed data sharing plan will be assessed by the reviewers who will provide their assessment of the proposed data sharing plan as an administrative note and will not factor it into the determination of scientific merit or the impact score. After the initial review, NHGRI program staff will be responsible for any additional administrative review of the plan for sharing data and may negotiate modifications of the data sharing plan with the prospective awardee before recommending funding of an application. The adequacy of the negotiated data sharing plan will be considered by program staff when making funding recommendations. The final negotiated version of the data sharing plan will become a term and condition of the award of the cooperative agreement with the expectation that the Consortium will develop a common plan for data release once the awards are funded, and that this common plan will be adopted by all awardees.
• In summary, in considering data sharing, applicants should understand that NHGRI’s interest is for the ENCODE Consortium going forward to again have a common data release policy to which all participants in the Consortium will adhere. NHGRI will negotiate an interim data release plan as appropriate with each prospective awardee before an award is issued. After all of the awards have been made, the ENCODE Steering Committee, of which all awardees will be members, will develop a final, common data release plan as appropriate for the Project that will address the interests of the data producers and analysts, as well as the users of the ENCODE catalogs. Applicants should indicate their willingness to participate in the development of such final plan and to accept it.
• The effectiveness of data sharing will be evaluated as part of the administrative review of the annual non-competing Grant Progress Report (PHS 2590).
• See Section VI.3. Reporting.
• Resource Sharing: As the ENCODE Project is generating a community resource, NHGRI intends that, in addition to data, resources generated by the ENCODE awards should be made rapidly available to the research community and that resource sharing plans should follow the same principles and spirit as data release plans. As demonstrated by previous genomics community resource projects, these resources are of high value to the broader biomedical research community in enabling scientific studies. Since the cost and effort involved of generating the resources can be high, rapid dissemination of these resources would accelerate scientific exploration since individual researchers would not have to replicate such efforts. The applicant should provide specific plans for resource sharing and distribution in the application. The reasonableness of the proposed resource sharing plan will be assessed by the reviewers who will provide their assessment of the proposed plan as an administrative note and will not factor it into the determination of scientific merit or the impact score. After the initial review, NHGRI program staff will be responsible for any additional administrative review of the plan for sharing resources and may negotiate modifications of the resource sharing plan with the prospective awardee before recommending funding of an application. The adequacy of the negotiated resource sharing plan will be considered by program staff when making funding recommendations. The final negotiated version of the resource sharing plan will become a term and condition of the award of the cooperative agreement. The effectiveness of the resource sharing plan will be evaluated as part of the administrative review of each non-competing Grant Progress Report (PHS 2590). See Section VI.3. Reporting.
• All applications, regardless of the amount of direct costs requested for any one year, should address Data and Resource Sharing Plans.

Appendix

Do not use the appendix to circumvent page limits. Follow all instructions for the Appendix as described in the SF424 (R&R) Application Guide.

Foreign (non-US) institutions must follow policies described in the NIH Grants Policy Statement, and procedures for foreign institutions described throughout the SF424 (R&R) Application Guide.

Part I. Overview Information contains information about Key Dates. Applicants are encouraged to submit in advance of the deadline to ensure they have time to make any application corrections that might be necessary for successful submission.

Organizations must submit applications via Grants.gov, the online portal to find and apply for grants across all Federal agencies. Applicants must then complete the submission process by tracking the status of the application in the eRA Commons, NIH’s electronic system for grants administration.

Applicants are responsible for viewing their application in the eRA Commons to ensure accurate and successful submission.

Information on the submission process and a definition of on-time submission are provided in the SF424 (R&R) Application Guide.

This initiative is not subject to intergovernmental review.

All NIH awards are subject to the terms and conditions, cost principles, and other considerations described in the NIH Grants Policy Statement.

Pre-award costs are allowable only as described in the NIH Grants Policy Statement.

Applications must be submitted electronically following the instructions described in the SF 424 (R&R) Application Guide. Paper applications will not be accepted.

Applicants must complete all required registrations before the application due date. Section III. Eligibility Information contains information about registration.

For assistance with your electronic application or for more information on the electronic submission process, visit Applying Electronically.

Important reminders:
All PD(s)/PI(s) must include their eRA Commons ID in the Credential field of the Senior/Key Person Profile Component of the SF 424(R&R) Application Package. Failure to register in the Commons and to include a valid PD/PI Commons ID in the credential field will prevent the successful submission of an electronic application to NIH.

The applicant organization must ensure that the DUNS number it provides on the application is the same number used in the organization’s profile in the eRA Commons and for the Central Contractor Registration (CCR). Additional information may be found in the SF424 (R&R) Application Guide.

See more tips for avoiding common errors.

Upon receipt, applications will be evaluated for completeness by the Center for Scientific Review and responsiveness by NHGRI, NIH. Applications that are incomplete and/or nonresponsive will not be reviewed.

In order to expedite review, applicants are requested to notify the NHGRI Referral Office by email at {[email protected]} when the application has been submitted. Please include the FOA number and title, PD(s)/PI(s) name, and title of the application.

Applicant Information Session

An Information Session for this FOA and related FOAs RFA-HG-11-024 and RFA-HG-11-026 will be held on October 31, 2011, from 12 noon-3 PM Eastern Standard Time. The Information Session will be conducted as a teleconference. No provisions will be made for in-person attendance. During the Information Session, NHGRI staff will present an overview of these FOAs and answer questions from prospective applicants. The Information Session is open to all prospective applicants, but participation is not a prerequisite to applying.

Prospective applicants who plan to participate in the Information Session should send an e-mail expressing their interest as soon as possible to NHGRI at [email protected] in order to receive logistical information about the Information Session, including dial-in numbers, which will be provided no later than October 27, 2011. In the Subject line of the e-mail request, please write: Information Session . The email message should contain:

Name,
Institution,
E-mail address,
Number of telephone lines that your group plans to use for the teleconference.

Prospective applicants are encouraged to submit their questions about the FOAs to [email protected] before October 27, 2011. Prospective applicants may ask additional questions during the Information Session, and NHGRI staff will respond to those questions. Following the Information Session, by November 4, 2011, NHGRI will post a summary of questions and answers at http://www.genome.gov/ENCODE. Prospective applicants with inquiries concerning these FOAs who are unable to participate in the Information Session are encouraged to view the summary of questions and answers after they are posted. For any additional questions that are not addressed in the summary, please contact the program contacts listed in the FOAs for which you plan to apply.

Applicants are required to follow the instructions for post-submission materials, as described in NOT-OD-10-115.

Only the review criteria described below will be considered in the review process. As part of the NIH mission, all applications submitted to the NIH in support of biomedical and behavioral research are evaluated for scientific and technical merit through the NIH peer review system.

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 review criteria and additional review criteria (as applicable for the project proposed).

Reviewers will consider each of the review criteria below in the determination of scientific 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? Will the proposed analyses enhance the utility of the ENCODE data?

Investigator(s)

Are the PD(s)/PI(s), 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(s)/PI(s), do the investigators have complementary and integrated expertise; are their leadership approach, governance and organizational structure appropriate for the project? Are the track records of the PD(s)/PI(s) and other key personnel in the analysis of high-throughput data adequate to conduct the proposed research successfully? Do the investigators have experience in working cooperatively with others and sharing data and methods in a timely manner?

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? Is the level of innovation appropriate for the proposed analyses in the Project?

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?

As applicable for the project proposed, reviewers will evaluate the following additional items while determining scientific and technical merit, and in providing an overall impact/priority score, 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. For additional information on review of the Human Subjects section, please refer to the Human Subjects Protection and Inclusion Guidelines.

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. For additional information on review of the Inclusion section, please refer to the Human Subjects Protection and Inclusion Guidelines.

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 on review of the Vertebrate Animals section, please refer to the Worksheet for Review of the Vertebrate Animal Section.

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.

Resubmissions

Not Applicable

Renewals

Not Applicable

Revisions

Not Applicable

As applicable for the project proposed, reviewers will consider 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

Reviewers will assess whether the project presents special opportunities for furthering research programs through the use of unusual talent, resources, populations, or environmental conditions that exist in other countries and either are not readily available in the United States or augment existing U.S. resources.

Select Agent 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 are reasonable: 1) Data Sharing Plan; 2) Sharing Model Organisms; and 3) Genome Wide Association Studies (GWAS).

Budget and Period of Support

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

Applications will be evaluated for scientific and technical merit by (an) appropriate Scientific Review Group(s) convened by the NHGRI , in accordance with NIH peer review policy and procedures, using the stated review criteria. Review assignments will be shown in the eRA Commons.

As part of the scientific peer review, all applications:

• May undergo a selection process in which only those applications deemed to have the highest scientific and technical merit (generally the top half of applications under review), will be discussed and assigned an overall impact/priority score.
• Will receive a written critique.

Appeals of initial peer review will not be accepted for applications submitted in response to this FOA.

Applications will be assigned to the appropriate NIH Institute or Center. Applications will compete for available funds with all other recommended applications submitted in response to this FOA. Following initial peer review, recommended applications will receive a second level of review by the National Advisory Council for Human Genome Research. The following will be considered in making funding decisions:

• Scientific and technical merit of the proposed project as determined by scientific peer review.
• Availability of funds.
• Relevance of the proposed project to program priorities.
• Adequacy of the proposed data and resource sharing plans.

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.

Information regarding the disposition of applications is available in the NIH Grants Policy Statement.

If the application is under consideration for funding, NIH will request "just-in-time" information from the applicant as described in the NIH Grants Policy Statement.

A formal notification in the form of a Notice of Award (NoA) will be provided to the applicant organization for successful applications. The NoA signed by the grants management officer is the authorizing document and will be sent via email to the grantee’s business official.

Awardees must comply with any funding restrictions described in Section IV.5. Funding Restrictions. 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.

Any application awarded in response to this FOA will be subject to the DUNS, CCR Registration, and Transparency Act requirements as noted on the Award Conditions and Information for NIH Grants website.

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 and Part II: Terms and Conditions of NIH Grant Awards, Subpart B: Terms and Conditions for Specific Types of Grants, Grantees, and Activities. More information is provided at Award Conditions and Information for NIH Grants.

Cooperative Agreement Terms and Conditions of Award

The following special terms of award are in addition to, and not in lieu of, otherwise applicable U.S. Office of Management and Budget (OMB) administrative guidelines, U.S. Department of Health and Human Services (DHHS) 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.

The PD(s)/PI(s) will have the primary responsibility for:

• Defining the details for the project within the guidelines of RFA-HG-11-025 and for performing the scientific activities.
• Ensuring that the appropriate analyses are developed, evaluated, and chosen for implementation.
• Coordinating the processing of particular data types with groups working with related data, both in the Project and outside of it.
• Sharing project activities within the ENCODE Consortium.
• Ensuring that the data produced as part of this project, as well as any resource datasets produced as part of developing the methods for data analysis, are released to the ENCODE Data Coordination and Analysis Center (EDCAC) by procedures developed by the Steering Committee and the AWG.
• Disclosing fully algorithms, software source code, and experimental methods to the other members of the Consortium for the purpose of scientific evaluation.
• Ensuring that software developed as part of this project is made freely available to the broad research community.
• Sharing results according to the data release policy developed for and by this project.
• Participating in group activities, including attending periodic workshops to discuss the ENCODE Project's progress and coordinating publication of research results.
• Serving as a member of the ENCODE Research Consortium Steering Committee.
• Not disclosing confidential information obtained from other members of the Consortium.
• Adhering to NHGRI policies regarding intellectual property and other policies that might be established during the course of this activity.
• Accepting and implementing the common guidelines and procedures approved by the Steering Committee, External Consultants Panel and NHGRI.

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 DHHS, PHS, and NIH policies.

NIH staff have substantial programmatic involvement that is above and beyond the normal stewardship role in awards, as described below:

An NIH Project Scientist is a scientist of the NHGRI extramural staff who will have substantial scientific and programmatic involvement that is above and beyond the normal stewardship role in awards, including providing technical assistance, advice, and coordination for the ENCODE Project and its component parts. 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 ENCODE Research Consortium Steering Committee 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 Steering Committee and will have one vote.

The Project Scientist will:

• Provide technical assistance, advice and coordination for the ENCODE Project and its component parts. However, the role of NIH staff will be to facilitate and not to direct the activities.
• Participate with the other Steering Committee members in the group process of setting research priorities, deciding optimal research approaches and protocol designs, and contributing to the adjustment of research protocols or approaches as warranted.
• Participate within the ENCODE AWG to provide advice and coordination for their activities.
• Serve as a liaison, helping to coordinate activities among and for the awardees, including acting as a liaison to the NHGRI, and as an information resource about extramural genome research activities.
• Coordinate the efforts of the entire Research Consortium, including other participating groups not funded through this FOA.
• Attend all Steering Committee meetings as a voting member and assist in developing operating guidelines, quality control procedures, and consistent policies for dealing with recurrent situations that require coordinated action. The Project Scientist must be informed of all major interactions of members of the Steering Committee.
• Report periodically on the progress of the ENCODE Project to the Director, NHGRI.
• Provide relevant expertise and overall knowledge of NIH-sponsored research to facilitate the selection of scientists not affiliated with the awardee institutions to serve on the External Consultants Panel.
• Serve as a liaison between the Steering Committee and the External Consultants Panel, attending External Consultants Panel meetings in a non-voting liaison member role.
• Serve on subcommittees of the Steering Committee and the External Consultants Panel, as appropriate.
• Assist awardees in the development, if needed, of policies for dealing with situations that require coordinated action.
• Provide advice in the management and technical performance of the investigation.
• Assist in promoting the availability of the ENCODE and related resources developed in the course of this project to the scientific community at large.
• Participate in data analyses, interpretations, and, where warranted, co-authorship of the publication of results of studies conducted through the ENCODE Research Consortium.

Additionally, an agency program official or IC program director will be responsible for the normal scientific and programmatic stewardship of the award and will be named in the award notice.

An External Consultants Panel will be established by the NHGRI to evaluate the progress of the ENCODE Research Consortium. The External Consultants Panel will provide recommendations to the Director, NHGRI about the progress and scientific direction of all components of the program. The External Consultants Panel 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 External Consultants Panel 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 Steering Committee to allow the members of the both the External Consultants Panel and the Steering Committees to interact directly with each other. Twice a year the External Consultants Panel will make recommendations regarding progress of the ENCODE Research Consortium and present advice to the Director of NHGRI about changes, if any, that may be necessary in the ENCODE Research Consortium program.

Areas of Joint Responsibility include:

The Steering Committee will serve as the main coordinating board of the ENCODE Research Consortium established under this FOA. It is anticipated that additional coordination mechanisms will be set up with other U.S. and international groups that may join this effort. The Steering Committee membership will include one NIH Project Scientist and the P.I. from each awarded cooperative agreement. The Steering Committee may add additional members. Other government staff may attend the Steering Committee meetings if their expertise is required for specific discussions.

The Steering Committee will be responsible for coordinating the activities being conducted by the ENCODE Research Consortium. To address particular issues, the Steering Committee 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 Project; 2) address data management issues; 3) analyze Project data; 4) develop quality standards and methods to assess data quality; and 5) handle communication issues and develop principles for reporting findings. Minutes of the Steering Committee meetings will be available to the Steering Committee members with 30 days after each meeting.

Each full member will have one vote. Awardee members of the Steering Committee will be required to accept and implement policies approved by the Steering Committee

Dispute Resolution:

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 regulation 42 CFR Part 50, Subpart D and DHHS regulation 45 CFR Part 16.

When multiple years are involved, 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.

A final progress report, invention statement, and the expenditure data portion of the Federal Financial Report are required for closeout of an award, as described in the NIH Grants Policy Statement.

The Federal Funding Accountability and Transparency Act of 2006 (Transparency Act), includes a requirement for awardees of Federal grants to report information about first-tier subawards and executive compensation under Federal assistance awards issued in FY2011 or later. All awardees of applicable NIH grants and cooperative agreements are required to report to the Federal Subaward Reporting System (FSRS) available at www.fsrs.gov on all subawards over $25,000. See the NIH Grants Policy Statement for additional information on this reporting requirement.

We encourage inquiries concerning this funding opportunity and welcome the opportunity to answer questions from potential applicants.

Grants.gov Customer Support (Questions regarding Grants.gov registration and submission, downloading or navigating forms)
Contact Center Phone: 800-518-4726
Email: [email protected]

GrantsInfo (Questions regarding application instructions and process, finding NIH grant resources)
Telephone 301-710-0267
TTY 301-451-5936
Email: [email protected]

eRA Commons Help Desk(Questions regarding eRA Commons registration, tracking application status, post submission issues)
Phone: 301-402-7469 or 866-504-9552 (Toll Free)
TTY: 301-451-5939
Email: [email protected]

Peter Good, Ph.D.
Program Director, Genome Informatics
Division of Extramural Research
National Human Genome Research Institute (NHGRI)
5635 Fishers Lane, Ste. 4076, MSC 9305
Bethesda, MD 20892-9305 (U.S Postal Service Express or regular mail)
Rockville, MD 20852 (for express/courier service; non-USPS service)
Telephone: 301-496-7531
FAX: 301-480-2770
E-mail: [email protected]

Ken Nakamura, Ph.D.
Scientific Review Officer
Scientific Review Branch
National Human Genome Research Institute (NHGRI)
5635 Fishers Lane, Ste. 4076, MSC 9305
Bethesda, MD 20892-9305 (U.S Postal Service Express or regular mail)
Rockville, MD 20852 (for express/courier service; non-USPS service)
Telephone: 301-402-0838
FAX: 301-435-1580
E-mail: [email protected]

Cheryl Chick
Grants Administration Branch
National Human Genome Research Institute (NHGRI)
5635 Fishers Lane, Suite 3058
Bethesda, MD 20892-9307
Phone: 301-435-7858
Fax: 301-451-5434
E-mail: [email protected]

Recently issued trans-NIH policy notices may affect your application submission. A full list of policy notices published by NIH is provided in the NIH Guide for Grants and Contracts. All awards are subject to the terms and conditions, cost principles, and other considerations described in the NIH Grants Policy Statement.

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 Part 52 and 45 CFR Parts 74 and 92.