Participating Organization(s)	National Institutes of Health (NIH)
Components of Participating Organizations	National Human Genome Research Institute (NHGRI)
Funding Opportunity Title	Informatics Tools for High-Throughput Sequence Data Analysis (U01)
Activity Code	U01 Research Project Cooperative Agreements
Announcement Type	New
Related Notices	None
Funding Opportunity Announcement (FOA) Number	RFA-HG-10-018
Companion FOA	RFA-HG-10-019, Informatics Tools for High-Throughput Sequence Data Analysis U43/44 SBIR
Number of Applications	See Section III. 3. Additional Information on Eligibility.
Catalog of Federal Domestics Assistance (CFDA) Number(s)	93.172
FOA Purpose	This FOA is intended to fund the further development of existing computational software tools for use with contemporary DNA sequencing technology in order to make those tools sufficiently robust, reliable, well-documented, and well-supported that they can be readily adopted by any biological or biomedical research laboratory. Potential applications for such tools include determination of sequence quality, alignment, assembly, variant calling, interpretation of variants, or any other application for which there is existing or likely future demand by many investigators or clinicians who work with large amounts of data from contemporary sequencing instruments. Proposals for producing stand-alone tools or integrated suites of programs for data processing or analysis will be responsive to this FOA. Applications responsive to this FOA will describe the further development of software tools (algorithms or programs) that have already been shown to be useful in the sequencing setting, but which are not readily transferable to others. Applications for the initial stages of software development will be considered non-responsive. Applicants may propose the further development of tools they have initially developed on their own, or that have been obtained from others. Because a major intent of this FOA is that such tools be widely useful and disseminated, NHGRI expects that applications will include information about how any tools developed will be disseminated, and made as readily available as possible, to the broader community.

Posted Date	December 13, 2010
Open Date (Earliest Submission Date)	Not Applicable
Letter of Intent Due Date	February 3, 2011
Application Due Date(s)	March 3, 2011
AIDS Application Due Date(s)	Not applicable.
Scientific Merit Review	July, 2011
Advisory Council Review	October, 2011
Earliest Start Date(s)	December, 2011
Expiration Date	March 4, 2011
Due Dates for E.O. 12372	Not Applicable

Required Application Instructions

It is critical that applicants follow the instructions in the PHS398 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. While some links are provided, 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 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

Purpose and Objectives

The DNA sequencing landscape has changed dramatically in the last few years. A new generation of genome sequencing platforms that produce high throughput genome sequence data has now made it possible for laboratories outside of large sequencing centers to generate enormous amounts of sequence data in their experiments. Often, however, such laboratories face a serious challenge because they do not have access to readily usable software tools or the informatics expertise necessary to take best advantage of the new sequencing capabilities. There is thus a need for robust, well-documented, and well-supported software tools for processing and analyzing the data that individual labs can now generate, and the demand for such software tools will only grow, with the increasing uptake of large-scale sequencing, and the development of new applications for sequence data.

Large sequencing centers, such as those supported by the NHGRI and similar efforts in the U.S. and abroad have faced similar software needs as they have converted their production efforts to the new sequencing technologies. The informatics components of those centers have, accordingly, been able to develop a large number of tools to manage, process, analyze, and interpret the large nucleic acid sequence data sets produced to address a number of scientific questions, including identifying human variants underlying disease, and comparative and functional genomic analyses. While the sequence analysis informatics tools they have developed are technically available to others, there are significant practical barriers to their use by the wider community. Most of the "in-house" informatics tools developed so far are optimized only for local applications. Furthermore, the software may not be well-documented, and it does not generally have adequate documentation or user support. It may only run on large, local computational clusters (something many researchers do not have), and may not, for example be useful for cloud applications, or operate on multiple platforms. It may require a dedicated group of local bioinformatics experts to maintain or update. In general, the centers have not been supported to develop their tools to make them readily transferrable to other groups, especially groups operating at a smaller scale and/or that do not have extensive dedicated local bioinformatics support. This situation has the potential to create a bottleneck to the ability of the growing number of investigators who wish to analyze sequence data that they have generated in pursuit of their own projects. The issue promises to become even more serious because the costs of producing sequence data continue to drop rapidly, and will soon be exceeded by the costs of analysis.

The NHGRI therefore seeks to support efforts to address this gap, and this FOA has been issued to solicit proposals to take existing software for management, analysis, or interpretation of large-scale DNA or RNA sequence data and make it into a robust, readily transferable software tool for wider use. The purpose of the FOA is to support the further development of existing tools to give them high utility in terms of the potential number of users and/or ease of use, high significance in terms of the specific capabilities they enable, and to make them readily transferrable, with excellent documentation for installation and use, and appropriate user support. Access to the tools and underlying code should be high as well, for example through deposition in a suitable repository (e.g. SourceForge).

The existing "in-house" software from which proposals for this FOA should start can come from any appropriate source, including software developed at existing sequencing centers (which NHGRI regards as a resource when developed through the NHGRI large-scale sequencing program), or from companies or academic laboratories that work with sequence data.

This FOA is being accompanied by a nearly identical FOA (RFA-HG-10-019) seeking SBIR applications for the same purpose.

Research Network. All of the investigators funded as a result of this FOA will be organized into a research network, that will also include NHGRI program staff, and other components of the NHGRI large-scale sequencing program, under the Cooperative Agreement Terms and Conditions (see Section VI). The major purposes of the research network will be:

• To establish guidelines for readiness for release of software tools
• To compare or benchmark software tools
• To cooperate on community awareness of software tools, and in obtaining community feedback about tools

NHGRI expects to evaluate this program in an ongoing manner during the award period, in order to determine priorities for specific software tool development.

Specific Areas of Research Interest

Applications are solicited to develop transferrable tools in any area related to the management, analysis or interpretation of large volumes of DNA or RNA sequence, from the point of data production through at least publication including, but not limited to, the following areas: sequencing pipeline management, basecalling, assignment of data quality values, alignment, assembly, variant calling, validation, visualization of data, functional interpretation of variants, etc. Applicants may propose to develop software tools that can be used in the study of any biomedical question that can be addressed through high-throughput sequencing, including for example RNA expression, metagenomics, and epigenomics.

Applications are sought that propose either to develop stand-alone tools, or to bundle software tools into a coherent suite or package. Applications that run in a cloud environment are encouraged.

Applicants must justify their selection of project and approach based on the existing or likely future demand for the proposed software tools by a breadth of investigators who work with large-scale sequence data.

Software tools to be further developed include those that are working in one or a few laboratories but are not readily transferable, or those that are at some advanced stage of development in the applicant's research group. Applications that propose development from the beginning of new tools, algorithms, etc., and which do not devote the majority of the effort to making them widely transferable and usable within the period of the award, will not be considered responsive.

Guidance for Applicants

Because this initiative seeks to foster the creation of robust, transferable software tools that will be useful to the community, applicants should address several points:

• The software should perform reliably and precisely according to the computing demands of end-users.
• The algorithms that are employed by the software should be well documented, as should be the assumptions underlying these algorithms.
• Contemporary software should be fully documented and easy to modify and extend. Defects that arise in any software must be correctable with limited effort.
• As the needs of a community of users change, the software that supports their research efforts must be easily modified. "Reparability" and "evolvability" are particularly important.
• Interoperability and portability are also a major concern. Where appropriate, software applications should operate on a variety of platforms employing different operating systems.

Plan for Sharing Software

A software dissemination plan, with appropriate timelines, is expected to be included in the application.  There is no prescribed single license for software produced, however reviewers will be asked to evaluate the dissemination plan based on its likely impact. A dissemination plan guided by the following principles is thought to promote the largest impact:

• The software should be freely available to biomedical researchers and educators in the non-profit sector, such as institutions of education, research institutions, and government laboratories. Software and underlying code should be deposited in an appropriate repository (e.g., SourceForge).
• The terms of software availability should include the ability of researchers outside the Center and its collaborating projects to modify the source code and to share modifications with other colleagues as well as with the Center.  The terms should also permit the dissemination and commercialization of enhanced or customized versions of the software, or incorporation of the software or pieces of it into other software packages.
• To preserve utility to the community, the software should be transferable such that another individual or team can continue development in the event that the original investigators are unwilling or unable to do so.
• An applicant should take responsibility for creating the original and subsequent official versions of a piece of software. Applicants are asked to propose a plan to manage and disseminate the improvements or customizations of their tools and resources by others.  This proposal may include a plan to incorporate the enhancements into the official core software, which may involve the creation of an infrastructure for plug-ins, or may describe some other solution.

Funding Instrument	Cooperative Agreement: A support mechanism used when there will be substantial Federal scientific or programmatic involvement. Substantial involvement means that, after award, scientific or program staff will assist, guide, coordinate, or participate in project activities.
Application Types Allowed	New The OER Glossary and the PHS398 Application Guide provide details on these application types.
Funds Available and Anticipated Number of Awards	Issuing IC and intends to commit an estimated total of $16M ($4M per year) for up to ten awards
Award Budget	Application budgets are limited to $750,000 direct costs, and need to reflect actual needs of proposed project.
Award Project Period	Maximum of 4 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 Organizations)

Foreign (non-U.S.) components of U.S. Organizations are allowed.

Applicant organizations must complete the following registrations as described in the PHS398 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
• eRA Commons

All Program Directors/Principal Investigators (PD/PIs) 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 Project Director/Principal Investigator (PD/PI) 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 PDs/PIs, visit the Multiple Program Director/Principal Investigator Policy and submission details in the Senior/Key Person Profile (Expanded) Component of the PHS398 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 are required to prepare applications according to the current PHS 398 application forms in accordance with the PHS 398 Application Guide.

It is critical that applicants follow the instructions in the PHS398 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.

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:

Adam L. Felsenfeld, Ph.D.
Program Director, Large-Scale Sequencing
National Human Genome Research Institute
5635 Fishers Lane
Suite 4076, MSC 9305
Bethesda, MD 20892
Telephone: 301-496-7531
Email: [email protected]

Applications must be prepared using the PHS 398 research grant application forms and 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)

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

Rudy Pozzatti, Ph.D.
Office of Scientific Review
National Human Genome Research Institute
5635 Fishers Lane
Suite 4076, MSC 9305
Bethesda, MD 20892
Telephone: (301) 496-7531
Email:[email protected]

All page limitations described in the PHS398 Application Guide and the Table of Page Limits must be followed. ,

All instructions in the PHS398 Application Guide must be followed, with the following additional instructions:

The applicant should describe the significance of the software tool proposed for further robust development including information about likely use in the community, and advantages over existing software. The applicant should also describe the current capabilities of the software tool and outline what additional work needs to be done to make it robust and readily transferrable. This must be included within the 12-page Research Strategy page limit.

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 PHS398 Application Guide.

Appendix

Do not use the appendix to circumvent page limits. Follow all instructions for the Appendix (please note all format requirements) as described in the PHS398 Application Guide, with the following modifications:

• Appendices should include any additional concise documentation relating to the potential demand for the proposed software tools that is not included in the Research Plan, for example letters of support from potential users.

Foreign (non-US) organizations must follow policies described in the NIH Grants Policy Statement, and procedures for foreign organizations described throughout the PHS398 Application Guide.

Part I. Overview Information contains information about Key Dates. 

Information on the process of receipt and determining if your application is considered on-time is described in detail in the PHS398 Application Guide.

Applicants may track the status of the application in the eRA Commons, NIH’s electronic system for grants administration.

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 received on or before the due dates in Part I. Overview Information. If an application is received after that date, it will not be reviewed.

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.

Applications that propose to develop wholly new software tools as a sole or majority component will not be considered to be responsive.

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?

If the proposed software tool development is successful, is it likely to be widely adopted and used?

Is the proposed software tool likely to be an improvement over existing similar tools that may be available, for example by superior technical performance or ease of use?

Investigator(s)

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

Have the PD/PI's demonstrated that they have had or will have sufficient interaction with and knowledge of large-scale sequencing laboratories that they will be aware of existing software and its promises and limitations?

Innovation

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

Approach

Are the overall strategy, methodology, and analyses well-reasoned and appropriate to accomplish the specific aims of the project? Are potential problems, alternative strategies, and benchmarks for success presented? If the project is in the early stages of development, will the strategy establish feasibility and will particularly risky aspects be managed? 

If the project involves clinical research, are the plans for 1) protection of human subjects from research risks, and 2) inclusion of minorities and members of both sexes/genders, as well as the inclusion of children, justified in terms of the scientific goals and research strategy proposed?

One of the major program aims of this FOA is that the software tools developed under this initiative should be useful and readily transferable to the community, and well-supported. . Is the plan adequate for making the software tool accessible? Are there adequate plans for delivering the developed research tool to potential users? Are plans for its ongoing support adequate to encourage broad use by the community (including user support, regular updates, etc.),? Will the software be customizable? Will it be interoperable with existing sequence analysis software? Are there plans for the long-term disposition of the software should the developers not be able to continue support?

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.

Software Sharing Plans

Reviewers will comment on whether there are adequate plans for making the software developed under this RFA available to the community. This includes licensing and distribution terms, whether the software should be open-source, deposition of software, etc.

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, or the rationale for not sharing the following types of resources, 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 (assignments will be shown in the eRA Commons), in accordance with NIH peer review policy and procedures, using the stated review criteria.

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

• 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.
• Receive a written critique.

Applications will be assigned on the basis of established PHS referral guidelines to the appropriate NIH Institute or Center and 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 on 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.
• Compliance with policies for resource sharing.
• Adequacy of plans to distribute software.
• Balance of the portfolio with regard to different types of sequencing software applications.

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 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.

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:

• Determining experimental approaches, design protocols, setting project milestones and conducting all project work;
• Accepting coordination, cooperation, and participation of NHGRI staff in those aspects of scientific and technical management of the project as described under "NIH Program Staff Responsibilities" and "Joint Responsibilities";
• Providing information about progress in annual reports and data in any other manner determined by the research network Steering Committee to be necessary, including data needed for benchmarking or comparisons;
• Adhering to the NHGRI policies regarding intellectual property and other policies that might be established during the course of this activity;
• Accepting and implementing any other common guidelines and procedures developed for the NHGRI large-scale sequencing program;
• Accepting and participating in the cooperative nature of the Research Network; generally, coordinating and collaborating with other groups that are funded as part of the NHGRI large-scale sequencing program
• Attending and participating in Steering Committee meetings. The Principal Investigator of each award will have one vote as a member of the Steering Committee.
• 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:

• NHGRI Program staff Project Scientists will be responsible during the conduct of this activity for technical assistance, advice and coordination. However, the role of NHGRI 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 Research Network and that NHGRI staff will be given the opportunity to offer input to this process. The larger NHGRI Large-Scale Sequencing Program, of which this FOA is part, retains and consults a Scientific Advisory Panel (SAP), which provides expert advice about progress and priorities within the program. NIH Project Scientists may add more expertise to the SAP, or divide SAP responsibilities in order to best guide this specific program.

The Project Scientist will:

• Participate (with the other Steering Committee members) in the group process of facilitating collaboration, establishing reporting formats for example for benchmarking, establishing guidelines for release of software tools, and for collaborative exchange of information;
• Negotiate priorities for specific software tool development with the awardees as necessary;
• Serve as a liaison between the awardees and the SAP to the Large-Scale Sequencing Program and the National Advisory Council for Human Genome Research for example for keeping informed of program priorities and guiding specific priorities for software tool development;
• Serve as a liaison to other elements of the NHGRI Large-Scale Sequencing Program in facilitating collaborative interactions (access to software tools; etc.);
• 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;
• Periodically report progress to the Director, NHGRI;
• Lend relevant expertise and overall knowledge of NHGRI- sponsored research to facilitate the selection of scientists not affiliated with the awardee institutions who are to serve on the Scientific Advisory Panel; serve as liaison between the Steering Committee and the Scientific Advisory Panel, and liaison between the Steering Committee and other components of the Large-Scale Sequencing Program Research Network;
• Serve on subcommittees of the Steering Committee and the SAP, as appropriate;
• Provide advice in the management and technical performance of the investigation;
• Assist in promoting the availability of 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 Research Network;
• Assist awardees in the development, if needed, of policies for dealing with situations that require coordinated action;
• Retain the option to recommend, with the advice of the SAP, the withholding or reduction of support from any cooperative agreement that substantially fails to achieve its goals, or fails to comply with the Terms and Conditions of the award.
• 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. The assigned program director may also serve as the NIH Project Scientist.
  
  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.

Areas of Joint Responsibility include:

Participate in the Steering Committee. A Steering Committee will serve as the main governing board of the Research Network participants funded by this FOA. The Steering Committee membership will include the NHGRI Project Scientist(s) and the P.I. of each awarded cooperative agreement under this FOA. The Steering Committee Chair will not be an NIH staff member. Additional members may be added by action of the Steering Committee. Other government staff may attend the Steering Committee meetings, if their expertise is required for specific discussions. The Steering Committee for this FOA will interact with the overall Large-Scale Sequencing Research Network Steering committee in a manner to be determined by NHGRI staff.

The Steering Committee will:

• Discuss progress in meeting the overall programmatic goals of this FOA;
• Develop recommendations for uniform procedures and policies necessary to meet the goals of the Research Network, for example for performance benchmarking, for establishing guidelines for software release, for determining high priority software applications, etc. Adoption of procedures and policies developed by the Steering Committee will require concurrence by the SAP;
• Serve as a venue for coordination, for example by disseminating best practices and collectively evaluating new procedures and resources.
• Schedule the time for, and prepare concise (3 to 4 pages) summaries of, the Steering Committee meetings, which will be delivered to members of the group within 30 days after each meeting.
• Each full member (limited to one person per awarded center, in the case of multiple PI’s per center) will have one vote except NHGRI Project Scientist(s), who will have one collective vote. Awardee members of the Steering Committee will be required to accept and implement policies approved by the Steering Committee.
• NHGRI and the grantees will work with and provide information to the SAP as needed to evaluate the progress of the overall program. The SAP will be responsible for reviewing and evaluating the progress of the members of the Research Network toward meeting their individual and collective goals. The SAP will make recommendations on any decisions about prioritizing software tools to be developed under this FOA. The SAP will provide recommendations to the Director, NHGRI, about continued support of the components of the Research Network. The SAP is composed of four to six senior scientists with relevant expertise who are not P.I.s of a cooperative agreement involved in the Research Network. The membership of the SAP may be enlarged permanently, or on an ad hoc basis, as needed. The SAP may be divided into sub-groups to better help manage the multiple different efforts that will compose the Large-Scale Sequencing program Research Network.
• The SAP will meet at least once a year. During part of this meeting, there may be a joint meeting with the Steering Committee of this FOA to allow the SAP members to interact directly with the awardees. Annually, the SAP will make recommendations regarding progress of the entire Genome Sequencing Research Network (of which this FOA will fund a part) and present advice about changes, if any, which may be necessary in the Genome Sequencing Research Network program to the Director, NHGRI.

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 Financial Status Report are required when an award is relinquished when a recipient changes institutions or when an award is terminated.

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.

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]

Adam Felsenfeld, Ph.D.
National Human Genome research Institute (NHGRI))
Telephone: 301-496-7531
Email: [email protected]

Rudy Pozzatti, Ph.D.
Office of Scientific Review
National Human Genome Research Institute
5635 Fisher Lane
Suite 4076
Bethesda, MD 20892
Telephone: (301) 496-7531
FAX: (301) 435-1580
Email: [email protected]

Cheryl Chick
Grants Management Branch()
National Human Genome Research Institute (NHGRI)
Telephone: 301-496-7531
Email: [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.