Department of Health and Human Services

Part 1. Overview Information
Participating Organization(s)

National Institutes of Health (NIH)

Components of Participating Organizations

National Institute of Allergy and Infectious Diseases (NIAID)

Funding Opportunity Title

Genomic Centers for Infectious Diseases (U19)

Activity Code

U19 Research Program – Cooperative Agreements

Announcement Type

New 

Related Notices

  • March 11, 2013 - See Notice NOT-AI-13-032. Notice of Clarification to the Composition of Required Research Projects.

Funding Opportunity Announcement (FOA) Number

RFA-AI-13-009

Companion Funding Opportunity

None  

Number of Applications

See Section III. 3. Additional Information on Eligibility.

Catalog of Federal Domestic Assistance (CFDA) Number(s)

93.855, 93.856   

Funding Opportunity Purpose

The purpose of this initiative is to establish 2-3 Genomic Centers for Infectious Diseases as a collaborative program that will utilize a combination of next generation sequencing and related genomic technologies, bioinformatics capabilities and computational analyses to understand infectious diseases, with a focus on the pathogen and its interaction with the host.  The knowledge generated, including research data, analytical software tools, computational models, experimental protocols, and reagents, is expected to be widely disseminated to the scientific community through publicly accessible databases and reagent repositories.

Key Dates
Posted Date

February 7, 2013

Letter of Intent Due Date(s)

May 24, 2013

Application Due Date(s)

June 24, 2013   

AIDS Application Due Date(s)

Not Applicable 

Scientific Merit Review

November, 2013   

Advisory Council Review

January, 2014 

Earliest Start Date

April, 2014

Expiration Date

June 25, 2013 

Due Dates for E.O. 12372

Not Applicable

Required Application Instructions

It is critical that applicants follow the instructions in the PHS 398 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.

Looking ahead: NIH is committed to transitioning all grant programs to electronic submission using the SF424 Research and Related (R&R) format and is currently investigating solutions that will accommodate NIH’s multi-project programs. NIH will announce plans to transition the remaining programs in the NIH Guide to Grants and Contracts and on NIH’s Applying Electronically website.

Table of Contents

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

Part 2. Full Text of Announcement

Section I. Funding Opportunity Description

Purpose

The purpose of this initiative is to establish Genomic Centers for Infectious Diseases as a collaborative program that will utilize a combination of next generation sequencing and related genomic technologies, bioinformatics capabilities and computational analyses to understand infectious diseases, with a focus on the pathogen and its interaction with the host.  The knowledge generated, including research data, analytical software tools, computational models, experimental protocols, and reagents, is expected to be widely disseminated to the scientific community through publicly accessible databases and reagent repositories.  

Background

The National Institute of Allergy and Infectious Diseases (NIAID) of the National Institutes of Health (NIH) supports research related to the basic understanding, treatment and ultimately prevention of infectious, immunologic and allergic diseases that threaten millions of human lives.  The NIAID Division of Microbiology and Infectious Diseases (DMID) supports a comprehensive extramural research portfolio focused on the prevention and control of diseases caused by virtually all infectious agents. This includes basic research, such as studies of microbial biology and physiology; applied research, including the development of medical diagnostics, therapeutics and vaccines; and clinical trials to evaluate experimental drugs and vaccines.

NIAID/DMID has made a significant investment in genomic-related activities that provide to the scientific community comprehensive resources for genome sequencing, transcriptomics, proteomics and bioinformatics, as well as rapid availability of data and reagents for basic and applied research in support of the Institute’s mission. NIAID-supported genomic research programs include the:

Over the last decade, NIAID has supported the sequencing of many genomes of pathogenic and related microorganisms, including those that are the cause of emerging infectious diseases, such as influenza, drug resistant tuberculosis, dengue fever, and potential agents of bioterrorism. During this time, the DNA sequences of the genomes of almost 5,000 microorganisms and invertebrate vectors of disease and an additional 15,000 viruses have been sequenced.  Coupled with other biochemical and microbiological information, this sequence data is facilitating the identification of novel and specific targets for improving both forensic strain identification and molecular genotyping, development of sequence-based detection technologies and diagnostics, and the development of therapeutic targets for new drugs and vaccines. In addition, comparative genomics (comparing the sequences of different strains, species and clinical isolates) has become vitally important, providing critical data that enable identification of genetic polymorphisms that correlate with phenotypes such as drug resistance, morbidity and infectivity.

This wealth of sequence information, as well as the availability of the human genome, provides a valuable resource for the research community. Specifically, the functional genomic analysis of DNA sequences from microbial pathogens is enhancing the understanding of a pathogen’s biology and its ability to cause disease. Human genome sequence analysis is enhancing the understanding of the host immune response and an individual’s genetic susceptibility to microbial pathogens.  These efforts may provide insights regarding how an individual may respond to drugs, treatments and vaccines.

Currently, NIAID supports contracts with the J. Craig Venter Institute, University of Maryland and the Broad Institute, which comprise the NIAID Genome Sequencing Centers. 

Research Objectives and Scope

This Program will be established to build upon and expand the sequence data, resources and technologies that have been generated through the current NIAID Genomic Sequencing Centers for Infectious Diseases and other programs. Through this FOA, two to three Genomic Centers for Infectious Diseases (hereinafter also referred to as “Program”) will be established to support a diverse set of genome sequencing activities using next generation sequencing and related genomic technologies.   In addition, this new effort will encourage a shift towards high-throughput genomic sequencing approaches to infectious diseases research that focuses on the pathogen and its interaction with the host.  This focus will provide insights into the biology of microbes, their role in pathogenesis, and their interactions with the host, including the microbiome.  To that end, the Program will use and develop or improve innovative applications of sequencing such as RNA sequencing and metagenomics, and provide rapid and cost-efficient production of high-quality genome sequences of microorganisms and invertebrate vectors of infectious diseases, host and microbiome. 

Moreover, the Program shall provide comparative genomics analyses to examine genetic variation in populations and communities of human pathogens and also across the human genome to identify genetic associations with observable phenotypes in the pathogen and in the human host.  Ultimately, it is anticipated that the Program will provide methods and protocols developed for next generation sequencing and genomic technologies and bioinformatics analyses that are applicable to studying infectious diseases and can be used by the broad infectious diseases community.

Genomes that will be sequenced include those from microorganisms from NIAID’s List of Emerging and Re-emerging Infectious Diseases (http://www.niaid.nih.gov/topics/emerging/Pages/list.aspx), which includes NIAID Category A-C Priority Pathogens, clinical isolates, closely related species and strains, and invertebrate vectors of diseases.  Emphasis will be placed on sequencing multiple strains and isolates of specific microbial species, populations and communities rather than on sequencing individual microorganisms.

For purposes of this initiative, genome sequencing activities include high throughput sequencing, comparative genomic sequencing, single nucleotide polymorphism identification, genotyping, and gene expression.  High throughput sequencing is defined as the capability to: a) produce high quality sequencing data in a highly efficient manner with continuous increase in efficiency and decrease in costs; b) generate a diverse variety of genome sequence products; c) develop and implement new technologies, bioinformatics resources, data analysis, and laboratory management systems; and d) maintain an automated production pipeline with at least a throughput of one terabyte (TB) successful sequence reads per year. Comparative genomics and genotyping are defined as using high throughput platforms to examine the whole genome or exomes for genetic variation.

NIAID recognizes that large-scale pre-publication DNA sequence and other genomic data and information are a unique research resource for the scientific community and that rapid and unrestricted sharing of genomic data sets are essential for advancing research on infectious diseases. Therefore, it is expected that pre-publication genome sequence data sets generated by the Centers will be made freely and publicly available through publicly accessible international databases, such as Genbank, as rapidly as possible.  NIAID strongly endorses the rapid release and public dissemination of experimental data, metadata, new analysis tools, novel reagents and other resources generated under the Program to enable the broad scientific community to utilize the available resources and pursue new research hypotheses.   The Centers funded under this FOA are expected to follow the guidelines and timelines described in the NIAID Data and Reagents Sharing and Release Guidelines (http://www.niaid.nih.gov/LabsAndResources/resources/dmid/gsc/Pages/data.aspx). 

Overall Structure

Each Center shall have a multi-disciplinary research and technology team with expertise in genomics, bioinformatics and data management and analysis, statistics, microbiology, epidemiology, and infectious diseases that includes the following: 

NOTE: This FOA will not support applications that focus exclusively on genomic technology development in the absence of use of the technology to sequence and characterize human pathogens and their interaction with the host. Applications of this type are unresponsive and will not be reviewed.

Required Components

Research Projects

Each application should describe the central theme of the proposed Center and propose four Research Projects that are centered around the themes of viruses, bacteria, fungi, and parasites and vectors (i.e., there should be one project on viruses, one on bacteria, one on fungi and one on parasites and vectors).  Each Research Project must utilize a combination of next generation, state-of-the-art genomics sequencing technologies and bioinformatics analyses to understand infectious diseases with a focus on human pathogens and their interaction with the host.  Applicants should explain how the proposed Research Projects are synergistic and fit under the Center’s overarching central theme. 

Applicants must provide milestones and timelines for each research project.

Note: Costs associated with prospective human sample collection will not be covered by the grant.

Technology Core

Each Center must include three or more high-throughput genomic technologies organized into a Technology Core to provide shared resources to the Research Projects.  Next-generation large scale high throughput sequencing, transcriptomics, metagenomics and related microbiome technologies must be included as three of the technologies in the core.

Data Management, Analysis, and Resources Dissemination Core

It is expected that a vast amount of data and other types of resources will be generated by the application of genomics and other related technologies on a large number of samples. The ability to perform sample tracking, laboratory data management, data storage, data access, data transfer, data analysis and integration and management of data and information from a variety of genomics technologies is essential for the efficient and successful performance of the Center.  Sample tracking may include managing and reviewing IRB documentation and clinical and meta data associated with clinical samples.  In addition, the core must have the capability to provide state of the art bioinformatic and computational infrastructure that is necessary for large scale, high throughput genomic sequencing and data analysis on data generated in the Center or independently, including implementation of new, improved and enhanced bioinformatic and computational platforms.

A primary objective for the Program is to maximize the public benefit of the data produced under the Centers  through the rapid release and public dissemination of genomic and related data, metadata,  new analysis tools, strains,  novel reagents (e.g., expression vectors, expression arrays, libraries), among other resources generated under the Program.  To achieve the objective of producing and broadly sharing the resources generated by Program, the Centers funded under this FOA are expected to follow the guidelinesdescribed in the NIAID Data Sharing and Release Guidelines (http://www.niaid.nih.gov/LabsAndResources/resources/dmid/gsc/Pages/data.aspx),

 and other NIH and NIAID sharing policies (see http://ott.od.nih.gov/policy/research_tool.html and http://sharing.nih.gov/).The Center should also assure that data is rapidly released according to approved criteria, that licensing and sharing practices ensure the availability of data and research resources for future use by the scientific community, and that research collaboration or sponsorship agreements are consistent with meeting the goals and the requirements of the Program.   The Data Sharing and Release Plan, once approved, will also become a Term and Condition of award.

Applications submitted in response to this FOA should provide details of the data integration, management and tracking activities of the Program and include a Plan for public dissemination of generated resources to the scientific community.

Administrative Core

Each Center must include an Administrative Core, headed by the PD/PI, which is responsible for managing, coordinating, and supervising all Center activities.  The Core should  include the following:

Milestones and Timelines

Applicants must provide milestones and timelines in a section of the Administrative Core entitled “Milestones and Timelines” that should address all Core activities.

Management Plan

The Administrative Core should provide a Management Plan that describes the organization of the proposed program and its management structure.  The Management Plan should include a Staffing Plan that describes the structure and roles of scientific and administrative staff; the committed level of effort; the training and experience of proposed staff; and the functions to be performed.

Training Program Plan

A Training Program will begin in the first year of the award and is expected to instruct and increase the number of infectious disease researchers that can use the approaches, methodologies and resources (datasets, analysis tools, etc.) generated under the Center.

Examples of appropriate training programs include workshops to promote the use of technologies and analysis tools developed by the Center, and short-term training appointments of undergraduate, graduate, post-doctoral candidates and junior faculty with expertise in microbiology and infectious diseases.

Supplemental Research Projects Plan (subject to availability of supplemental funds)

NIAID is interested in supporting Supplemental Research Projects during the period of grant award.  Supplemental Research Projects will focus on one of the four thematic areas and will take advantage of genomic sequencing technologies and new and innovative opportunities to study infectious agents and their interaction with the host. To that end, the Administrative Core should include a Supplemental Research Project Plan that describes procedures to be used by the Centers for identifying and selecting Supplemental Research Projects to be recommended to NIAID Program Staff. Applicants should not submit descriptions of Supplemental Research Projects in their application.

Annual Programmatic Meetings

Each year a one-two day meeting will be held and each awarded Center will assume responsibility for the meetings’ organization at least once over the award period. These meetings are anticipated to be held at a location at/near Bethesda, MD or at another NIAID-approved site. Each awardee should budget for travel to the yearly meeting. Costs for organizing the annual meeting should not be included in the budget. Funds for hosting a meeting will be provided via an administrative supplement.  Each Center should ensure that support for meeting attendance by the PD/PI, the Project Leaders and Cores leaders, and other key personnel is included in the budget.

Steering Committee

A Steering Committee will be established by the NIAID in collaboration with the awardees to review the progress in meeting the goals of all Centers funded under the Program and will make recommendations for the continuation or re-direction of all projects and activities of the funded Centers on an ongoing basis and in consultation with the NIAID staff.  In addition, the Steering Committee will make recommendations about Supplemental Research Projects (see Supplemental Research Projects).  The Steering Committee is expected to consist of investigators who are not current collaborators of the funded programs.  Names of Steering Committee members should not be proposed as part of the application since Steering Committee members will be independent, non-affiliated experts and will be selected in collaboration with NIAID.

Optional Components

Other Scientific Cores

These cores should provide scientific services or resources that are justified and not duplicative of other services or facilities available in the required cores. 

Note: Applications lacking any of the required projects, cores or Data Sharing and Release Plan will be deemed not responsive and will not be reviewed.

Section II. Award Information
Funding Instrument

Cooperative Agreement: A support mechanism used when there will be substantial Federal scientific or programmatic involvement. Substantial involvement means that, after award, NIH staff will assist, guide, coordinate, or participate in project activities.

Application Types Allowed

New

The OER Glossary and the PHS 398 Application Guide provide details on these application types.

Funds Available and Anticipated Number of Awards

NIAID intends to commit $14 million in FY 2014 to fund 2-3 awards.

Award Budget

Application budgets are not limited, but need to reflect actual needs of the proposed project .

Award Project Period

Scope of the proposed project should determine the project period. The maximum period is 5 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.

Section III. Eligibility Information

1. Eligible Applicants

Eligible Organizations

Higher Education Institutions

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

Nonprofits Other Than Institutions of Higher Education

For-Profit Organizations

Governments

Other

Foreign Institutions

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.

Required Registrations

Applicant organizations must complete the following registrations as described in the PHS 398 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.

All Program Directors/Principal Investigators (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 least6 weeks prior to the application due date.

Eligible Individuals (Program Director/Principal Investigator)

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 PDs/PIs, visit the Multiple Program Director/Principal Investigator Policy and submission details in the Senior/Key Person Profile (Expanded) Component of the PHS 398 Application Guide.     

2. Cost Sharing

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

3. Additional Information on Eligibility

Number of Applications

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

NIH will not accept any application that is essentially the same as one already reviewed within the past thirty-seven months (as described in the NIH Grants Policy Statement), except for submission:

Section IV. Application and Submission Information

1. Address to Request Application Package

Applicants are required to prepare applications according to the current PHS 398 application forms in accordance with the PHS 398 Application Guide.

2. Content and Form of Application Submission

It is critical that applicants follow the instructions in the PHS 398 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.

Letter of Intent

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:


The letter of intent should be sent to:

Eleazar Cohen, Ph.D.
National Institute of Allergy and Infectious Diseases (NIAID)
Room 3129, MSC 7616
6700-B Rockledge Drive
Bethesda, MD 20892-7616
FedEx zip code:  20817
Phone: (301) 435-3564
Email:  ecohen@niaid.nih.gov

Application Submission

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:

Eleazar Cohen, Ph.D.
National Institute of Allergy and Infectious Diseases (NIAID)
Room 3129, MSC 7616
6700-B Rockledge Drive
Bethesda, MD 20892-7616
FedEx zip code:  20817
Phone: (301) 435-3564
Email:  ecohen@niaid.nih.gov

Page Limitations

All page limitations described in the PHS 398 Application Guide and the Table of Page Limits must be followed, in addition to the following limitations to the Research Strategy section of each component of the application.

Supplemental Instruction for the Preparation of Multi-Project Applications

The following section supplements the instructions found in Form PHS 398 for preparing a multi-project grant application. Additional instructions are required because the Form PHS 398 is designed primarily for individual, free-standing research project grant applications, and has no specific instructions for multi-project applications consisting of Research Projects interrelated by a common theme. All applications must be submitted on Form PHS 398.  The multi-project grant application should be assembled and paginated as one complete document. Instructions for the Overall Component are presented first, followed by instructions for Research Projects, followed by instructions for Cores.

The application should consist of the following components:

All instructions in the PHS398 Application Guide must be followed, with the following additional instructions, as noted.

Specific Instructions for Overall Component

Form Page 1. Face Page (Overall)

Items 1 - 14: complete these items as instructed. This should be the first page of the entire application and all succeeding pages should be numbered consecutively.

Form Page 2. Summary, Relevance, Project/Performance Site, Senior/Key Personnel, Other Significant Contributor, and Human Embryonic Stem Cells (Overall)

Description: Using Page 2 of Form 398; provide a succinct but accurate description (abstract) of the OVERALL multi-project application addressing the major, common theme of the program.  Do not exceed the space provided.

Project/Performance Sites: List the performance sites where the research will be conducted.

Senior/Key Personnel: Under "Key Personnel", list the PD/PI of the multi-project application, followed by the Project and Core Leaders of the component Research Projects and cores, and other key personnel and then other significant contributors.

Form Page 3. Table of Contents (Overall)

Do not use Form Page 3 of the PHS 398; a more comprehensive table of contents is needed for a multi-project application.

Bearing in mind that the application will be scientifically reviewed project by project and core by core, prepare a detailed Table of Contents that will enable reviewers to readily locate specific information pertinent to the overall application as well as to each component research project and core.  A page reference should be included for the budget for each project and each core.  Further, each research project should be identified by number (e.g. Project 1), title, and responsible Project Leader, and each Core should be identified by letter (e.g. Core A), title, and responsible Core Leader.  The page location of a COMPOSITE BUDGET should be indicated in the "Table of Contents."

Form Page 4. Composite Budget (Overall)

Do not use Form Page 4 of PHS Form 398.  Instead, using the suggested format presented below, prepare a Composite Budget for All Proposed Years of Support. (Justification for budget elements should not be presented here but in the individual budgets of the projects and cores.)

SAMPLE: Consolidated Direct Cost Budget for All Proposed Years of Support. Add other Projects and Cores as appropriate to the FOA.

Component

Year 1

Year 2

Year 3

Year 4

Year 5

All Years

Project 1.Virues

125,000

125,000

125,000

125,000

125,000

650,000

Project 2. Bacteria

125,000

125,000

125,000

125,000

125,000

650,000

Project 3. Fungi

100,000

100,000

100,000

100,000

100,000

500,000

Project 4.Parasites and vectors

125,000

125,000

125,000

125,000

125,000

650,000

Core A.  Technology Core

250,000

250,000

250,000

250,000

250,000

1,250,000

Core B.  Admin. Core

50,000

50,000

50,000

50,000

50,000

250,000

Totals

775,000

775,000

775,000

775,000

775,000

3,875,000

 

 

 

 

 

 

 


Form Page 5. Total Direct Costs for the Entire Budget Period

Complete the Total Direct Cost line entries for all requested budget periods (years) and the Total Direct Cost for Entire Period of Support entry. Detailed budgets are required within the descriptions of each project and core (see below).  If the FOA allows for budget requests beyond 5 years, use a second Form Page 5 to reflect the additional budget years requested. 

PI(s)/PD(s) funded under this FOA are expected to devote at least 3.6 person/months, based on a 12-month calendar (equivalent to 30% of his/her time and effort) to the project.

Costs for organizing the annual meeting should not be included in the budget. Funds for hosting a meeting will be provided via an administrative supplement.  Each Center should ensure that support for meeting attendance by the PD/PI, the Project Leaders and Cores leaders, and other key personnel is included in the budget.

Biographical Sketch Format Page

Biographical sketches of all professional personnel for all components should be placed at the end of the application with the PD/PI first, followed by those of other key personnel in alphabetical order.

Resources Format Page

Do not complete.  Essential information is to be presented in the individual research project and core sections of the application.

Research Plan (Overall)

Specific Aims

List in priority order, the broad, long-range objectives and goals of the proposed Program. Concisely and realistically describe the hypothesis or hypotheses to be tested.

Research Strategy

This narrative section summarizes the overall research objectives and strategic plan for the multi-project application and explains how the proposed Program satisfies the purpose and all objectives of this FOA as delineated in Section I.  Applications responding to this FOA should describe the central theme of the proposed Program and explain how the proposed Research Projects are synergistic and fit under the overarching Program theme.

This is an important section for it provides the group of investigators an opportunity to give conceptual wholeness to the overall program – by giving a statement of the general problem area and by laying out a broad strategy for addressing the problems.  As the strategy develops, each project and core should be cited briefly as to its place in the overall scheme.  Summarize the special features in the environment and/or resources that make this application strong or unique. This section should also describe the PD(s)/PI(s) track record in large-scale sequencing and managing a large scale genomic sequencing program using next generation sequencing technologies and bioinformatics to study infectious diseases, with a focus on human pathogens and their interaction with the host. 

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 PHS 398 Application Guide, with the following modification:

Checklist (Overall)

One Checklist, placed at the end of the application, is to be submitted for the entire application.

Specific Instructions for Research Projects

A minimum of four individual research projects are required.  Each application should describe the central theme of the proposed Center and propose four Research Projects that are centered around the themes of viruses, bacteria, fungi, and parasites and vectors (i.e., there should be one project on viruses, one on bacteria, one on fungi and one on parasites and vectors).  Each Research Project must utilize a combination of next generation, state-of-the-art genomics sequencing technologies and bioinformatics analyses to understand infectious diseases with a focus on human pathogens and their interaction with the host.  Applicants should explain how the proposed Research Projects are synergistic and fit under the Center’s overarching central theme. 

Applicants must provide milestones and timelines for each research project.

Each individual research project should include the following forms.

Cover Page (Research Projects)

The Face Page of the 398 Form should not be used as a cover page for individual Research Projects within a multi-project application.  Instead, use the PHS 398 continuation page to create a "Cover Page" containing selected data about each individual research project.  This Cover Page will demarcate each individual research project and should contain the following information items (these are a subset of the information provided on a PHS 398 Face Page):

Form Page 2. (Research Projects)

Description: Provide a Description (abstract) of the research proposed in the individual research project according to the instructions on Form Page 2 of PHS Form 398.  In addition, the abstract should contain a brief description of how the individual research project will contribute towards attainment of the multi-project objectives.

Project/Performance Sites: List the performance sites where the research will be conducted.

Key Personnel: Under "Key Personnel", list the Project Leader, followed by other key project personnel, and then other significant contributors.

Form Page 3. Table of Contents (Research Projects)

Prepare a Table of Contents for the research project using Form Page 3 of the PHS 398.

Form Page 4 and 5. Detailed Budget for Initial Budget Period (Research Projects)

Prepare a detailed budget and justification for the research project using Form Pages 4 and 5 of the PHS 398.

Note: Costs associated with prospective human sample collection will not be covered by the grant.

Research Plan (Research Projects)

Specific Aims: List, in priority order, the broad, long-range objectives and goals of the proposed Research Project. Concisely and realistically describe the hypothesis or hypotheses to be tested. In addition, state the individual research project's relationship to the Program’s goals and how it relates to other projects or cores.

Research Strategy: Use this section to describe how the proposed research will contribute to meeting the Center’s goals and objectives and explain the rationale for selecting the methods to accomplish the specific aims. In addition to stating the biological significance of the research, indicate the project's relevance to the primary theme of the application.

Organize the Research Strategy in the specified order as stated in the PHS 398 Instructions, Section 5.5.  Make sure to start each section with the appropriate section heading in order, Significance, Innovation, Approach, and include the appropriate information.  Experimental details should be cited using the Bibliography and Reference Cited section and need not be detailed in the Research Strategy.  Preliminary Studies for projects should be included as part of the approach section and must be contained within the page limits of the Research Strategy section.

Each Research Project should include as many of the characteristics delineated below as scientifically appropriate.

Indicate the targeted microbial organism/s and the related human host, microbiome and infectious disease to be studied. Describe the research design conceptual procedures, and analyses to be used to accomplish the specific aims of the proposed Research Project. Describe any new methodology and its advantage over existing methodologies. Describe any novel concepts, approaches, tools, or technologies for the proposed studies. Discuss the potential difficulties and limitations of the proposed procedures and alternative approaches to achieve the aims.  Provide milestones and timelines for each Research Project.

Research Projects should be justified in terms of their significance by using genomic technologies and bioinformatics analyses to understand infectious diseases. This should include studying the pathogen and its interaction with the host, how the sequence information will be used, and how they are appropriate for a large-scale program—for example, how they take best advantage of the current state-of-the- art in high-throughput sequencing; how they drive the development of important new project capabilities; and how they are distinct from other projects going on at lower scale or by other means. 

Include a brief discussion of proposed samples, and availability of the samples for each Research Project.  Ideally, the choice of ongoing and newly proposed Research Projects will illustrate the overall scientific goals and priorities of the Program, as described elsewhere in the application. It should be clear how each Research Project will take the best advantage of current high-throughput sequencing, and their potential contribution to defining or refining how similar projects could be done, will be considered in the review.

Select Agent Research (if applicable)

As directed in the PHS 398 Instructions, provide a description of all facilities where the Select Agent(s) will be used in the project.  Describe the procedures that will be used to monitor possession, use, and transfer of the Select Agent(s).  Describe plans for appropriate biosafety, biocontainment, and security of the Select Agent(s).  Describe the biocontainment resources available at all performance sites.

Resource Sharing Plan

Individuals are required to comply with the instructions for the Resource Sharing Plans (Sharing Model Organisms, and Genome Wide Association Studies (GWAS)) as provided in the PHS 398 Application Guide, with the following modification:

In addition, the Centers funded under this FOA are expected to follow the guidelines and timelines described in the NIAID Data Sharing and Release Guidelines (http://www.niaid.nih.gov/LabsAndResources/resources/dmid/gsc/Pages/data.aspx).

Resources Format Page (Research Projects)

Provide information on resources available for the project.  Describe how the scientific environment in which the research will be done contributes to the probability of success (e.g., institutional support, physical resources, and intellectual rapport.)  For Early Stage Investigators, describe institutional investment in the success of the investigator.  If there are multiple performance sites, describe the resources available at each site. Describe any special facilities used for working with biohazards or other potentially dangerous substances.

Biographical Sketch Format Page (Research Projects)

Do not repeat the biographical sketches of participating investigators since this information will be included at the end of the overall application (and therefore will be referenced in the Overall Table of Contents). 

Specific Instructions for Core(s)

Each individual core should include the following forms.

Cover Page (Cores)

The Face Page of the 398 Form should not be used as a cover page for cores within a multi-project application.  Instead, use the 398 continuation page to create a "Cover Page" containing selected data about each individual core.  This Cover Page will demarcate each core and should contain the following information items (which are a subset of the information provided on a Face Page - see PHS 398):

Form Page 2. (Cores)

Description: Provide a Description (abstract) of the core activities and services according to the instructions on Form Page 2 of the PHS 398. In addition, the abstract should contain a brief description of how the core services will contribute towards attainment of the objectives.

Project/Performance Sites: List the performance sites where the core activities and services will be conducted.

Key Personnel: Under "Key Personnel", list the Core Leader, followed by other key core personnel, and then other significant contributors.

Form Page 3. Table of Contents (Cores)

Prepare a Table of Contents for the core using page 3 of Form PHS 398. 

Form Page 4 and 5. Budget Pages (Cores)

Prepare a detailed budget and justification for the core using Form Pages 4 and 5 of the PHS 398.

Research Plan (Cores)

Specific Aims: For each of the required and optional cores, list in priority order the broad, long-range objectives and goals of the proposed core. In addition, state the core’s relationship to the Program’s goals and how it relates to two or more individual Research Projects or other proposed cores.

Research Strategy: Technology Core (required) Each Center must include three or more high-throughput genomic technologies organized into a Technology Core to provide shared resources to the Research Projects.  Next-generation large scale high throughput sequencing, transcriptomics, metagenomics and related microbiome technologies must be included as three of the technologies in the core.

Use this section to describe how the proposed core activities will contribute to meeting the Program's goals and objectives and explain the rationale for selection of the general methods and approaches proposed to accomplish the specific aims.  In addition, this section should indicate the relevance of the core to the primary theme of the application.

Organize the Core Services Plan in the specified order as stated in the PHS 398 Instructions, Section 5.5.  Make sure to start each section with the appropriate section heading in order, Significance, Innovation, Approach, and include the appropriate information.  Experimental details should be cited using the Bibliography and Reference Cited section and need not be detailed in the Research Strategy.  Preliminary Studies for new cores must be included as part of the approach section and must be contained within the page limits of the Core Services Plan section.

The Technology Core should include the following:

Note: It is anticipated that whole human genomes will not be sequenced and that sequencing would be targeted to areas of the human genome such as exomes and epigenetic or other modifications of DNA sequence.  However, further decreases in sequencing costs may arise during the course of the Program, and may result in the use of whole human genome sequencing as a more efficient strategy.

Research Strategy: Data Management, Analysis and Resources Dissemination Core (required)

Applications submitted in response to this FOA are expcted to provide details of the data integration, management and tracking activities of the Program and  discuss how reagents and resources (e.g. microorganisms, nucleic acids, physical clones, expression constructs, monoclonal antibodies, and polyclonal sera) obtained and generated under this Program shall be rapidly deposited into public repositories, such as the NIAID Biodefense and Emerging Infections Research Resources Repository (http://www.beiresources.org/), consistent with the requirements and timelines described in the NIAID Data Sharing and Release Guidelines (http://www.niaid.nih.gov/LabsAndResources/resources/dmid/gsc/Pages/data.aspx).   In addition, applications are expected to include a plan that describes how data generated under this Program shall be released to a publicly accessible database such as Genbank or selected databases, as specified by the NIAID and/or NIAID Bioinformatics Resource Centers (http://www.niaid.nih.gov/dmid/genomes/brc/default.htm).  Applicant should discuss how the plan shall adhere to current NIAID and NIH policies and guidances on genomic data, including:  http://www.niaid.nih.gov/LabsAndResources/resources/dmid/gsc/Pages/data.aspx   and NIH guidance and instructions for NIH-Supported or Conducted Genome-Wide Association Studies (GWAS): http://grants.nih.gov/grants/guide/notice-files/NOT-OD-08-013.html.

Research Strategy:  Administrative Core (required)

The Administrative Core is responsible for the following Center activities including;

The application should describe the Management Plan for the proposed program, and how it will support the goals proposed.  It should describe the organization of the proposed program and its management structure, including integration of the separate components to form an efficient pipeline, key personnel, section leaders, and reporting relationships. The applicant should discuss project management including how s/he would manage what are likely to be multiple, ongoing and collaborative relationships across many types of projects.  The Plan should discuss how human subjects approvals associated with sequencing projects will be handled.  The plan should describe how the various components of the proposed program will be integrated. The issue of how any other, ongoing large-scale sequencing projects would be integrated with the one to be funded under this FOA should be discussed.  In addition, applicants should provide overall Program milestones, timelines and performance objectives for all Research Projects and cores (required and optional).

As part of the Management Plan, include a Staffing Plan, which should include a discussion of the structure and roles of administrative and scientific staff, including, the committed level of effort; the training and experience of proposed staff and the functions to be performed; and how resources will be prioritized, allocated and managed

Outline plans to establish a Training Program beginning with the first year of the award that will promote the use of next generation genomic technologies and bioinformatic analyses generated under the Program.

Describe the identification and resolution of problems, and engagement of the Steering Committee and NIAID, including details of how to interact with the Steering Committee aside from the required annual review meetings.  Names of Steering Committee members should not be proposed as part of the application since Steering Committee members will be independent, non-affiliated experts and will be selected in collaboration with NIAID.

Provide a Supplemental Research Project Plan that describes procedures for identifying and selecting Supplemental Research Projects to be recommended to the Program Officer for approval.  The Supplemental Research Project Plan should include: a description of the review process and evaluation criteria that will be used to select the most promising projects for funding; proposed timeframe for project identification, review and delivery of recommendations to the COR; plans for managing progress and monitoring the success/productivity of funded projects; and a discussion of how funds associated with each Supplemental Research Project will be managed.

As noted previously, subject to the availability of supplemental funds, Supplemental Research Projects will focus on one of the four thematic areas and will take advantage of genomic sequencing technologies and new and innovative opportunities to study infectious agents and their interaction with the host.   These Supplemental Research Projects will be related to the overall scope of the Center and should not duplicate projects already undertaken by any other Center in the Program. Do not suggest potential Supplemental Research Projects in the application. 

Research Strategy: Other Scientific Cores (optional) Provide details of the services or resources provided by the optional cores to at least two Research Projects and clarify how the optional cores are not duplicative of other services or facilities provided by the required cores.

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 modification:

In addition, the Centers funded under this FOA are expected to follow the guidelines and timelines described in the NIAID Data Sharing and Release Guidelines (http://www.niaid.nih.gov/LabsAndResources/resources/dmid/gsc/Pages/data.aspx).

Biographical Sketch Format Page (Cores)

Do not repeat the biographical sketches of participating investigators since this information will be included at the end of the overall application (and therefore will be referenced in the Overall Table of Contents).

Resources Format Page (Cores)

Provide information on resources available for the core.  Describe how the scientific environment in which the research will be done contributes to the probability of success (e.g., institutional support, physical resources, and intellectual rapport.)  For Early Stage Investigators, describe institutional investment in the success of the investigator.  If there are multiple performance sites, describe the resources available at each site.  Describe any special facilities used for working with biohazards or other potentially dangerous substances.

Appendix for the Entire Application

Do not use the Appendix to circumvent page limits. Follow all instructions for the Appendix (please note all format requirements) as described in the PHS 398 Application Guide, with the following modification:

Foreign Institutions

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

3. Submission Dates and Times

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 PHS 398 Application Guide.

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

4. Intergovernmental Review (E.O. 12372)

This initiative is not subject to intergovernmental review.

5. Funding Restrictions

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

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

6. Other Submission Requirements and Information

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 NIAID, NIH. Applications that are incomplete and/or nonresponsive will not be reviewed.  

Annual Program Meetings

The Project Leaders and key technical and scientific staff shall present an update on progress and a summary of results generated on each Research Project at Annual Program Meetings, including a discussion of problems/obstacles encountered and proposed approaches taken or planned to overcome them. Annual meetings shall also address the application of policies and procedures for monitoring the direction of specific projects. A kick-off meeting will be held within 3 months of award and will be organized by the NIAID Project Scientist in coordination with all funded Centers at a location at/near Bethesda (MD) to provide opportunities for the awarded centers to present their research plans and initiate discussions with other awarded centers under the Program. The PD(s)/PI(s) and all Research Project leaders are expected to attend this kick-off meeting and include this in the first year budget.    

Post Submission Materials

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

Section V. Application Review Information

1. Criteria

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.

Overall Impact - Overall

Reviewers will provide an overall impact/priority score to reflect their assessment of the likelihood for the Center 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 Center proposed).

Overall Impact - Individual Research Projects

Reviewers will provide an overall impact 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).

Scored Review Criteria– Individual Research Projects

Reviewers will consider each of the review criteria below in the determination of scientific merit for each project, and provide an aggregate score for each project. 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?   Do the proposed plans ensure that the Center has a high probability of success and will make significant contributions to applying state-of-the-art, next generation sequencing technology and bioinformatics analyses to study infectious diseases, including new applications and/or project designs for diverse types of sequencing projects? Is there a high likelihood that the applicant can accomplish this at and beyond the current state-of-the-art levels of sequencing throughput, data quality and cost?

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?  Do(es) the PD(s)/PI(s) have documented training, leadership skills, scientific and technical skills, and managerial competence to successfully plan, manage, conduct and direct a Program and Research Projects having goals, size and complexity similar to those of the proposed Program, including experience in successfully managing a large scale genome sequencing program for infectious diseases,  have time commitment as well as demonstrated ability to manage this program and establish collaborations and to obtain microbial and human clinical samples for genomic projects?  Is there an adequate staffing plan appropriate to the scope of the proposed work? If collaborations are proposed, with diverse infectious diseases and organism communities and investigators with human sample collections, are the plans adequate to ensure a productive collaboration, especially to execute conceiving, designing, organizing, and managing a successful sequencing project completed within the milestones and timelines for the project proposed?  Does the PD(s)/PI(s) have a successful record of collaborations with infectious diseases and organism communities and appropriate track record for collaborative activities and public dissemination of generated resources?

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? Will the proposed sequencing and related genomic technology platforms and bioinformatics analysis pipelines and related developmental technologies provide innovative new tools or paradigms for using genomics strategies for the study of infectious diseases?     

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?

Overall Impact– Individual Cores

Reviewers will provide an overall impact/priority score to reflect their assessment of the likelihood for the core 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 core proposed).

Review Criteria – Individual Cores

Reviewers will consider each of the review criteria below, as appropriate for the individual core, in the determination of scientific merit and provide an overall impact score, but will not give separate scores for these items. An application does not need to be strong in all categories to be judged likely to have major scientific impact. For example, a core that by its nature is not innovative may be essential to advance a field.

Technology; Data Management, Analysis and Resources Dissemination; and Other Scientific Cores

Administrative Core

Optional Scientific Cores

Additional Review Criteria - Overall, Project, Core

As applicable for the Center, project or core proposed, reviewers will evaluate the following additional items while determining scientific and technical merit, and in providing an overall impact 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 Center, project or core 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 .

Additional Review Considerations - Overall, Projects, Cores

As applicable for the Center, project or core 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 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, 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).

Is the Plan for public dissemination of generated resources adequate and consistent meeting the NIAID Data and Reagents Sharing and Release Guidelines (http://www.niaid.nih.gov/LabsAndResources/resources/dmid/gsc/Pages/data.aspx).

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.   

2. Review and Selection Process

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

As part of the scientific peer review, all applications:

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

Applications will be assigned 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  Allergy and Infectious Diseases Council. The following will be considered in making funding decisions:

3. Anticipated Announcement and Award Dates

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.

Section VI. Award Administration Information

1. Award Notices

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, SAM Registration, and Transparency Act requirements as noted on the Award Conditions and Information for NIH Grants website.

2. Administrative and National Policy Requirements

All NIH grant and cooperative agreement awards include the NIH Grants Policy Statement as part of the NoA. For these terms of award, see the NIH Grants Policy Statement Part II: Terms and Conditions of NIH Grant Awards, Subpart A: General  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 OMB administrative guidelines, HHS grant administration regulations at 45 CFR Parts 74 and 92 (Part 92 is applicable when State and local Governments are eligible to apply), and other HHS, PHS, and NIH grant administration policies.

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

Principal Investigator Rights and Responsibilities

PD(s)/PI(s), will have the primary responsibility for coordinating the Projects and Cores within the overall Program. Specifically, the PD(s)/PI(s) have primary responsibility as described below.

The PD(s)/PI(s) will be responsible for defining the research objectives, approaches and details of the projects within the guidelines of the FOA and retains primary responsibility for the planning, directing, and executing the proposed scientific activities.

The PD(s)/PI(s) will be responsible for:

The multi-disciplinary and collaborative nature of the Programs funded under this FOA creates an extraordinary opportunity for information exchange and scientific advancement of genomics sequencing technologies and strategies to study infectious diseases research.  Programs’ investigators are expected to take advantage of this opportunity by participating in both formal events established expressly for this purpose and informal investigator-initiated dialogues.

NIH Responsibilities

An NIAID/NIH Project Scientist will have substantial programmatic involvement that is above and beyond the normal stewardship role in awards, as described below.

The role of the NIAID/NIH Project Scientist in the cooperative agreement is to support and encourage the recipient's activities by substantial involvement as partners and facilitators in the process without assuming responsibilities that remain with the PDs/PIs.  The NIAID Project Scientist will work closely with the PD(s)/PI(s) and other Program member scientists to facilitate collaborations and to leverage the resources available to the Program.

The NIAID Project Scientist will monitor the progress of the Program, help coordinate research approaches among all Programs funded through the FOA, and contribute to the shaping of Research Projects or approaches as warranted. The NIAID Project Scientist will support and facilitate this process but will not direct it. 

The NIAID Project Scientist will keep the Program informed about other ongoing studies supported by NIAID to avoid duplication of effort and encourage sharing/collaboration in infectious diseases research.  The NIAID Project Scientist will coordinate access for the Program to other NIAID resources, as well as assist the research efforts of the Program by facilitating access to fiscal and intellectual resources provided by industry, private foundations, NIH intramural scientists and other federal government agencies as appropriate.

The NIAID Project Scientist will serve as a non-voting member of the Steering Committee and will assist in developing the operating guidelines and consistent policies for dealing with situations that require coordinated action.

The NIAID Project Scientist will review, make recommendations and provide suggestions for Supplemental Research Project proposals.

The NIAID Project Scientist will retain the option to recommend, with the advice of the Steering Committee, the withholding or reduction of support from any cooperative agreement that substantially fails to achieve its goals according to the milestones agreed to at the time of the award or fails to comply with the Terms and Conditions of the award.

Additionally, a NIAID 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 official may also serve as the NIAID Project Scientist.

Areas of Joint Responsibilities

The NIAID Project Scientist will provide overall coordination across all funded Programs, will coordinate with the PD(s)/PI(s) and hold regular program-wide discussions to facilitate the achievement of program goals. In the event that some members of the Programs develop common research interests working groups may be formed to pursue collaborative activities.

In addition, PD(s)/PI(s), Research Project and Core Leaders and the NIAID Project Scientist will participate in the Steering Committee activities as needed. 

Annual Site Visits

These visits will be used by NIAID program staff to review and discuss progress; problems and obstacles and approaches to overcoming identified problems and obstacles; recommendations for modifications in project timelines, objectives, and research approaches/ methodologies based on outcomes to date; and future plans. 

Bimonthly Teleconferences

These teleconferences will be held to discuss progress, problems, proposed solutions and any matter that is relevant to the scientific and financial administration of the Center and future activities. The schedule for those meetings will be established by the PD(s)/PI(s) and the NIAID Project Scientist. 

Steering Committee

A Steering Committee will be established by the NIAID to review the progress in meeting the goals of all Programs funded under this FOA, including also the activities of all Training and Supplemental Research Projects as well as the data/other resources’ dissemination activities.  The PD(s)/PI(s) of the awarded programs will provide NIAID with suggestions for members of the Steering Committee within the first 6 months from award. The Steering Committee is expected to consist of approximately 10 individuals who are not key personnel or collaborators of the key personnel of any of the awardees. The Steering Committee will make recommendations for the continuation or re-direction of all projects and activities of the funded Programs on an ongoing basis and in consultation with the NIAID staff. The NIAID may re-budget individual U19 funds based on recommendations of the Steering Committee.

The Steering Committee will prepare concise (3-4 pages) summaries of the Steering Committee meetings which will be delivered to members of the group and NIAID within 30 days. The Committee will meet on an annual basis in conjunction with the Annual Programmatic Meetings and on ad-hoc basis by conference calls, as needed. Committee’s meetings will include NIAID staff, and may include   PD(s)/PI(s) and other members of the funded Programs as necessary.

The Steering Committee will select one member to be the Chair of the Committee and the Chair will not be a NIAID staff member. 

Federally Mandated Regulatory Requirements for Clinical Research

Each Institution engaged in human subjects research is required to meet DHHS regulation for the protection of human subjects. At a minimum, this includes: 

Intellectual Property

The awardee is solely responsible for the timely acquisition of all appropriate propriety rights, including intellectual property rights, and all materials needed for the awardee to perform the project.

Before, during, and subsequent to the award, the U.S. Government is not required to obtain for the awardee any propriety rights, including intellectual property rights, or any materials needed by the awardee to perform the project.

The awardee is required to report to the U.S. Government all inventions made in the performance of the project, as specified by 35 U.S.C. Sect. 202 (Bayh-Dole Act).

Program Generated Data, Software and Other Resources

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

The Programs funded under this FOA are expected to follow the requirements and timelines described in the NIAID Data Sharing and Release Guidelines (http://www.niaid.nih.gov/LabsAndResources/resources/dmid/gsc/Pages/data.aspx).  Program-generated data and software should be made available through publicly accessible web and database sites, including the Web Portal, the BRCs (http://www.niaid.nih.gov/dmid/genomes/brc/default.htm), the NCBI (http://www.ncbi.nlm.nih.gov/) and/or other public repositories, as identified by the Steering Committee in consultation with the NIAID.

Program-generated data and software include, for example:

Whenever possible, the awardee shall provide software certified by the Open Source Initiative (http://www.opensource.org/licenses/), to guarantee the right of others to read, redistribute, modify, and freely use the software.

Program-generated novel reagents (e.g., expression vectors, mutant strains, libraries, protein clones), should be made available through NIAID-supported repositories, such as the NIAID BEI Resources (http://www.beiresources.org/) or in other repositories as identified by the Steering Committee in consultation with the NIAID.

Publications

The PD(s)/PI(s) will be responsible for the timely submission to the NIAID of all abstracts, manuscripts and reviews (co)authored by members of the grant and supported in whole or in part under this Cooperative Agreement.  The PD(s)/PI(s) are requested to provide manuscripts to the NIAID Program staff prior to the submission to the Journal and abstracts prior to submission to conferences and meeting so that an up-to-date summary of program accomplishments can be maintained.  Publications and oral presentations of work conducted under this Cooperative Agreement are the responsibility of the PD(s)/PI(s) and appropriate Research Project and Core Leaders and will require appropriate acknowledgement of NIAID support.  Awardees are expected to make new information and materials known to the research community in a timely manner through publications, web announcements, and reports to the NIAID, or other mechanisms.

Arbitration Process
Any disagreements that may arise in scientific or programmatic matters (within the scope of the award) between award recipients and the NIH may be brought to arbitration. An Arbitration Panel composed of three members will be convened. 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 arbitration procedure in no way affects the awardee's right to appeal an adverse action that is otherwise appealable in accordance with PHS regulations 42 CFR Part 50, Subpart D and HHS regulations 45 CFR Part 16.

3. Reporting

When multiple years are involved, awardees will be required to submit the Non-Competing Continuation Grant Progress Report (PHS 2590 or RPPR) 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. 

Section VII. Agency Contacts

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

Application Submission Contacts

GrantsInfo (Questions regarding application instructions and process, finding NIH grant resources)
Telephone 301-435-0714
TTY 301-451-5936
Email: GrantsInfo@nih.gov

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: commons@od.nih.gov

Scientific/Research Contact(s)

Maria Y. Giovanni, Ph.D.
National Institute of Allergy and Infectious Diseases (NIAID)
Telephone: 301-496-1884
Email: mgiovanni@niaid.nih.gov

Peer Review Contact(s)

Eleazar Cohen, Ph.D.
National Institute of Allergy and Infectious Diseases (NIAID)
Telephone: 301-496-1884
Email: ecohen@niaid.nih.gov

Financial/Grants Management Contact(s)

Regina Kitsoulis
National Institute of Allergy and Infectious Diseases (NIAID)
Telephone: 301-402-6245
Email: kitsoulisre@niaid.nih.gov

Section VIII. Other Information

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.

Authority and Regulations

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.


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