Participating Organization (PO)
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National Institutes of Health (NIH)
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National Institute of Allergy and Infectious Diseases (NIAID)
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Title
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Genomic Centers for Infectious Diseases (U19)
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FOA
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RFA-AI-13-009
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Funding Opportunity Purpose
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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.
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Posted Date
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February 7, 2013
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Letter of Intent Due Date(s)
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May 24, 2013
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Application Due Date(s)
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June 24, 2013
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Scientific Merit Review
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November, 2013
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Advisory Council Review
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January, 2014
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Earliest Start Date
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April, 2014
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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.
| Note: A new version of the paper PHS 398 application form and instructions (revised 6/2009) must now be used. Download the new application form and instructions from http://grants.nih.gov/grants/forms.htm. |
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
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
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:
- Genomic Sequencing Centers for Infectious Diseases -- provide rapid and cost-efficient production of high-quality genome sequences of human pathogens and related organisms, invertebrate vectors of infectious diseases, human and microbial genotyping and metagenomics analysis.
- Bioinformatics Resource Centers -- collect, integrate and provide open access to research data of microbial organisms and vectors of infectious diseases in a user-friendly format, develop and share open source software tools, and provide bioinformatics services and training to the scientific community.
- Clinical Proteomics Centers for Infectious Diseases and Biodefense -- identify candidate pathogen and host biomarkers important for infectious diseases.
- Systems Biology Centers for Infectious Diseases -- identify and analyze molecular interaction networks of microbial pathogens and their host cells through a combination of computational and experimental high-throughput technologies.
- Structural Genomics Centers for Infectious Diseases -- focus on experimentally characterizing the three-dimensional atomic structure of proteins of pathogenic organisms.
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:
- Program Director(s)/Principal Investigator(s) (PDs/PIs) who will serve as the Center Director to oversee, manage and coordinate the research and ensure that the individual projects and cores are synergized to advance the goals of the Center. The PD(s)/PI(s) must have experience in managing a high throughput, large scale genomic sequencing center for infectious diseases.
- Four thematic Research Projects, focused on viruses, bacteria, fungi, and parasites and vectors, respectively. A Project Leader with relevant expertise is expected to be named for each thematic area.
- Three required cores, including a Technology Core; a Data Management, Analysis and Resources Dissemination Core; and an Administrative Core.
- Other Scientific Cores (optional).
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.
Funding Instrument
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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.
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Application Types Allowed
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New
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Funds Available and Anticipated Number of Awards
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NIAID intends to commit $14 million in FY 2014 to fund 2-3 awards.
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Award Budget
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Application budgets are not limited, but need to reflect actual needs of the proposed project .
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Award Project Period
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Scope of the proposed project should determine the project period. The maximum period is 5 years.
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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.
1. Eligible Applicants
Foreign Institutions
Non-domestic (non-U.S.) Entities (Foreign Institutions) are eligible to apply.
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.
- System for Award Management (SAM)– must maintain an active entity registration (formerly CCR registration), to be renewed at least annually. Use the Sam.gov “Manage Entity” function to manage your entity registrations. See the Grants Registration User Guide at SAM.gov for additional information.
- eRA Commons
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.
