Department of Health and Human Services

Part 1. Overview Information

Participating Organization(s)

National Institutes of Health (NIH)

Components of Participating Organizations

National Human Genome Research Institute (NHGRI)

Funding Opportunity Title
Informatics Tools for the Pangenome (U01 Clinical Trial Not Allowed)
Activity Code

U01 Research Project – Cooperative Agreements

Announcement Type
New
Related Notices
  • August 31, 2022 - Implementation Changes for Genomic Data Sharing Plans Included with Applications Due on or after January 25, 2023 - See Notice NOT-OD-22-198
  • August 5, 2022 - Implementation Details for the NIH Data Management and Sharing Policy - see Notice NOT-OD-22-189.  
Notice of Funding Opportunity (NOFO) Number
RFA-HG-23-026
Companion Funding Opportunity
RFA-HG-23-024 , UM1 Research Project with Complex Structure Cooperative Agreement
RFA-HG-23-025 , U41 Biotechnology Resource (Cooperative Agreements)
Assistance Listing Number(s)
93.172
Funding Opportunity Purpose

This NOFO seeks applications for the development of informatics tools to facilitate uptake and scientific use of the human pangenome reference being developed and maintained by the NHGRI Human Genome Reference Program (HGRP).  Emphasis for this RFA will be on development of tools to advance compelling use cases that are relevant to different broad sectors of the genomics community, e.g., clinical, population, and functional genomics. These tools will use pangenome datasets and build on systems developed by the Human Pangenome Coordinating Center (see below), which will support general computational infrastructure for pangenome use. 

This informatics tools RFA will fund one component of an overall HGRP, which will also include two other components: High Quality Reference Genomes (herein called “Genomes Center”), and a Human Pangenome Coordinating Center (Herein called “Coordinating Center”). (See Companion Funding Opportunities). Awardees under all three RFAs will work collaboratively within a consortium towards production and community adoption of the human pangenome reference.   

Key Dates

Posted Date
June 20, 2023
Open Date (Earliest Submission Date)
October 01, 2023
Letter of Intent Due Date(s)

October 01, 2023; February 3, 2025

Application Due Dates Review and Award Cycles
New Renewal / Resubmission / Revision (as allowed) AIDS - New/Renewal/Resubmission/Revision, as allowed Scientific Merit Review Advisory Council Review Earliest Start Date
November 01, 2023 Not Applicable Not Applicable March 2024 May 2024 July 2024
March 03, 2025 March 03, 2025 Not Applicable July 2025 October 2025 December 2025

All applications are due by 5:00 PM local time of applicant organization. 

Applicants are encouraged to apply early to allow adequate time to make any corrections to errors found in the application during the submission process by the due date.

No late applications will be accepted for this Funding Opportunity Announcement.

Expiration Date
March 04, 2025
Due Dates for E.O. 12372

Not Applicable

Required Application Instructions

It is critical that applicants follow the instructions in the Research (R) Instructions in the SF424 (R&R) Application Guide, except where instructed to do otherwise (in this NOFO or in a Notice from NIH Guide for Grants and Contracts).

Conformance to all requirements (both in the Application Guide and the NOFO) is required and strictly enforced. Applicants must read and follow all application instructions in the Application Guide as well as any program-specific instructions noted in Section IV. When the program-specific instructions deviate from those in the Application Guide, follow the program-specific instructions.

Applications that do not comply with these instructions may be delayed or not accepted for review.

There are several options available to submit your application through Grants.gov to NIH and Department of Health and Human Services partners. You must use one of these submission options to access the application forms for this opportunity.

  1. Use the NIH ASSIST system to prepare, submit and track your application online.
  2. Use an institutional system-to-system (S2S) solution to prepare and submit your application to Grants.gov and eRA Commons to track your application. Check with your institutional officials regarding availability.

  3. Use Grants.gov Workspace to prepare and submit your application and eRA Commons to track your application.


  4. Table of Contents

Part 2. Full Text of Announcement

Section I. Notice of Funding Opportunity Description

Purpose 

The National Human Genome Research Institute (NHGRI) plans to renew the Human Genome Reference Program (HGRP), which is a flagship effort to transform the original genome reference to incorporate population-scale data in a pangenome representation. This RFA seeks applications for the development of informatics tools to facilitate uptake and scientific use of the human pangenome reference being developed and maintained by the HGRP. This informatics tools NOFO will fund one component of an overall HGRP, which will also include two other components: High Quality Reference Genomes (“Genomes Center”) and a Human Pangenome Coordinating Center (“Coordinating Center”; see Companion Funding Opportunities).  

Emphasis for this RFA will be on development of tools for compelling use cases for the pangenome that are relevant to different broad sectors of the genomics community, e.g., clinical, population, and functional genomics. Tools are intended to enable other genomics researchers to adopt and use the pangenome in their scientific endeavors. These tools will build on datasets and systems developed by the Coordinating Center, which will support general computational infrastructure for pangenome use.

Awardees under all three NOFOs will work collaboratively within a consortium towards production and community adoption of the human pangenome reference.

Background

A human genome reference sequence is an accepted representation of the human genome used as a standard to align and assemble genome sequence data. It also serves as a consensus coordinate system for reporting results. Since the completion of the Human Genome Project, the genome reference has been steadily improved by resolving errors and adding information from new assemblies. Improved or updated reference versions are curated and released to the community by the Genome Reference Consortium (GRC), a collaboration between the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI). The existing reference, however, has limitations including assembly gaps, lack of haplotype resolution and — most importantly — inadequate representation of genetic diversity that perpetuates reference bias and risks exacerbating health disparities across populations. 

The HGRP  was established by NHGRI in 2019 to improve the human genome reference by using new methods for more complete assemblies, by increasing genetic diversity and by transforming the reference to represent hundreds of genomes in an accessible and usable resource.   In the ensuing three years, funded investigators formed the Human Pangenome Reference Consortium (HPRC), established an embedded ELSI team which guided the HPRC on issues such as consent and participant community engagement, and initiated collaborations with international partners to develop a resource representative of global populations.  An initial draft pangenome consisting of nearly 50 human genome assemblies was recently released. These efforts constitute a strong foundation for the further improvement of the human pangenome reference.   

In October 2022, NHGRI hosted a workshop to identify future directions for the HGRP. Meeting participants strongly encouraged the continuation of the program, with key recommendations emerging from the participants' individual input including:

  • Prioritize utility over quantity and focus on sample selection and data generation of highest benefit to the broader genomics research community.
  • Emphasize adoption of the new pangenome by identifying use cases, building user-friendly tools, and minimizing disruption to existing workflows.
  • Establish partnerships with international organizations and global participant communities and strive to ensure equitable benefit of the pangenome.
  • Integrate ethical, legal and social implications (ELSI) at all stages of research including project design, recruitment, adoption, dissemination, and access.

Considering these recommendations, NHGRI plans to renew the HGRP. The goals for the renewal include: 1) continuing to maintain and improve the pangenome reference, adding diverse, reference quality sequence assemblies; 2) facilitating adoption of the pangenome reference by the research and clinical genomics communities; 3) fostering the development and deployment of informatics tools for the pangenome; 4) embedding  ELSI  research; and 5) forming international partnerships to maximize the chances that the human pangenome reference will represent populations worldwide, and encourage the collaboration of scientists worldwide in its creation and use. Overall, there will be a shift in emphasis towards evaluating HGRP progress in terms of how useful the pangenome resource is for clinical and basic genomics research communities.  The overall goal of the HGRP during the renewal will be to produce a human pangenome reference that optimizes both the population genetic diversity represented, and also the utility for, and adoption by, the genomics research community.

Based on the subsequent Concept for this program presented to the National Advisory Council on Human Genome Research the components of the renewal will be:  

  1. High Quality Reference Genomes (“Genomes Center,” see RFA-HG-23-024), a limited competition NOFO that focuses on generating high-quality human genome sequence data and assemblies to fill gaps in genetic variation and diversity, and includes the embedded ELSI component;
  2. Human Pangenome Coordinating Center (“Coordinating Center,” see RFA-HG-23-025), a limited competition NOFO that will serve as the logistic and scientific coordinating center for the HGRP and will create, improve, release, and maintain new pangenome reference versions and organize community outreach and resource adoption;
  3. Informatics Tools for the Pangenome (“Tools Projects,” this NOFO: RFA-HG-23-026), consistent with the overall emphasis of the renewed program on utility and adoption, this NOFO is an open competition that will fund multiple investigators to develop computational tools to address the need to facilitate uptake and use of the pangenome reference with an emphasis on tools for common use cases of the pangenome relevant to broad sectors of the genomics community.

All awardees of the program are expected to work together closely to achieve the goals of HGRP.

In addition to these three NOFOs. NHGRI will encourage investigator-initiated applications on topics related to the development of the pangenome.  

Research Objectives

Tools for using the pangenome

For this RFA NHGRI seeks applications proposing to develop informatics tools that will allow the full range of the genomics community to use the human pangenome reference being developed by the HGRP. Proposed projects can be wholly new tools that take advantage of the new information in the pangenome reference, and its graph representation to produce improved results, or modifications of existing tools to enable important use cases of the pangenome. The current representation is graph-based, but other representations (e.g. k-mer) may evolve to accommodate scale and complexity and strategies for compression and efficient data structures may be relevant. 

NHGRI supports development of methods, tools and technologies that can be used by other biomedical researchers. This RFA has a focus on developing tools that will catalyze routine use of the human pangenome by other researchers. Emphasis will be on tools for compelling use cases that are relevant to different broad sectors of the genomics research community: clinical, population, functional genomics, etc. These tools are expected to break the path for other scientists to benefit from the pangenome reference. Ideally such tools will be usable by investigators or clinicians with a range of genomics informatics expertise and resources. Although it is likely that each individual application will need to focus on one or a few uses, ideally, across all the awards, the tools developed will address a range of topics that represent the major use cases for the pangenome.  

Further, this RFA will focus on tools that have the greatest utility to the genomics research community. Best practices in software development (see NIH Best Practices for Sharing Research Software) are expected, including documentation, testing and robust design principles. Tools and software should be reproducible and interoperable with other methods and tools. When appropriate, the tools should integrate into existing pipelines, use existing standards and ontologies, and contribute to the larger genomic data science and computational genomics ecosystem.

Possible examples of tools include applications that best use the pangenome reference for: 

  • Selecting the best subset of linear genomes or paths along the pangenome graph for use in genome alignments of short read sequence data 
  • Creating a data visualization tool to aid in identifying structural variation in the pangenome
  • Using the distribution of genetic variation in the pangenome to inform population genetic or comparative genomic analysis
  • Integrating the pangenome with multi-omic or functional genomic data to improve variant characterization in genomically diverse populations
  • Visualizing regulatory elements, or other functional genomic features within the pangenome
  • Using the pangenome reference to improve fine mapping and polygenic risk scores
  • Using the pangenome to annotate disease associations or clinically relevant variants
  • Integrating controlled access genomic data with open access pangenome data in ways that enable secure and private use of protected data. 

Applicants are expected to work closely with the Coordinating Center, which will also be developing informatics systems and tools for the pangenome. The distinction is that this tools RFA seeks development of user applications, while the Coordinating Center will support informatics infrastructure for the construction and delivery of a human pangenome reference. Both NOFOs share the mission of encouraging and supporting use and adoption of the pangenome by the broader genomic research community.  

Project management and integration with the HGRP consortium

The project management structure should ensure the efficient planning, initiation, implementation, and timely completion of all activities. Specific timelines and milestones should be developed and may be updated over the course of the funding period.  

Project management should involve frequent interactions and communications with NHGRI staff, including preparing additional reports as requested by NHGRI staff.

Work under this RFA will be closely integrated with the work done under the companion RFAs to ensure that the higher-level goals of the HGRP towards producing a useful community resource are realized. During the renewal period of the HGRP, the program will place a new emphasis on outreach to the user community in order to facilitate adoption of the pangenome. Awardees can expect to be closely involved in these adoption efforts.  Applications must plan to attend annual in-person consortium meetings.

The HGRP as a whole will include a Steering Committee, composed of representatives from all funded awards under this program (see Terms and Conditions), which will meet on a regular basis (at least monthly) to discuss and evaluate progress and challenges, form and revise working groups as needed, and otherwise coordinate activities across the consortium. Major decisions affecting the output of the consortium (including e.g. criteria and priorities for sample selection; data quality and incorporation of new sequencing platforms or assembly methods, etc.) must be approved by the Steering Committee level.  

The HGRP collectively is expected to recruit external scientific consultants (ESCs) who can, based on their individua expertise, assess different aspects of the program’s operations, scientific progress, and plans. Assesments from individual ESCs will be made available to the Steering Committee and NHGRI staff. ESCs will be independent, have expertise in a broad range of topics relevant to genomic medicine and genomic research including genomic technologies, computational genomics, data science, cloud computing, data management, data sharing concerns (such as participant protection issues), and Ethical Legal Social Implication issues. ESCs must be approved by NHGRI program staff; NHGRI may require additions to the ESCs e.g. to balance expertise. Any ESCs who have been already providing input to the applicants regarding pangenome reference-related work should be listed in the application; however applicants should refrain from recruiting or naming any additional ESCs until after the new program is funded.

Applicants are strongly encouraged to contact NIH Staff (see Agency Contacts) to discuss the alignment of their proposed work with the goals of this RFA.

Data and resource sharing in this initiative. Consistent with achieving the goals of this program, NIH expects that all products of the HGRP will be appropriately made available to the community. This includes (but may not be limited to): 

  • Samples (e.g. cell lines) used for sequencing through an established repository
  • Sequence and metadata for the high-quality genomes, publicly available and unrestricted for use (with specific exceptions to be approved by NHGRI for e.g., data from international collaborators)   
  • Data that are the products of processing or analysis of the primary data
  • Quality standards developed for producing high-quality genome assemblies, particularly for newer platforms.
  • Software developed and shared according to NIH Best Practices for Sharing Research Software.    

Recipients must comply with the NIH Data Management and Sharing Policy (NOT-OD-21-013) and NIH Genomic Data Sharing Policy (NOT-OD-14-124). Data should be released through the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL), and other resources as appropriate to enhance dissemination. The Informatics Tools component of the HPRC will work collaboratively with the other HGRP recipients to ensure compliance with the NIH data sharing policies (sharing.nih.gov), and NHGRI’s expectations which are summarized at (www.genome.gov/data-sharing). For the specific purposes of this NOFO, informatics tools developed under the program should be made available to the community via the HGRP Coordinating Center.            

Because the overall goal of the HGRP will be to produce a community resource, Resource Sharing and Data Management and Sharing plans are critical.  Prior to funding, NHGRI program staff will conduct an  administrative review of any plan for sharing data and resources and may negotiate modifications of the data sharing plan with the prospective recipient. The final negotiated version of the data sharing plan will become a term and condition of the award of the cooperative agreement. 

Responsiveness

The following applications will be considered non-responsive to this NOFO:

  • Applications that do not focus on developing tools for use of the pangenome produced by the HGRP 
  • Applications that do not develop tools that will be shared and that can be used by others
  • Applications that propose tools that are applicable to only one or a small number of diseases or biological systems
  • Applications that propose extensive wet-lab data generation, other than a small amount (10% of direct costs) that may be needed to validate the tool.  

Webinar

All applicants are strongly encouraged to contact NHGRI Staff to discuss the responsiveness and alignment of their proposed work with the goals of this program. An informational webinar will be held on July 20, 2023 at 12PM EDT for potential applicants. NIH staff will be available to answer questions related to this NOFO. Time, date, and dial in information will be provided at https://www.genome.gov/Funded-Programs-Projects/Human-Genome-Reference-Program#events.  During the webinar, NHGRI staff will present overviews of the program and answer RFA-related questions from prospective applicants. The informational webinar is open to all prospective applicants, but participation is not a prerequisite for submission of an application.   

See Section VIII. Other Information for award authorities and regulations.

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 scientific or program staff will assist, guide, coordinate, or participate in project activities. See Section VI.2 for additional information about the substantial involvement for this NOFO .

Application Types Allowed
New
Resubmission

The OER Glossary and the SF424 (R&R) Application Guide provide details on these application types. Only those application types listed here are allowed for this NOFO.

Clinical Trial?

Not Allowed: Only accepting applications that do not propose clinical trials.

Funds Available and Anticipated Number of Awards

NHGRI  intends to commit $2M in FY 2024, and a further $2M in FY2026 to fund up to 6 awards. 

Award Budget

Application budgets are limited to $400,000 direct costs per year, but need to reflect the actual needs of the proposed project.

Award Project Period

The maximum project period is 3 years. 

NIH grants policies as described in the NIH Grants Policy Statement will apply to the applications submitted and awards made from this NOFO.

Section III. Eligibility Information

1. Eligible Applicants

Eligible Organizations

Higher Education Institutions

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

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

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

Nonprofits Other Than Institutions of Higher Education

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

For-Profit Organizations

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

Local Governments

  • State Governments
  • County Governments
  • City or Township Governments
  • Special District Governments
  • Indian/Native American Tribal Governments (Federally Recognized)
  • Indian/Native American Tribal Governments (Other than Federally Recognized)

Federal Governments

  • Eligible Agencies of the Federal Government
  • U.S. Territory or Possession

Other

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

Applicant organizations must complete and maintain the following registrations as described in the SF 424 (R&R) Application Guide to be eligible to apply for or receive an award. All registrations must be completed prior to the application being submitted. Registration can take 6 weeks or more, so applicants should begin the registration process as soon as possible. The NIH Policy on Late Submission of Grant Applications states that failure to complete registrations in advance of a due date is not a valid reason for a late submission.

  • System for Award Management (SAM)– Applicants must complete and maintain an active registration, which requires renewal at least annually. The renewal process may require as much time as the initial registration. SAM registration includes the assignment of a Commercial and Government Entity (CAGE) Code for domestic organizations which have not already been assigned a CAGE Code.
    • NATO Commercial and Government Entity (NCAGE) Code – Foreign organizations must obtain an NCAGE code (in lieu of a CAGE code) in order to register in SAM.
    • Unique Entity Identifier (UEI)- A UEI is issued as part of the SAM.gov registration process. The same UEI must be used for all registrations, as well as on the grant application.
  • eRA Commons - Once the unique organization identifier is established, organizations can register with eRA Commons in tandem with completing their Grants.gov registrations; all registrations must be in place by time of submission. eRA Commons requires organizations to identify at least one Signing Official (SO) and at least one Program Director/Principal Investigator (PD/PI) account in order to submit an application.
  • Grants.gov – Applicants must have an active SAM registration in order to complete the Grants.gov registration.

Program Directors/Principal Investigators (PD(s)/PI(s))

All PD(s)/PI(s) must have an eRA Commons account.  PD(s)/PI(s) should work with their organizational officials to either create a new account or to affiliate their existing account with the applicant organization in eRA Commons. If the PD/PI is also the organizational Signing Official, they must have two distinct eRA Commons accounts, one for each role. Obtaining an eRA Commons account can take up to 2 weeks.

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 their organization to develop an application for support. Individuals from diverse backgrounds, including underrepresented racial and ethnic groups, individuals with disabilities, and women are always encouraged to apply for NIH support. See, Reminder: Notice of NIH's Encouragement of Applications Supporting Individuals from Underrepresented Ethnic and Racial Groups as well as Individuals with Disabilities, NOT-OD-22-019.

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 SF424 (R&R) Application Guide.

2. Cost Sharing

This NOFO 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.

The NIH will not accept duplicate or highly overlapping applications under review at the same time, per 2.3.7.4 Submission of Resubmission Application. This means that the NIH will not accept:

  • A new (A0) application that is submitted before issuance of the summary statement from the review of an overlapping new (A0) or resubmission (A1) application.
  • A resubmission (A1) application that is submitted before issuance of the summary statement from the review of the previous new (A0) application.
  • An application that has substantial overlap with another application pending appeal of initial peer review (see 2.3.9.4 Similar, Essentially Identical, or Identical Applications).

Section IV. Application and Submission Information

1. Requesting an Application Package

The application forms package specific to this opportunity must be accessed through ASSIST, Grants.gov Workspace or an institutional system-to-system solution. Links to apply using ASSIST or Grants.gov Workspace are available in Part 1 of this NOFO. See your administrative office for instructions if you plan to use an institutional system-to-system solution.

2. Content and Form of Application Submission

It is critical that applicants follow the instructions in the Research (R) Instructions in the SF424 (R&R) Application Guide except where instructed in this notice of funding opportunity 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:

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

The letter of intent should be sent to:

Adam L. Felsenfeld, Ph.D.
Telephone: 301-496-7531
Email: felsenfa@mail.nih.gov

Page Limitations

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

Instructions for Application Submission

The following section supplements the instructions found in the SF424 (R&R) Application Guide and should be used for preparing an application to this NOFO.

SF424(R&R) Cover

All instructions in the SF424 (R&R) Application Guide must be followed.

SF424(R&R) Project/Performance Site Locations

All instructions in the SF424 (R&R) Application Guide must be followed.

SF424(R&R) Other Project Information

All instructions in the SF424 (R&R) Application Guide must be followed.

SF424(R&R) Senior/Key Person Profile

All instructions in the SF424 (R&R) Application Guide must be followed.

R&R or Modular Budget

All instructions in the SF424 (R&R) Application Guide must be followed.

R&R Subaward Budget

All instructions in the SF424 (R&R) Application Guide must be followed.

PHS 398 Cover Page Supplement

All instructions in the SF424 (R&R) Application Guide must be followed.

PHS 398 Research Plan

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

Research plan

Applicants should clearly describe the tool they will develop and explain what its applications are and why they are important. Applicants should justify the significance of the proposed tool in terms of the following: 1. How will the proposed tool  enable important or significant uses of the pangenome in one or more broad areas (e.g. functional, population or clinical genomics), including considerations of which sectors of the genomics community will use the proposed tool? 2. How will the proposed tool catalyze the use and adoption of the human pangenome reference by the community of investigators that use genomics data?  3. How will the tool take advantage of the pangenome reference to allow improved or novel analyses compared to what can be done with existing human references e.g. GRCh38?

If the application is focused on revision of existing tools, then applicants should present data that the tool is of high value, including describing current use of the tool by the appropriate sectors of the genomics community.

Applicants  should discuss innovative elements of their proposal, for example, in the kind of applications the tool allows (e.g. something that cannot be readily done without a pangenome reference), in the design (e.g. novel ways to use the pangenome resource to obtain a result), or in the degree of advance over current methods/references.  

Where applicable, applicants should describe in detail plans for rigorous validation, benchmarking, comparisons to existing tools, and/or evaluations that will be performed to assess the quality or utility of the developed approaches. Applicants should demonstrate how their methods substantially outperform similar methods.

Applicants should discuss ways in which the proposed tool can accommodate, or be robust to, changes in the pangenome reference over time (changes in number of genomes, different representations, etc.), including updates or multiple versions of the reference, including  how their tools will scale to work with a human pangenome that will include an estimated 350 individuals (twice that many haplotypes) at the time of award and scaling up to add another 200 individuals over the next five years. Applicants should also discuss  how the proposed tool will scale to handle anticipated increases to the size and complexity of the data and studies available to the research community for analyses using the pangenome over the length of the award.

Applicants should  describe how their planned tools will take advantage of the genetic diversity of the pangenome resource and the very high quality of the constituent genome assemblies. If applicable, applicants should describe how the distribution of genetic variation in the pangenome will be taken into account in tool development or application. Also, applicants should address how their tool works with current graph-based pangenomes representations, and how their proposed tools could work with, and adapt to, other ways in which the pangenome may be represented (e.g. k-mer or other data structures).

Applicants should describe plans to incorporate best practices and robust design principles in their software development to enhance re-use of the software. This should include a description of how the methods, tools, or approaches will be developed such that they are reproducible, robust, well-documented, and can be readily adopted, applied, and extended or modified by other biomedical researchers.

Applicants should describe the utility of their tool to the broader genomics research community, including a description of any testing or documentation needed in relation to, or interdependencies with, other tools or methods. Applicants should also describe how the proposed tools and approaches, or resulting outputs or analyses, are standards-compliant to be interoperable with other methods, including plans for using existing relevant data and meta-data standards and ontologies.

Applicants should describe plans to enable broad uptake of the proposed tool, including portable solutions. Applicants should also describe how they will work with the Coordinating Center to help aggregate tools and promote community adoption. See also the Resource Sharing section below.

Management and integration: Applicants should provide timelines and milestones. Applicants should describe how they will work within the HGRP consortium towards the larger program goal of developing a human pangenome reference that is useful to the community. This includes participation in the HGRP Steering Committee and relevant working group calls and attending annual consortium meetings.

Where appropriate, applicants should describe how the methods or software they are developing will protect any human subjects data while allowing access to those data by qualified users. Innovative approaches to enable secure and private use of the pangenome are invited if they enable important scientific use cases.

Resource Sharing Plan:

Individuals are required to comply with the instructions for the Resource Sharing Plans as provided in the SF424 (R&R) Application Guide.

Resource Sharing Plan:

 Individuals are required to comply with the instructions for the Resource Sharing Plans as provided in the SF424 (R&R) Application Guide, with the following modification:

  • A major goal of this NOFO is the development of informatics methods and tools that are enabling for the genomics community. Applicants should therefore include detailed plans for open dissemination of methods, software, and tools to the community such that they are readily usable and extensible, where applicable. These should be made freely available to biomedical researchers and educators. There is no prescribed license for software produced by applications responding to this announcement, but any software license selected by applicants should allow for unrestricted redistribution and modification of software. Usable informatics tools will be aggregated by the Coordinating Center to enhance their uptake.
  • Methods, tools, and software should be well-documented and where applicable made available via version-controlled public repositories.
  • Solutions that enhance reproducibility when used by the community and ability of the community to integrate into automated pipelines should be emphasized.

Other Plan(s):

Note: Effective for due dates on or after January 25, 2023, the Data Management and Sharing Plan will be attached in the Other Plan(s) attachment in FORMS-H application forms packages.


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

  • All applicants planning research (funded or conducted in whole or in part by NIH) that results in the generation of scientific data are required to comply with the instructions for the Data Management and Sharing Plan. All applications, regardless of the amount of direct costs requested for any one year, must address a Data Management and Sharing Plan.
  • Recipients must comply with the NIH Data Management and Sharing Policy (NOT-OD-21-013) and NIH Genomic Data Sharing Policy (NOT-OD-14-124). NHGRI supports the broadest appropriate data sharing with timely data release through widely accessible data repositories. Please follow the NIH guidance on writing a Data Management and Sharing (DMS) Plan here, and ensure the Plan is in alignment with NHGRI’s data sharing expectations, which are summarized at genome.gov/data-sharing. If the proposed work will generate any data that are the results of data processing or analyses of the initial sequence data, these should be shared.

Appendix:

Only limited Appendix materials are allowed. Follow all instructions for the Appendix as described in the SF424 (R&R) Application Guide.

  • No publications or other material, with the exception of blank questionnaires or blank surveys, may be included in the Appendix.

PHS Human Subjects and Clinical Trials Information

When involving human subjects research, clinical research, and/or NIH-defined clinical trials (and when applicable, clinical trials research experience) follow all instructions for the PHS Human Subjects and Clinical Trials Information form in the SF424 (R&R) Application Guide, with the following additional instructions:

If you answered “Yes” to the question “Are Human Subjects Involved?” on the R&R Other Project Information form, you must include at least one human subjects study record using the Study Record: PHS Human Subjects and Clinical Trials Information form or Delayed Onset Study record.

Study Record: PHS Human Subjects and Clinical Trials Information

All instructions in the SF424 (R&R) Application Guide must be followed.

Delayed Onset Study

Note: Delayed onset does NOT apply to a study that can be described but will not start immediately (i.e., delayed start). All instructions in the SF424 (R&R) Application Guide must be followed.

PHS Assignment Request Form

All instructions in the SF424 (R&R) Application Guide must be followed.

Foreign Institutions

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

3. Unique Entity Identifier and System for Award Management (SAM)

See Part 1. Section III.1 for information regarding the requirement for obtaining a unique entity identifier and for completing and maintaining active registrations in System for Award Management (SAM), NATO Commercial and Government Entity (NCAGE) Code (if applicable), eRA Commons, and Grants.gov

4. Submission Dates and Times

Part I. Overview Information contains information about Key Dates and times. Applicants are encouraged to submit applications before the due date to ensure they have time to make any application corrections that might be necessary for successful submission. When a submission date falls on a weekend or Federal holiday, the application deadline is automatically extended to the next business day.

Organizations must submit applications to Grants.gov (the online portal to find and apply for grants across all Federal agencies). Applicants must then complete the submission process by tracking the status of the application in the eRA Commons, NIH’s electronic system for grants administration. NIH and Grants.gov systems check the application against many of the application instructions upon submission. Errors must be corrected and a changed/corrected application must be submitted to Grants.gov on or before the application due date and time.  If a Changed/Corrected application is submitted after the deadline, the application will be considered late. Applications that miss the due date and time are subjected to the NIH Policy on Late Application Submission.

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

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

5. Intergovernmental Review (E.O. 12372)

This initiative is not subject to intergovernmental review.

6. 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.

7. Other Submission Requirements and Information

Applications must be submitted electronically following the instructions described in the SF424 (R&R) Application Guide. Paper applications will not be accepted.

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

For assistance with your electronic application or for more information on the electronic submission process, visit How to Apply – Application Guide. If you encounter a system issue beyond your control that threatens your ability to complete the submission process on-time, you must follow the Dealing with System Issues guidance. For assistance with application submission, contact the Application Submission Contacts in Section VII.

Important reminders:

All PD(s)/PI(s) must include their eRA Commons ID in the Credential field of the Senior/Key Person Profile form. Failure to register in the Commons and to include a valid PD/PI Commons ID in the credential field will prevent the successful submission of an electronic application to NIH. See Section III of this NOFO for information on registration requirements.

The applicant organization must ensure that the unique entity identifier provided on the application is the same identifier used in the organization’s profile in the eRA Commons and for the System for Award Management. Additional information may be found in the SF424 (R&R) Application Guide.

See more tips for avoiding common errors.

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

In order to expedite review, applicants are requested to notify the NHGRI  Referral Office by email at grahambj@exchange.nih.gov when the application has been submitted. Please include the NOFO number and title, PD/PI name, and title of the application.

Post Submission Materials

Applicants are required to follow the instructions for post-submission materials, as described in the policy

Any instructions provided here are in addition to the instructions in the policy.

Section V. Application Review Information

1. Criteria

Only the review criteria described below will be considered in the review process.  Applications submitted to the NIH in support of the NIH mission are evaluated for scientific and technical merit through the NIH peer review system.

Overall Impact

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

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

 

Does the project address an important problem or a critical barrier to progress in the field? Is the prior research that serves as the key support for the proposed project rigorous? 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?

Specific to this NOFO:

What is the potential for this project to result in development of informatics tools that will address important or significant uses of the human pangenome reference in one or more broad areas (e.g. functional, population or clinical genomics)?   

What is the potential for this tool   to catalyze the adoption of the human pangenome resource by the genomics research community?  

How well will  the proposed tool take advantage of key aspects of the human pangenome reference to allow improved or novel analyses?

If the application is focused on revision of existing genomics tools for use with the pangenome reference, what is the value of   the existing software and tools to the appropriate  sectors of the genomics community? 

 

Are the PD(s)/PI(s), collaborators, and other researchers well suited to the project? If Early Stage Investigators or those 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?

 

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?

Specific to this NOFO:

How well will the  proposed tool allow novel analyses (i.e., something that cannot be readily done without a pangenome reference) because it is using the human pangenome reference? 

What elements of the proposal are innovative e.g. is there innovation in the design, or in the degree of advance over current methods/references? 

 

Are the overall strategy, methodology, and analyses well-reasoned and appropriate to accomplish the specific aims of the project? Have the investigators included plans to address weaknesses in the rigor of prior research that serves as the key support for the proposed project? Have the investigators presented strategies to ensure a robust and unbiased approach, as appropriate for the work proposed? 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? Have the investigators presented adequate plans to address relevant biological variables, such as sex, for studies in vertebrate animals or human subjects? 

If the project involves human subjects and/or NIH-defined clinical research, are the plans to address 1) the protection of human subjects from research risks, and 2) inclusion (or exclusion) of individuals on the basis of sex/gender, race, and ethnicity, as well as the inclusion or exclusion of individuals of all ages (including children and older adults), justified in terms of the scientific goals and research strategy proposed?

Specific to this NOFO:

How do the proposedir approaches compare to existing tools and/or outperform similar methods? 

How well does  the application  address capabilities to handle scale of data at the appropriate level (including both the number of genomes comprising the human pangenome reference, and the number of human genomes potentially available for analysis using the pangenome?

How well do the   proposed methods and tools take advantage of the genetic diversity of the pangenome and high quality genome assemblies? If applicable, has the application adequately considered how the distribution of genetic variation in the pangenome will be taken into account in tool development or application?  

What is  the potential of the proposed tool  to be robust to changes in the pangenome reference over time (eg, number of genomes, different representations, etc.), and changes in the genomic datasets that will be available to the scientific community for analysis?

To what degree does  the proposed project  incorporate best practices and robust software development approaches that will  enhance re-use of software? Does the application demonstrate a commitment to reproducible, robust, well-documented approaches and formats?

To what extent will  the tools  be of utility to the broader research community?  Does the application adequately address any needed testing and documentation and  or the use of appropriate standards and ontologies?

How likely is it adequate discussion of how that the applicants will integrate with the HGRP to aggregate tools, promote community adoption  and work towards the larger program goal of developing a human pangenome reference that is useful to the community? 

 

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?

Additional Review Criteria

As applicable for the project proposed, reviewers will evaluate the following additional items while determining scientific and technical merit, and in providing an overall impact score, but will not give separate scores for these items.

 

Not applicable

 

For research that involves human subjects but does not involve one of the 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 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 Guidelines for the Review of Human Subjects.

 

When the proposed project involves human subjects and/or NIH-defined clinical research, the committee will evaluate the proposed plans for the inclusion (or exclusion) of individuals on the basis of sex/gender, race, and ethnicity, as well as the inclusion (or exclusion) of individuals of all ages (including children and older adults) to determine if it is justified in terms of the scientific goals and research strategy proposed. For additional information on review of the Inclusion section, please refer to the Guidelines for the Review of Inclusion in Clinical Research.

 

The committee will evaluate the involvement of live vertebrate animals as part of the scientific assessment according to the following criteria: (1) description of proposed procedures involving animals, including species, strains, ages, sex, and total number to be used; (2) justifications for the use of animals versus alternative models and for the appropriateness of the species proposed; (3) interventions to minimize discomfort, distress, pain and injury; and (4) justification for euthanasia method if NOT consistent with the AVMA Guidelines for the Euthanasia of Animals. Reviewers will assess the use of chimpanzees as they would any other application proposing the use of vertebrate animals. For additional information on review of the Vertebrate Animals section, please refer to the Worksheet for Review of the Vertebrate Animals Section.

 

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.

 

For Resubmissions, the committee will evaluate the application as now presented, taking into consideration the responses to comments from the previous scientific review group and changes made to the project.

 

Not applicable

 

Not applicable

Additional Review Considerations

As applicable for the project proposed, reviewers will consider each of the following items, but will not give scores for these items, and should not consider them in providing an overall impact score.

 

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.

 

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).

 

Reviewers will comment on whether the Resource Sharing Plan(s) (e.g., Sharing Model Organisms) or the rationale for not sharing the resources, is reasonable.

 

For projects involving key biological and/or chemical resources, reviewers will comment on the brief plans proposed for identifying and ensuring the validity of those resources.

 

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 National Human Genome Research Institute, 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 will receive a written critique.

Applications may undergo a selection process in which only those applications deemed to have the highest scientific and technical merit (generally the top half of applications under review) will be discussed and assigned an overall impact score.

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

  • Scientific and technical merit of the proposed project as determined by scientific peer review.
  • Availability of funds.
  • Relevance of the proposed project to program priorities.
  • Program balance across topics.

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. Refer to Part 1 for dates for peer review, advisory council review, and earliest start date.

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 recipient's business official.

Recipients must comply with any funding restrictions described in Section IV.6. 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 NOFO will be subject to terms and conditions found on the Award Conditions and Information for NIH Grants website.  This includes any recent legislation and policy applicable to awards that is highlighted on this website.

Institutional Review Board or Independent Ethics Committee Approval: Recipient institutions must ensure that protocols are reviewed by their IRB or IEC. To help ensure the safety of participants enrolled in NIH-funded studies, the recipient must provide NIH copies of documents related to all major changes in the status of ongoing protocols.

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, Recipients, and Activities, including of note, but not limited to:

If a recipient is successful and receives a Notice of Award, in accepting the award, the recipient agrees that any activities under the award are subject to all provisions currently in effect or implemented during the period of the award, other Department regulations and policies in effect at the time of the award, and applicable statutory provisions.

Should the applicant organization successfully compete for an award, recipients of federal financial assistance (FFA) from HHS will be required to complete an HHS Assurance of Compliance form (HHS 690) in which the recipient agrees, as a term and condition of receiving the grant, to administer their programs in compliance with federal civil rights laws that prohibit discrimination on the basis of race, color, national origin, age, sex and disability, and agreeing to comply with federal conscience laws, where applicable. This includes ensuring that entities take meaningful steps to provide meaningful access to persons with limited English proficiency; and ensuring effective communication with persons with disabilities. Where applicable, Title XI and Section 1557 prohibit discrimination on the basis of sexual orientation, and gender identity. The HHS Office for Civil Rights provides guidance on complying with civil rights laws enforced by HHS. Please see https://www.hhs.gov/civil-rights/for-providers/provider-obligations/index.html and https://www.hhs.gov/civil-rights/for-individuals/nondiscrimination/index.html

HHS recognizes that research projects are often limited in scope for many reasons that are nondiscriminatory, such as the P rincipal I nvestigator’s scientific interest, funding limitations, recruitment requirements, and other considerations. Thus, criteria in research protocols that target or exclude certain populations are warranted where nondiscriminatory justifications establish that such criteria are appropriate with respect to the health or safety of the subjects, the scientific study design, or the purpose of the research. For additional guidance regarding how the provisions apply to NIH grant programs, please contact the Scientific/Research Contact that is identified in Section VII under Agency Contacts of this NOFO.

Please contact the HHS Office for Civil Rights for more information about obligations and prohibitions under federal civil rights laws at https://www.hhs.gov/ocr/about-us/contact-us/index.html or call 1-800-368-1019 or TDD 1-800-537-7697.

In accordance with the statutory provisions contained in Section 872 of the Duncan Hunter National Defense Authorization Act of Fiscal Year 2009 (Public Law 110-417), NIH awards will be subject to the Federal Awardee Performance and Integrity Information System (FAPIIS) requirements. FAPIIS requires Federal award making officials to review and consider information about an applicant in the designated integrity and performance system (currently FAPIIS) prior to making an award. An applicant, at its option, may review information in the designated integrity and performance systems accessible through FAPIIS and comment on any information about itself that a federal agency previously entered and is currently in FAPIIS. The Federal awarding agency will consider any comments by the applicant, in addition to other information in FAPIIS, in making a judgement about the applicant’s integrity, business ethics, and record of performance under Federal awards when completing the review of risk posed by applicants as described in 45 CFR Part 75.205 and 2 CFR Part 200.206 “Federal awarding agency review of risk posed by applicants.” This provision will apply to all NIH grants and cooperative agreements except fellowships.”

Cooperative Agreement Terms and Conditions of Award

The following special terms of award are in addition to, and not in lieu of, otherwise applicable U.S. Office of Management and Budget (OMB) administrative guidelines, U.S. Department of Health and Human Services (DHHS) grant administration regulations at 45 CFR Part 75, and other HHS, PHS, and NIH grant administration policies. 

The administrative and funding instrument used for this award will be managed as a cooperative agreement, an "assistance" mechanism (rather than an "acquisition" mechanism), in which substantial NIH programmatic involvement with the recipients 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 recipient.  Specific tasks and activities may be shared among the recipients; within the consortium and the NHGRI staff as defined below.

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

  • Determining research approaches, designing protocols, setting project milestones and timelines, and conducting research.
  • Ensuring that the software, resources, materials, etc. produced as part of this project are released appropriately according to the Resource Sharing Plan.
  • Ensuring that the data produced as part of this project are released appropriately according to the Data Management and Sharing Plan.
  • Preparing abstracts, presentations and publications in a timely manner.
  • Adhering to policies regarding sharing of genomic and other types of data, data access, and standardized formats; timely publication; and intellectual property established by the NIH, NHGRI, and the Steering Committ ee (SC).
  • Not disclosing confidential information.
  • Interacting with other relevant NHGRI and NIH activities, as needed, to promote synergy and consistency among similar or related projects.
  • Collaborating with the Coordinating Center (CC). Recipients that are part of a consortium will work collaboratively with a CC that is tasked with a variety of roles, such as: ensuring that the products are the highest quality, developing standards; disseminating information; providing logistics, outreach and training, etc. In order for the collaboration to be effective, PDs/PIs are responsible for:
    • Ensuring that the recipient receives the appropriate approvals for sharing data between the CC and selected data repositories, including the NHGRI Analysis Visualization and Informatics Lab-space (AnVIL), and other appropriate public databases.
    • Transferring, in a timely manner, detailed sequence, variant, other genomic and related data and metadata, as appropriate, to the Human Pangenome Coordinating Center (HPCC), using agreed-upon formats and processes, to facilitate dissemination of data more broadly through databases such as AnVIL and other appropriate databases.
    • Sharing the informatics tools through the HPCC, which will maintain a list of pangenome tools for dissemination to the community. 
    • Collaborating with the HPCC to   track and document collaborations and incoming samples, report findings, etc. in a FAIR (Findable, Accessible, Interoperable, Reusable) manner.
    • Submitting periodic progress reports in a standard format, including metrics of the use and impact on the community, agreed on with the NHGRI Project Scientist/Scientific Officer (PS/SO) and the SC.
    • Providing reports, summary statistics, and data, as appropriate, in a timely fashion. 
    • Sharing research resources, tools, and data of interest as described in the NOFO and consistent with achieving the goals of the project.
    • Assessing and disseminating data, protocols, consent materials, and methods developed for or derived from the CC within and outside the Consortium.
    • Abiding by common definitions, protocols, and procedures.
    • Attending and participating in SC and other working group meetings and accepting and implementing decisions made by the SC.

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

The Project Scientist/Scientific Officer (PS/SO) at NHGRI is a dual role held by a NHGRI Program Director. In the Project Scientist role, the Program Director will have substantial scientific and programmatic involvement during the conduct of this activity through technical assistance, advice, and coordination. In the Scientific Officer role, the Program Director will be responsible for the normal scientific and programmatic stewardship of the award and manages concerns about bias as it affects the project. The role of NHGRI PS/SO will be to facilitate and not to direct the activities. The PS/SO will be named in the Notice of Award.

The PS/SO will have the following substantial involvement:

  • Serving as a liaison, helping to coordinate activities among and for the recipients, including acting as a liaison to the NHGRI and as an information resource for the recipients about genome research activities. The PS/SO will also coordinate the efforts of the recipients) with other groups conducting similar studies.
  • Reporting periodically on the progress of the recipients to the NHGRI Director and to the National Advisory Council for Human Genome Research.
  • Assisting recipient(s) in the development, if needed, of policies for dealing with situations that require coordinated action.
  • Providing advice on the management and technical performance of the award.
  • Assisting in promoting the availability of the data and related resources developed in the course of the award to the scientific community.
  • Being responsible for the normal scientific and programmatic stewardship of the award, including assessments of how well the recipient has met any milestones required for each year of funding. 
  • Curtailing, withholding or reducing support for any recipient that fails to make satisfactory progress toward the work scope that NHGRI approved, has ethical or conflict of interest issues, or fails to comply with the Terms and Conditions of Award.
  • Involving NIH or NHGRI staff who may assist the recipient(s) as designated by the PS/SO.
  • Where warranted and consistent with authorship and conflict of interest requirements of journals in which the Consortium/Network decides to publish, co-authoring manuscripts through their role in scientific program management.

External Scientific Consultants  (ESCs) : The NHGRI PS/SO may engage external scientists with relevant scientific and consortium experience, who are not funded as part of the project and who agree to a confidentiality policy, to provide input and advice to the NHGRI PS/SO about the project. The PS/SO will work with the SC to appoint scientists as ESCs  and will determine the durations of service.  Activities of individual ESCs  could include:

  • Participating, as appropriate, in consortium meetings, Steering Committees calls, and the annual recipients'’ meetings; a subset of ESCs may also meet remotely at other times during the project period, as needed.
  • Reviewing and evaluating the progress of recipients (individually or as a group) in achieving the goals of the project.
  • Recommending changes in priorities based on scientific advances within and outside the consortium.
  • Providing individual recommendations regarding any changes in the project or grant(s) as necessary.

The PS/SO will use  recommendations from individual ESCs to make project changes, as appropriate.

Areas of Joint Responsibility:

If there are multiple awards working toward a common goal, close interaction between the participating recipients(s) and the PS/SO will be required, to manage, assess, and implement th e consortium. This is accomplished by:

  • Meeting monthly with the consortium SC to share information on data resources, methodologies, analytical tools, data analyses, preliminary results, etc.
  • Establishing best practices for data integration and collaborative analyses as appropriate.
  • Setting research priorities, deciding optimal research approaches and protocol designs, and contributing to the adjustment of research protocols or approaches as warranted.
  • Generating responses to ESP recommendations.
  • In addition to the PD(s)/PI(s), key co-investigators and pre- and postdoctoral scholars , including  those who are members of under-represented  groups or those from different but related disciplines, are eligible to attend these meetings. NHGRI encourages these co-investigators and scholars  to become involved in key consortium working groups, to lead and report on analyses, etc. 

The PS/SO will assist and facilitate the group process and not direct it.

  • Steering Committee (SC): The SC will be the main governing body of the Consortium. The purpose of the SC will be to maintain an overview of progress and the activities of any working groups that may be formed to implement the consortium, recommend directions for a consortium consistent with achieving the project goals, develop consortium policies to build synergy and improve communication and collaboration between the projects, and to provide a forum for discussing progress, challenges and opportunities for the consortium.

The SC will be composed of one representative from each of the grants awarded in the consortium. Each PD/PI will decide who will be its representative. Multi-PI grants will have one representative. Each representative will have one vote; The PS/SO will be a voting member.

  • The SC will develop its own operating procedures.
  • The SC may establish subcommittees to oversee the development and implementation of consortium policies including data releases, publications and standards, etc. Subcommittees may be either permanent or time limited, may include additional experts, depending on the needs of the research.
  • The PD(s)/PI(s) will be expected to play an active role in these working groups, as appropriate.
  • It is expected that most of the decisions on the activities of the SC will be reached by consensus. If a vote is needed, at least 60% of the voting members most vote in favor of the proposal.
  • NIH staff will review and approve policies developed by the SC.
  • Recipients will be required to accept and implement policies approved by the SC.

Dispute Resolution:

Any disagreements that may arise in scientific or programmatic matters (within the scope of the award) between award recipients and the NHGRI may be addressed by convening a Dispute Resolution Panel.  It will be composed of three members: a designee of the SC 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 disagreement for one award, the first member may be chosen by that recipient. This special dispute resolution procedure does not alter the recipient's right to appeal an adverse action that is otherwise appealable in accordance with PHS regulation 42 CFR Part 50, Subpart D and DHHS regulation 45 CFR Part 16.

3. Data Management and Sharing

Note: The NIH Policy for Data Management and Sharing is effective for due dates on or after January 25, 2023.

Consistent with the NIH Policy for Data Management and Sharing, when data management and sharing is applicable to the award, recipients will be required to adhere to the Data Management and Sharing requirements as outlined in the NIH Grants Policy Statement. Upon the approval of a Data Management and Sharing Plan, it is required for recipients to implement the plan as described.

4. Reporting

When multiple years are involved, recipients will be required to submit the Research Performance Progress Report (RPPR) annually and financial statements as required in the NIH Grants Policy Statement.

A final RPPR, 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. NIH NOFOs outline intended research goals and objectives. Post award, NIH will review and measure performance based on the details and outcomes that are shared within the RPPR, as described at 45 CFR Part 75.301 and 2 CFR Part 200.301.

The Federal Funding Accountability and Transparency Act of 2006 (Transparency Act), includes a requirement for recipients of Federal grants to report information about first-tier subawards and executive compensation under Federal assistance awards issued in FY2011 or later.  All recipients 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 the threshold.  See the NIH Grants Policy Statement for additional information on this reporting requirement.

In accordance with the regulatory requirements provided at 45 CFR 75.113 and 2 CFR Part 200.113 and Appendix XII to 45 CFR Part 75 and 2 CFR Part 200, recipients that have currently active Federal grants, cooperative agreements, and procurement contracts from all Federal awarding agencies with a cumulative total value greater than $10,000,000 for any period of time during the period of performance of a Federal award, must report and maintain the currency of information reported in the System for Award Management (SAM) about civil, criminal, and administrative proceedings in connection with the award or performance of a Federal award that reached final disposition within the most recent five-year period.  The recipient must also make semiannual disclosures regarding such proceedings. Proceedings information will be made publicly available in the designated integrity and performance system (currently FAPIIS).  This is a statutory requirement under section 872 of Public Law 110-417, as amended (41 U.S.C. 2313).  As required by section 3010 of Public Law 111-212, all information posted in the designated integrity and performance system on or after April 15, 2011, except past performance reviews required for Federal procurement contracts, will be publicly available.  Full reporting requirements and procedures are found in Appendix XII to 45 CFR Part 75 and 2 CFR Part 200 – Award Term and Condition for Recipient Integrity and Performance Matters.

Section VII. Agency Contacts

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

Application Submission Contacts

eRA Service Desk (Questions regarding ASSIST, eRA Commons, application errors and warnings, documenting system problems that threaten submission by the due date, and post-submission issues)

Finding Help Online: https://www.era.nih.gov/need-help (preferred method of contact)
Telephone: 301-402-7469 or 866-504-9552 (Toll Free)

General Grants Information (Questions regarding application instructions, application processes, and NIH grant resources)
Email: GrantsInfo@nih.gov (preferred method of contact)
Telephone: 301-637-3015

Grants.gov Customer Support (Questions regarding Grants.gov registration and Workspace)
Contact Center Telephone: 800-518-4726
Email: support@grants.gov

Scientific/Research Contact(s)

Adam L. Felsenfeld, Ph.D. National Human Genome Research   Institute (NHGRI)
Telephone: 301-496-7531
Email: Adam_felsenfeld@nih.gov 

Peer Review Contact(s)

Rudy Pozzatti, Ph.D. National Human Genome Research  Institute (NHGRI)
Telephone: 301-496-7531
Email: pozzattr@exchange.nih.gov

Financial/Grants Management Contact(s)

Maricella Trujillo National Human Genome Research  Institute (NHGRI)
Telephone: 301-480-7716
Email: Maricella.trujillo@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 Part 75 and 2 CFR Part 200.

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