Funding Opportunity Announcement - ATLAS-D2K Opportunity Pool 2024
This announcement was posted on Monday, January 8, 2024.
Applications are due Friday, March 15th, 2024.
- Application Instructions
- Eligible Project Directors/Principal Investigators
- Eligible Organizations
- Peer Review
- Additional Information
- Progress Reports
- Scientiﬁc/Research Contact(s)
The ATLAS-D2K Opportunity Pool funding program aims to address gaps or catalyze new partnerships in kidney and genitourinary research. This specific funding opportunity invites “glue grant” applications from investigators who are working in areas of high relevance to the GenitoUrinary Development Molecular Anatomy Project (GUDMAP) or the (Re)Building a Kidney (RBK) consortium and are currently supported by other signiﬁcant non-GUDMAP/RBK funding sources. Examples of other signiﬁcant funding sources include, but are not limited to, an NIH R01, RC2, R21, ISAC award, DP3, U01 award, or a VA MERIT award.
Successful glue grants are expected to be mutually beneficial. Applicants should describe how their “parent” project will benefit from being part of GUDMAP or RBK and how GUDMAP or RBK will benefit from partnering with the “parent” project. Specifically, glue grant funding will provide $100,000 total costs per year to the “parent” project to support sharing, harmonization, and integration with GUDMAP or RBK of relevant data, software, analytic pipelines, expertise, etc.
Of particular interest are applications to perform integrative and novel bioinformatic analyses that will yield helpful community resources adhering to FAIR principles (ﬁndable, accessible, interoperable, and reusable). Projects are expected to integrate data such as single-cell RNA-seq, single-cell ATAC-seq, spatial transcriptomic, imaging, and other molecular modalities. Integration efforts may include data generated by multiple entities, including but not limited to GUDMAP, RBK, the Kidney Precision Medicine Project (KPMP), the Human BioMolecular Atlas Program (HuBMAP), and the Human Cell Atlas (HCA). Moreover, it is expected that additional publicly accessible data from the Gene Expression Omnibus (GEO) would also be useful in data integration to construct comprehensive datasets for the research community. Ultimately, these datasets are intended to act as a starting point for the community to build upon, fostering the development of hypotheses, seeding new research directions, and expanding the ﬁeld.
Integrating diverse datasets presents a multitude of challenges that necessitate innovative computational approaches. These challenges encompass technical variations in the extensive array of scRNA-seq platforms and protocols, the presence of non-standard cell-type annotations, variations in sample sizes and sequencing depths, and the intricate implications of diverse biological factors, including tissue source, genetic background, and disease state, all of which impact gene expression proﬁles and must be carefully managed during integration. This funding opportunity encourages utilizing and advancing novel computational approaches using FAIR principles to harmonize large, heterogeneous datasets.
ATLAS-D2K Opportunity Pool projects aim to benefit a wider research community in several ways. Integrating numerous and disparate datasets to construct more comprehensive datasets will help identify quality issues and could lead to new standards. For example, a project merging multiple datasets into a uniﬁed integrated dataset could contribute to the delineation and discovery of novel cell types and cellular states, facilitating the recognition of commonalities and differences in disease states between mice and humans. Ultimately, products of the Opportunity Pool projects will expedite discoveries, bolster research in kidney and genitourinary development and disease, amplify the impact of existing data, and streamline data access and sharing within the broader biomedical community.
Limited funds are expected to be expended on generating new experimental data. Potential applicants are encouraged to use the ATLAS-D2K website and may contact current GUDMAP and RBK investigators to understand the scope of available data:
Since glue grants are expected to be mutually beneficial to GUDMAP/RBK and the parent grant, research products from the Opportunity Pool will be made publicly available upon completion of the project on or via the ATLAS-D2K website via the parent grant’s sharing infrastructure and in a public repository. These products could include integrated datasets and analyses (e.g., Seurat objects), data visualizations (e.g., Shiny apps), and/or white papers (e.g., reporting on issues of data quality and the potential for standardization).
Examples of potential Opportunity Pool projects include, but are not limited to:
Harmonizing Data for Comprehensive Development and Disease Datasets:
a. Objective: Employ new and inventive computational techniques not previously used with extensive datasets, experiment with integration methods, and build a comprehensive atlas of the mouse urinary tract throughout different developmental stages. Alternatively, establish a kidney disease atlas to advance our understanding of kidney injury and the mechanisms involved in kidney repair.
b. Data Sources: Utilize existing datasets from GUDMAP, RBK, KPMP, and HuBMAP in conjunction with external data sourced from repositories such as the Mouse Genome Informatics (MGI) database, Chan Zuckerberg Tabula Muris project or publicly accessible datasets within the Gene Expression Omnibus (GEO). Leverage these resources to create a comprehensive multi-omics dataset through data integration.
c. Expected Outcomes: Identify key molecular players, cell surface markers, and regulatory networks involved in urinary tract development and build a comprehensive single-cell transcriptomic atlas of the mouse lower urinary tract throughout different developmental stages or establish a kidney disease atlas to improve our understanding of kidney injury and repair mechanisms. Identify pre-analytical or analytical sources of variability that could inform community standards.
Synergizing Basic and Translational Research with Clinical and Molecular Data for Enhanced Discovery:
a. Objective: Integrate clinical data concerning human urinary tract developmental disorders and disease progression with findings from mouse models. Leverage extensive population-based whole exome sequencing or a similar approach such as GWAS whenever possible.
b. Data Sources: Examples of potential datasets include GWAS genomic sequencing studies from CAKUT patients, Prune Belly Syndrome or other kidney or urologic diseases available from the Gabriella Miller Kids First Data Resource Center (GMKF), or relevant data from the database of Genotypes and Phenotypes (dbGaP), 1000 Genomes Project, the NCBI Single Nucleotide Polymorphism Database (dbSNP), or through collaboration with clinicians who research these diseases and disorders.
c. Expected Outcomes: Evaluate the translational relevance of animal models, particularly mouse models, in the context of urinary tract development disorders and enhance our understanding of disease mechanisms.
Harnessing Data Integration for Evolutionary Insights and Translation in Comparative Developmental Studies:
a. Objective: Compare lower urinary tract development and disease in mice versus other model organisms or humans to identify conserved and divergent mechanisms.
b. Data Sources: Utilize data from mice and other species, such as Xenopus or other model systems, and incorporate human datasets from initiatives such as GMKF. Applicants may also explore resources available through the Pediatric Centers of Excellence in Nephrology (https://www.niddk.nih.gov/research-funding/research-programs/kidney-disease-centers).
c. Expected Outcomes: Discover evolutionary insights and potential translational applications.
Unlocking Cell Interactions: Harmonizing Data Integration, Spatial Transcriptomics, and Neighborhood Analysis:
a. Objective: Integrate spatial transcriptomic data with other molecular data to visualize gene expression patterns within the developing mouse urinary tract or disease states to better understand cell-cell interactions and the importance of cellular context.
b. Data Sources: Utilize existing datasets from GUDMAP, RBK, KPMP, and HuBMAP in conjunction with external data from repositories such as MGI, Chan Zuckerberg Tabula Muris project, or publicly accessible datasets within GEO. Leverage these resources to create a comprehensive multi-omics dataset through data integration.
c. Expected Outcomes: Generate visualizations and spatial relationships between genes and tissues, aiding in understanding tissue development and cellular interactions.
Data Integration with Machine Learning Predictive Models:
a. Objective: Apply novel machine learning models such as tensor decomposition (TD) strategies that predict developmental or disease outcomes based on integrated multi-omics data.
b. Data Sources: Utilize existing datasets from GUDMAP, RBK, KPMP, and HuBMAP in conjunction with external data sourced from repositories such as MGI, Chan Zuckerberg Tabula Muris project or other publicly accessible datasets within GEO. Leverage these resources to create a comprehensive multi-omics dataset through data integration.
c. Expected Outcomes: The establishment of novel approaches in integrating various data to predict developmental outcomes and identify potential therapeutic pathways and targets in treating disease.
Applications may request up to $100,000 (total costs) for one year and are due Friday, March 15th, 2024.
The application is the standard PHS 398 form, including face, abstract, detailed budget, biosketches (up to 5 pages each), and research plan. The research plan is limited to 5 pages, including specific aims.
All applications must be milestone-driven and include a detailed list of expected deliverables and a well-deﬁned timeline.
Applicants must state a willingness to provide key personnel travel at least once to the Bethesda, MD area for a GUDMAP or RBK consortia meeting.
Applicants must be willing to participate in the GUDMAP Bioinformatic Working Group.
Applicants must state a willingness to adhere to all GUDMAP/RBK practices, protocols, and policies. All awardees and the participating institution(s) must sign the GUDMAP/RBK Confidential Disclosure Agreement (CDA) and Material Transfer Agreement (MTA) documents. No edits to either the CDA or MTA will be allowed.
All applications must be submitted via the application portal available at the link below:
If you have any questions about using the portal, please contact email@example.com.
The costs must include the travel of key personnel to at least one of the GUDMAP annual or RBK semi-annual meetings in the Bethesda, MD, area.
Awards will be made as subcontracts from the ATLAS-D2K Center based at Brigham and Women’s, not directly by the NIH.
Eligible Project Directors/Principal Investigators
Individuals with the skills, knowledge, and resources necessary to carry out the proposed research are invited to work with their institution 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.
Early-stage investigators (ESIs) are encouraged to apply but must have a full-time faculty position or an equivalent position at a non-academic institution.
Foreign Institutions are eligible to apply.
Higher Education Institutions:
Public/State Controlled Institutions of Higher Education
Private Institution of Higher Education
The following types of Higher Education Institutions are encouraged to apply for 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; Nonprofit with 501(c)(3) IRS Status
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 Institution of Higher Education)
For-Proﬁt Organization (Other than Small Businesses) 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.
All applications will be peer-reviewed by non-conflicted reviewers.
Reviews will be coordinated by the ATLAS-D2K Center, not the NIH/NIDDK, but will follow the NIH grant application scoring system.
The NIH grant application scoring system uses a 9-point rating scale (1 = exceptional; 9 = poor) in whole numbers (no decimals) for Overall Impact and Criterion scores for all applications. NIH expects that scores of 1 or 9 will be used less frequently than the other scores. 5 is for a good medium-impact application and considered an average score. No formula is used to derive the overall impact score from the individual criterion scores, and reviewers are instructed to weigh the different criteria as they see fit in deriving their overall scores. Note that an application does not need to be strong in all categories to be judged likely to have major scientific impact and thus, deserve a high impact score. Reviewers will score an application as presented in its entirety and may not modify their scores on the assumption that a portion of the work proposed will be deleted or modified according to the review group’s recommendations.
Reviewers will score applications based on three scoring criteria:
Factor 1: Importance of the Research (Significance and Innovation)
Should it be done?
Scored (1-9), affects overall impact score
Factor 2. Feasibility & Rigor (Approach)
Can it be done well?
Scored (1-9), affects overall impact score
Factor 3: Expertise and Resources (Investigator, Environment)
Will it be done?
Considered in overall impact; no individual score
Reviewers will also strongly consider the following review criteria:
Does the application address a significant scientific knowledge gap in kidney and genitourinary research?
Does the application provide explicit details of what will be shared, when it will be shared, how much of it will be shared, and who will use it?
Does the application propose to use FAIR principles?
Are the proposed milestones, deliverables, and timeline appropriate and feasible?
- Incomplete, non-compliant, and/or nonresponsive applications will not be reviewed.
- No additional materials may be submitted after the receipt date.
- Conflicts of interest will be managed at all stages of review.
- Scientists from the applicant institution are in conflict and excluded from peer review.
- Written comments will be provided for all reviewed applications.
- Funding decisions will be made in consideration of the applicant’s ability to complete the scope of work and associated costs described in applications.
- Funding decisions will be made in consideration of the scientific merit, availability of funds, and programmatic balance. The ATLAS-D2K Center intends to make approximately 3 awards.
- Final funding decisions will be made in conjunction with the NIDDK.
- All decisions are final, and appeals will not be accepted for applications submitted in response to this solicitation.
- The number of awards will depend upon the number, quality, duration, and cost of the applications received.
- Funded awards are not allowed to submit a competitive renewal application.
- Unfunded applications are not allowed to revise and resubmit an amended application.
Awardees will become GUDMAP or RBK consortium members depending on the data integration eﬀorts proposed. Awardees will have the same responsibilities and access to data and results as other GUDMAP/RBK awardees and must follow the GUDMAP/RBK sharing policies. As such, **all awardees and the participating institution(s) must sign the GUDMAP/RBK Confidential Disclosure Agreement (CDA) and Material Transfer Agreement (MTA) documents. No edits to either the CDA or MTA will be allowed. **Per the General Collaborations policy regarding the roles of Collaborators, the GUDMAP/RBK Steering Committee will be deﬁned by the initially funded GUDMAP/RBK FOAs. As such, collaborators funded by this FOA will not be voting members of either Steering Committee.
A written summary of the accomplishments from the funded projects is due after the funding period.
The NIDDK intends the resource-sharing plans for the data and samples generated under the GUDMAP/RBK to follow the policy and objectives stated in the original GUDMAP/RBK FOAs. Specifically, consistent with achieving the objectives of the GUDMAP/RBK, all study data (including, but not limited to, raw data, metadata, digital pathology images, and computational datasets), protocols (including analytical methods), technologies, biological samples, and other research resources are to be shared immediately across the consortium, and made publicly available to the larger community as soon as quality control procedures have been completed, and per GUDMAP/RBK SC policies, subject to approval by the NIDDK.
Limited exceptions to the requirement for community dissemination may be identified by the GUDMAP/RBK SC and are subject to approval by the NIDDK. The NIDDK, in consultation with the SC for this project, will make all final decisions concerning data and sample deposition and data access policies, and all policies are subject to change by the NIDDK as deemed necessary to sustain program principles and priorities or to ensure the highest standards for responsible research conduct within the project.
Awardees will comply with and implement the recommendations and decisions of the SC concerning the sharing of information, data, biosamples, protocols, resources, methods, and analyses developed by the GUDMAP/RBK investigators under the GUDMAP/RBK.
Awardees must acknowledge the GUDMAP/RBK in all posters, manuscripts, or scientific materials generated in part or whole using funds from the GUDMAP/RBK using the following text:
“Research reported in this [poster/manuscript] was supported by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) Rebuilding a Kidney (RBK) Opportunity Pool, www.rebuildingakidney.org, under award number U24DK135157.
“Research reported in this [poster/manuscript] was supported by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) GenitoUrinary Development Molecular Anatomy Project (GUDMAP) Opportunity Pool, www.gudmap.org, under award number U24DK135157.
Eric W. Brunskill Ph.D.
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Anna Sadusky, Ph.D.
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Danny Gossett, Ph.D.
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)