Human BioMolecular Atlas Program (HuBMAP) Frequently Asked Questions (FAQs)
We appreciate your interest in the Human BioMolecular Atlas Program (HuBMAP) and hope that you and your team will choose to submit an application. In order to maximize your chances of success, we would like to provide some guidance that may be helpful. For additional clarification of these or other issues, we encourage you to send an email to HuBMAP@mail.nih.gov (link sends e-mail) or talk with the scientific contacts listed in the RFA to which you are applying.
1. What is the NIH Common Fund?
The NIH Common Fund, managed by the Office of Strategic Coordination in the Office of the Director, supports cross-cutting, trans-NIH programs that require participation by multiple Institutes and Centers. Common Fund programs are intended to be transformative, catalytic, synergistic, cross-cutting, and unique. This program is funded as a short-term, goal-driven strategic investment, with deliverables intended to catalyze research across multiple biomedical research disciplines. More information can be found at http://www.commonfund.nih.gov.
2. Why was the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) created?
Understanding how tissue organization influences a cell’s molecular state, interactions, and history is critical for enhancing our understanding of variation in organ function across the lifespan and health-disease continuum. Despite vastly improved imaging and omics technologies and many important foundational discoveries, our understanding of how tissues are organized is restricted to a very limited number of microscopic structures. Better insights into the principles governing organization-function relationship will potentially lead to better understanding of the significance of inter-individual variability, changes across the lifespan, tissue engineering, and the emergence of disease at the biomolecular level. However, integrating imaging and omics analysis to comprehensively profile biomolecular distribution and morphology of tissues in a high-throughput manner and placing this information into 3D tissue maps amenable to modelling has yet to be fully realized.
In a June 2016 meeting (Summary of the HuBMAP Planning Meeting) organized by the NIH, experts from the research community identified the following scientific priorities necessary to develop these tissue maps: 1) sourcing high-quality tissue from multiple human normal organ sites, 2) processing and preserving tissue for multiple imaging and omics assays, 3) quality control, validation, and variation in data generation, 4) data coordination across multiple acquisition techniques, 5) annotation, curation, and archiving of the data, 6) browsing, visualizing, and searching the data, 7) building statistical and analytic techniques and models for nonlinear analysis of highly multidimensional data and 8) community engagement.
3. What is the goal of HuBMAP?
The goal of the Human BioMolecular Atlas Program (HuBMAP) is to catalyze development of a framework for mapping of the human body with cellular resolution to enhance our understanding of tissue organization and function. This goal will be achieved by:
- Accelerating the development of the next generation of tools and techniques for constructing high-resolution spatial tissue maps that quantify multiple types of biomolecules either sequentially or simultaneously;
- Generating foundational 3D tissue maps using validated high-content, high-throughput imaging and omics assays;
- Establishing an open data platform that will develop novel approaches to integrating, visualizing and modelling imaging and omics data to build multi-dimensional maps, and making data rapidly findable, accessible, interoperable, and reusable by the global research community;
- Coordinating and collaborating with other funding agencies, programs, and the biomedical research community to build the framework and tools for mapping the human body;
- Supporting pilot projects that demonstrate the value of the resources developed by the program to study individual variation and tissue changes across the lifespan and the health-disease continuum.
For additional information about how HuBMAP is structured, see Program Goals and Initiatives.
4. How is the program structured?
HuBMAP will scale-up the scope of tissues, technologies, data management, and community engagement that are being addressed during the eight-year duration of the program. The program will have four stages: a setup phase in FY18, a scale-up phase FY19-21, a production phase FY22-24 and a transition phase in FY25. The five research initiatives that compose the program are:
- Transformative Technology Development - This set of initiatives, the first of which was issued in FY2018, is to seek to establish proof-of-principle with initial validation of transformative new tools, techniques and methods for mapping the human body at high-resolution.
- Rapid Technology Integration - This set of initiatives, the first of which was issued in FY2019, will focus on enhancing, validating, and integrating promising technologies into the HuBMAP Consortium. The goal is to improve the quality and throughput of map generation at key steps of the production pipeline including sample collection, tissue mapping, and data integration and analysis.
- Tissue Mapping Centers – The goal for this set of initiatives, the first of which was funded in FY2018, is to build, benchmark, standardize, validate, and generate extensive data from high-content, high-throughput imaging, and omics technologies to produce 3D human tissue maps at high-resolution. Centers are expected to integrate and optimize all parts of the data generation pipeline, from tissue collection and preservation through to data integration, analysis, and interpretation.
- The HuBMAP Integration, Visualization, and Engagement (HIVE) Collaboratory - This multi-component collaboratory, funded in FY2018, has responsibility for: 1) managing the data generated by the Consortium, 2) coordinating internal and external Consortium activities, 3) developing novel tools for visualizing, searching and modelling data, and 4) building an atlas of tissue maps.
- Demonstration Projects - The goal of this initiative, which is expected to start half way through the program pending the availability of funds, is to demonstrate how HuBMAP resources, in combination with new or other datasets or biospecimens as needed, can be used to build better statistical and analytic tools and models of cellular organization and communication in tissues.
4a. What is expected to happen during each of the four phases of the program?
Pending the availability of funds and dependent on progress, the budget for the program is expected to increase significantly over the first half of the program as the scale and complexity of Consortium activities increase.
During the first year of the program, the Setup Phase, the focus of the Consortium will be on establishing working groups, policies, SOPs, joint activities, and the infrastructure to support these activities. Individual projects will be expected to recruit needed staff, carry out calibration and benchmarking experiments, and build collaborations with other Consortium members.
During years 2-4 of the program, the Scale-up Phase, the Consortium will develop and populate the data matrix using data generated from validated assays, to carry out joint projects such as cross-validation studies or integrated analysis, and to establish collaborations with similar national and international programs. Individual projects will be expected to generate validation and pilot data by the end of the Scale-up Phase. The projects will optimize the resolution, content, and throughput of their assays to generate publication-quality data from human tissues, and rapidly share their research products with the Consortium.
During years 5-7 of the program, the Production Phase, the Consortium will be expected to have regular data releases of publication-quality data, to work with the wider research community to establish data and resource sharing policies, as well as creating tools and engaging in activities that will accelerate awareness and re-use of Consortium data. Individual projects will validate and implement emerging technologies into their data generation pipelines, regularly contribute significant amounts of well annotated, high-quality data to the HIVE in standardized formats, and analyze the generated data for new insights into inter-individual variability, changes in tissue organization across the lifespan, and changes across the health-disease continuum.
The goal of the final stage of the program in year 8, the Transition Phase, is to achieve long-term sustainability of the high-value resources generated by the Consortium by implementing a pathway that will maintain and curate the resources using other sources of funding.
5. What is the relationship between HuBMAP and other similar programs?
The goal of HuBMAP is to catalyze development of a framework for mapping of the human body with cellular resolution to enhance our understanding of tissue organization and function. This Consortium will be managed by NIH staff and a Steering Committee of funded investigators that will establish its own policies and procedures. At NIH there are several related atlas programs, including the NIH Common Fund GTEx Program, BRAIN Initiative, NCI’s Human Tumor Atlas Network, the NIDDK Kidney Precision Medicine Program (KPMP) and GUDMAP, and NHLBI’s LungMAP. In addition, HuBMAP researchers are coordinating with international programs and initiatives, including the Human Cell Atlas and the Human Protein Atlas, to make their data interoperable across the consortia. While each program has separate and specific scientific interests, goals and governance, there is significant interest in sharing expertise, developing synergies, and building collaborations among the programs that is realized through joint meetings, cross-consortia working groups, and collaborative projects.
6. Where can I find more information?
Announcements and regular updates will be posted on the program website: https://commonfund.nih.gov/hubmap and on the Consortium website itself https://hubmapconsortium.org
7. Who should I contact with questions?
General inquiries can be sent to HuBMAP@mail.nih.gov (link sends e-mail). For individual RFAs, Scientific and Research contacts are indicated in each announcement and these individuals should be your first contact for questions related to that RFA. In addition, the Common Fund HuBMAP Program is administered via a team of NIH program experts. The NIH HuBMAP Program Working Group members and their affiliations are listed below and at: https://commonfund.nih.gov/HuBMAP/members.General Questions General Questions
8. What do you mean by “tissue”, “organ”, and “organ system”?
Tissue is any aggregate of cells that have similar structure and function. An organ is typically a self-contained component of the body that has a specific vital function; an organ is composed of a collection of tissues; a tissue is an ensemble of similar cells. An organ system is a group of organs that act together to perform a bodily function.
9. What do you mean by “healthy” human tissue?
The focus of this program is on solid tissues with a defined spatial organization, collected from human donors without any diseases that are known to significantly impact the morphology, function or biomolecular profile of the tissue to be analyzed.
10. Will HuBMAP fund projects that do not use “healthy” human tissue?
No. The focus of the program is on understanding the intrinsic intra-, inter-, and extra- cellular biomolecular distribution in human tissue. The program will focus on fresh, fixed, or frozen healthy human tissue using in situ and dissociative techniques that have high-spatial resolution. Projects must propose to generate or analyze spatial data related to human tissues, including both cellular and extracellular compartments. In the case of the Transformative Technology Development initiative, during the UG3 phase, mammalian tissue may be used to reduce experimental variability while establishing feasibility, however, the UH3 phase must propose using human tissue.
11. What is a 3D tissue map and a biomolecular atlas?
For HuBMAP, a 3D tissue map is a high-resolution, representation of the quantitative distribution of intrinsic biomolecules found in human tissue. These biomolecules fall into many classes including but not limited to DNA, RNA, proteins, and metabolites. A biomolecular atlas is a collection of related biomolecular maps. Applicants are strongly encouraged to propose assays that can be easily multiplexed to produce comprehensive maps of the 3D spatial distribution of multiple classes of biomolecules across a tissue, including both intracellular and extracellular compartments.
Tissue Mapping Centers are responsible for generating individual maps in Cartesian space. The HIVE is responsible for integrating these maps together body-wide using a Common Coordinate Framework, generating maps in non-Cartesian space, and providing a framework for generating atlases of functional, structural, and biomolecular data that enable studies of inter-individual variability, changes across the lifespan, and across the health-disease continuum.
12. What tissue or organs are within the scope of the program?
Projects that propose studying non-human, diseased or dysfunctional tissues are not within the scope of the program. Projects that propose studying bodily fluids are not within the scope of the program. Motile human cells in the context of a tissue, such as tissue resident macrophages, are within the scope of the program. Projects may generate information from bodily fluids, or about microbiome interactions, the virome or exogenous compounds to enhance their understanding of tissue organization and function, though they should not be the focus of the project. There are no preferences or limitations to the tissues that will be analyzed as part of HuBMAP, beyond each project being expected to work with non-diseased human tissue. Given (1) technology limitations, (2) availability of high-quality tissue, and (3) tools, data, and analysis available from similar programs, applicants are strongly encouraged to consider: (1) how their choice of tissues provides a unique and synergistic opportunity for HuBMAP, (2) the rationale and synergy between the technologies, tissues and analysis tissues and organs proposed, and (3) the significance of the biological insights that will be gained from the data generated and analyzed. Additional details can be found in each RFA. There are no specific requirements for the collection, preservation, and processing of tissue. However, it is expected that high-quality tissue will be used and degradation will be characterized and minimized particularly if existing tissue specimens will be used, that specimens are of a sufficient size, and there is adequate information about the location and orientation of tissue blocks, so they can be accurately positioned in the human body using anatomical landmarks, and that donor consent does not inhibit the sharing and re-use of information within the Consortium. Although there are no specific requirements for preservation and pre-analytical processing (e.g. fixation and sectioning), these steps should minimize perturbation of the tissue, maximize compatibility with multiple downstream assays, and make sharing with other Consortium members practical. Projects are encouraged to develop, compare, and optimize preservation and pre-analytical techniques for each of the tissues they propose studying.
13. What tools and technologies are within the scope of the program?
HuBMAP supports the development and application of high-content, high-throughput, cost-effective assays that generate high-quality quantitative data for characterizing cells and the extracellular structures at high-resolution. The focus of the program is on in-situ analysis of the biomolecular composition and morphology of tissue, using unbiased, qualitative assays that can be readily multiplexed with other assays and used for analyzing multiple human tissues. Technologies that only assay a small number of biomolecules, have low sensitivity or specificity, are not generally applicable to all tissues or require significant optimization for each tissue, do not provide a reproducible quantitative readout, are not capable of high-throughput analysis, do not preserve information about spatial organization and have high-resolution, do not identify specific biomolecules, or are not cost-effective will be considered as low priority. Tools and technologies which require significant pre-processing of the tissue that results in significant biomolecular degradation, or that work with dissociated or fragmented cells and do not accurately recover spatial organization with high-resolution will also be considered a low priority.
Although the focus is on technologies that provide quantitative readout of the spatial organization of specific biomolecules, such as proteins, RNA, DNA, and metabolites, projects can propose generating data from technologies that will enhance scientific understanding, including from but not limited to MRI, micro-CT, photoacoustic imaging, Raman spectroscopy, histology, and mechanical imaging.
14. What is meant by “high-resolution”, “high-content”, and “high-throughput”?
For HuBMAP, a high-resolution assay is one that can reliably and reproducibly assign detected biomolecules to individual cells or extracellular compartments of a tissue. This dimension is typically understood to be at a length scale of around a micron, though projects may propose techniques within an order of magnitude depending on the biomolecules and tissues being studied. A high-content approach is one that maximizes identification of tissues features through a combination of biomolecular depth, spatial resolution, and multiplexing of complementary, multi-parameter assays. A high-throughput pipeline is one that maximizes the bandwidth of data production to result in any or all of the following: 1) accelerated speed of analysis, so that hundreds or thousands of samples can be analyzed at once, 2) greater depth of analysis, so that hundreds or thousands of molecules can be analyzed in a single sample, or 3) enhanced capacity for volume, so that a given set of molecules can be analyzed in all the cells within a larger tissue sample. Approaches that maximize the volume of tissue that will be analyzed while maintaining cellular resolution and high-biomolecular content are strongly encouraged.
14a. What will be considered unresponsive?
The focus of the program is to understand the spatial distribution of identifiable biomolecules in non-diseased human tissue, including both intracellular and extracellular space. Therefore, projects proposing to study cell lines, organoids, diseased or non-human tissues will be considered unresponsive (the exception is for the UG3 phase of TTD projects where mammalian tissues can be used). Projects proposing to use a combination of assays that do not generate high-spatial resolution, high-content, and high-throughput data on a diverse range of biomolecules will be considered unresponsive. Likewise, projects that use a preponderance of assays that do not generate maps of identifiable biomolecules (e.g. anatomical or morphological imaging or functional or physiological assays) will be considered unresponsive.
14b. Will HuBMAP fund projects using dissociative techniques?
Projects that propose to use only dissociative techniques that do not capture spatial information or only examine intracellular compartments will be considered unresponsive. Projects can use dissociative techniques in combination with complementary imaging approaches or propose dissociation assays where the spatial organization of the tissue can be inferred, and the conditions varied to analyze intracellular and extracellular regions. Projects can propose starting with intracellular transcript-only assays, though will be expected to broaden their range of assays during the project to include other biomolecules and extracellular compartments. Investigators are strongly encouraged to use multiple assays that can be cross validated, to minimize perturbation and degradation of tissue during pre-analytical process, and to optimize and standardize their assays.Science-Related Questions Science-Related Questions
Funding Related Questions
15. Does HuBMAP use the NIH grant mechanism?
HuBMAP will use cooperative agreements, contracts, and Other Transactional Authority (OTA) as appropriate for each initiative to reach its goal and milestones. All the Principal Investigators (PIs) funded through the Program will work together as a Consortium, with substantial NIH input.
16. What are cooperative agreements?
A cooperative agreement funding mechanism supports discrete, specified, circumscribed projects to be performed by investigators in an area representing their specific interest and competencies. It is used when substantial NIH programmatic involvement is anticipated. In addition to a Program Officer from the administering Institute, each award will be assigned a Project Scientist(s) from NIH who will participate with the Principal Investigators on a Steering Committee. NIH staff will not direct the research but will assist in aligning progress with the goals of the program and promote interaction with other members of the Consortium. There are several key expectations described in each RFA such as:
- Attendance at Consortium meetings, workshops, and conference calls
- All investigators are under a confidential disclosure agreement regarding all private information within the Consortium
- Participate in cross-validation of their own and others’ tools/technologies
17. What are Other Transaction (OT) awards?
Other Transactions (OTs) are funding mechanisms, which are not grants, cooperative agreements, or contracts, authorized under the Other Transaction Authority (OTA) as authorized by the 21st Century Cures Act, 2016 (P.L. 114-255). Section 2036.
OTs are used by components within the NIH, including the Common Fund, which have been authorized by Congress to use them. They allow the NIH to:
- Seek participation by non-traditional research partners
- Foster innovation and nimbleness to quickly develop and engage in programmatic activities
- Alter the course of the project in real-time to meet the overarching goal
- Conduct objective review
- Expand, modify, partner, not support, or discontinue awarded activities based on performance and programmatic need.
For additional information, please see the HuBMAP Other Transactions Policy Guide.
18. Is funding based on a payline?
No. Funding decisions are based on scientific merit and programmatic needs, as defined in the funding announcement, and on the availability of funds.
19. Who is eligible to apply for funding?
Academic organizations, small businesses, large businesses, non-profit organizations, and eligible agencies of the Federal Government (e.g. NIH intramural, the FDA) are eligible to apply as described in the “Eligible Applicants” or “Eligibility” section of each announcement.
20. My organization is an XYZ or I am an ABC investigator. Does that mean I have any special preference or disadvantage?
All applications will be evaluated solely based on the evaluation criteria described in the funding announcement. We encourage applications from nearly any organization (domestic or foreign), see the “Eligible Applicants” or “Eligibility” section of the relevant announcement. NIH policies such as Continuous Submission or New Investigator status do not apply to RFAs. There is no preference or disadvantage for organizations beyond the review criteria listed in the relevant announcement.
21. Can work be performed outside the United States?
Yes, for several of the HuBMAP initiatives applications can be submitted by a foreign institution as the primary applicant or as a subcontract to the US-based institution. Justification for inclusion of work to be performed outside the US must be provided in the grant application and if selected for funding, foreign clearance will be required prior to release of a Notice of Award (NoA). Please refer to the eligibility section of each announcement for further information.
22. Is there a recommended period of performance and budget level?
Period of performance and budget should be driven by scope and scientific need. Budgets and timelines are expected to vary from project to project.
23. Can an institution/research team submit more than one application to a one RFA or submit related applications to different RFAs?
For a specific RFA there is no prohibition on the number of applications an institution or team may submit, provided the applications are scientifically distinct. In the case of the HIVE RFA, a coordinated set of applications can be submitted as described in the announcement. However, it is not possible to submit coordinated applications across multiple RFAs.
24. Can research teams span institutions?
Yes. Team members may span multiple institutions, and it is possible that the full range of expertise needed for a proposal may not exist at one institution. Teams are expected to assemble the expertise across labs, disciplines, institutions needed to achieve the goals of the project and the HuBMAP.
25. What makes a good application for a Common Fund Program?
Common Fund Programs are designed to support actively managed, milestone-driven projects that are different from mainstream studies. These projects are expected to work together to address key roadblocks in emerging fields that will transform the way biomedical research is conducted. Applicants must explicitly address how the proposed research will have an impact which cuts across the interests of individual NIH Institutes and Centers and the reviewers will evaluate whether the project proposes an incremental improvement or a significant advancement which will transform the field. Applicants must also provide compelling justification for Common Fund support rather than from an individual NIH Institute or Center.Funding Related Questions Funding Related Questions
HuBMAP Consortium Questions
26. What is the HuBMAP Consortium?
The HuBMAP Consortium is made up of HuBMAP awardees, NIH staff, External Program Consultants, and other scientists and groups the Steering Committee agrees to include within the Consortium. The purpose of the Consortium is to enable groups to effectively collaborate with each other to maximize the chances of overall success of the program. In addition to completing the research goals outlined in their applications, successful applicants will be expected to work collaboratively with all members of the Consortium to contribute to developing SOPs, data and metadata standards, metrics for data generation, participate in cross-site studies, engage in cross-training, and guide development of data analysis and visualization tools that can be used by the broader scientific community.
27. What is the HUBMAP Steering Committee?
The HUBMAP Steering Committee (SC) is the governing body for the HUBMAP Consortium. The purpose of the SC is to recommend direction for the HuBMAP Consortium consistent with the program goals, develop Consortium policies and projects 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 includes PDs/PIs of each of the funded awards and NIH WG members. The SC is chaired by two PD/PIs that are approved by the NIH WG. An Executive Committee (EC) composed of the co-chairs and the NIH Program Team Leads meets monthly to set the agenda for SC meetings. The SC has established subcommittees to oversee the development and implementation of Consortium policies including data release, publications and standards. Current working groups include:
- Communication and Engagement
- Tissues, Technology and Data Collection
- Data Science
- Tools & Models
28. Who are the External Program Consultants?
As part of the HuBMAP program, NIH staff engage 5-10 external program consultants (EPCs) not funded as part of the program but with relevant scientific and consortium experience to provide input and advice to the NIH WG. This guidance could include reviewing and evaluating the progress of the entire HuBMAP Program or individual awardees as well as recommending changes in priorities for the HuBMAP Program based on scientific advances within and outside of the Consortium. The EPCs are senior, scientific experts who are not directly involved in the activities of the HuBMAP Program and who agreement to a confidentiality policy, engaged on an as-needed basis to advise on specific issues. NIH is solely responsible for appointing EPCs for variable durations of service. EPCs are invited to participate in Consortium meetings and Steering Committees calls and the Annual Investigators’ Meeting. A subset of EPCs may also meet by phone or web at other times of the year, as needed. Annually, the EPCs will provide individual assessments to the NIH of the progress of the Consortium and will present individual expert recommendations regarding any changes in the HuBMAP Program as necessary. The assessments and recommendations will be provided through the NIH WG to the Director of the Office of Strategic Coordination.
29. What role does the NIH have in the HuBMAP Consortium?
NIH staff has substantial programmatic involvement that is above and beyond the normal stewardship role in grants, providing technical assistance, advice and coordination. The roles of NIH are described in each Funding Opportunity Announcement.
30. What are the expectations for new investigators participating in the Consortium?
New investigators funded as part of the program will be expected to participate in a variety of Consortium activities, agree to existing policies and implement agreements. The Consortium has a range of regular teleconferences, including Steering Committee and Working Group calls. In addition, investigators will be expected to attend the Annual Investigator Meeting in-person and other appropriate face-to-face meetings and workshops organized by the Consortium and should budget accordingly. Funded projects will be expected to participate in Consortium projects, that may include development of SOPs and metadata standards, cross-site validation studies using the same tissue specimens, joint analysis projects, multi-site training programs, or coordinated outreach initiatives. Applicants are strongly encouraged to propose and budget for these activities as part of their applications.
In addition, the Consortium has established a range of policies and expectations, including the use of pre-print servers for rapid dissemination of results, regular data submissions, and publication of experimental protocols. A more complete list of Consortium policies can be found here: https://hubmapconsortium.org/policies/
31. Can investigators not funded though HuBMAP collaborate with the Consortium?
The Consortium has established an Associate Member policy, to facilitate collaborations with researchers who are not funded directly through the HuBMAP program. Details of the policy can be found here: https://hubmapconsortium.org/policies/HuBMAP Consortium Questions HuBMAP Consortium Questions
32. What are the plans for data and resource sharing for this program?
NIH intends that the products of the HuBMAP be broadly available to the research community to establish the foundations for a human body map that other programs and the international community to build upon, including methods, tools, reagents, biospecimens, datasets, and software. All funded investigators must facilitate the public release and dissemination of results, data, reagents, technologies, and other products generated through their HuBMAP awards in a timely manner and abide by Consortium and NIH policies. Awardees will be expected to develop policies for public access; data sharing; protocol, tool, and reagent sharing; intellectual property; and software sharing to work collectively with the NIH to harmonize and implement these policies across the Consortium. Applicants are expected to be conversant with the NIH Genomic Data Sharing Policy and to share data, protocols, and analytical tools rapidly with Consortium members, disclose publications before submission for review, regularly submit data to the HIVE (e.g. quarterly), and are strongly encouraged to make advances rapidly known through preprint servers.
32a. What are the expectations for data security and privacy?
NIH takes data security and privacy very seriously. Although applicants are not expected to be compliant with FISMA and FEDRAMP requirements, they are encouraged to propose working with infrastructures that have experience and credentials for handling detailed human sequencing data, and to propose a data management plan that includes security assurance and testing assessment, access control with appropriate user verification, and appropriate approaches for de-identifying data.
33. Are milestones the same as specific aims?
No, a milestone is a defined event, achievement, or important stage that is used to indicate the progress of a project. Milestones are expected to be:
- Major steps or events (e.g., activities or outcomes) with a clearly defined purpose.
- Specific targets that depict progress toward project goals.
- Descriptive of what will be done and when it will be completed.
- Collectively organized in a logical order (e.g. sequentially, simultaneously, or iteratively).
- Associated with a timeframe (e.g., end of the fiscal year).
Common Fund initiative milestones are not specifics aims or broadly aspirational statements of what a project is expected to achieve.
34. Can changes be made to the Research Plan during the project period?
Since this is an actively managed program, investigators should expect that their goals and budgets will be modified during the project period. For example, funds may be withheld each year and released only when Consortium activities have been proposed and approved. To promote synergy and collaboration between projects in the Consortium, NIH staff may also work with awardees to amend and refine goals and milestones. As tools and techniques are developed within the Consortium and other programs, investigators may also be asked to cross-validate these approaches. Investigators can also propose minor changes to the research approach as needed during the course of the project.
35. Can HuBMAP select only certain portions of an application to fund?
Yes. NIH staff may choose to fund a portion of an application based on reviewer feedback. This option may result in a reduction in project budget and project period. Projects may also be funded as pilot projects with a reduced budget and duration, with funds being restored for later years if the work is of high programmatic priority and milestones have been met or exceeded.Award Related Questions Award Related Questions
RFA Specific Questions
TTD: What tissues can projects propose?
The goal of the TTD initiative is to accelerate the development of the next generation of tissue analysis tools. While the HuBMAP program is interested in the whole body, TTD projects are encouraged to: 1) choose a practical mammalian tissue during the UG3 phase that best exemplifies the capabilities of their technology, and 2) to propose a range of human tissues that shows the generalized nature of the technology and its potential for scale-up and future incorporation into the Tissue Mapping Centers during the UH3 phase. Projects may choose and acquire their own tissue or may consider working with one of the Tissue Mapping Centers to access human tissue biospecimens. For projects funded during the UH3 phase, there will be an expectation that they participate in cross-validation studies with other Consortium projects and to submit significant high-quality data on human tissues to the HIVE. TTD applicants are encouraged to use existing data and metadata standards where possible and to develop a plan and roadmap for data handling, including a timeline with milestones for generating different tiers of data including feasibility data, validation data and publication quality data, and how they will work with the HIVE to successfully submit publication-quality data to the HIVE during the UH3 phase.
TTD: Is preliminary data required?
If significant preliminary data already exists for feasibility to study mammalian tissues or technologies with similar capabilities have already published, then the RTI initiative may be more appropriate and applicants are strongly encouraged to talk with NIH program staff.
What is the difference between Transformative Technology Development and Rapid Technology Implementation initiatives?
HuBMAP will support technology development relevant to meeting the goals of the program using different initiatives based on the “readiness” level as described below:
Technology Readiness Level (TRL)
Transformative Technology Development – UG3 phase
Basic principles observed
Technology concept formulated
Experimental proof of concept
Transformative Technology Development – UH3 phase
Technology validated in lab
Rapid Technology Implementation
Technology validated in relevant environment
Technology demonstrated in relevant environment
System prototype demonstration in operational environment
System complete and qualified
Actual system proven in operational environment
The Transformative Technology Development (TTD) initiative began in FY18, while the Rapid Technology Implementation (RTI) initiative began in FY19. Applicants are strongly encouraged to only apply for the initiative that best describes their stage of readiness. TTD applications with significant preliminary results that demonstrate proof of concept or validation in mammalian tissue will be considered a low programmatic priority. While TTD projects are encouraged to motivated by an unaddressed biological challenge, the focus of these projects should be on development of novel, high-impact technologies that significantly expand our capabilities. Likewise, this expansion may involve improving the sensitivity, specificity, or throughput of an assay by at least an order of magnitude over any similar technology in the peer-reviewed literature at time of submission or developing the capability to analyze specific biomolecules of interest at the single cell level that currently cannot be assayed. Conversely, high-risk technologies that have not generated publication-quality data from at least one human tissue will be considered a low-priority for the RTI initiative. RFAs for the RTI initiative are expected to focus on specific technological needs of the Consortium.
TMC: Are there preferred tissues or approaches?
NIH expects to fund at least one Center focused in each of the following areas: 1) analysis of multiple discrete, complex organs from the same individual or a region of the body composed of multiple tissues, 2) analysis of a complete organ or system and 3) analysis of rare, dynamic or motile cell types and their microenvironments or tissue neighborhoods.
Higher programmatic priority will be given to: 1) applications that propose to study complete human organs that are currently studied by existing TMCs, 2) that propose a synergistic and well-validated set of assays for multiscale and multi-modal analysis and 3) that have existing informed consent from a diverse range of donors or their families for explicit sharing of genomic data. Programmatic priority will also be given to approaches that maximize the volume of tissue that will be analyzed while maintaining cellular resolution and high biomolecular content.
TMC applicants are strongly encouraged to: 1) optimize or adapt appropriate existing tissue collection protocols, assays, and analytical methods, 2) plan a prospective tissue collection strategy, including collecting appropriate clinical data, 3) develop enrollment criteria and acquisition strategies that will minimize the risk of abnormal or degraded tissue as part of a quality management strategy, 4) pursue explicit consent from the donor or their family for unrestricted sharing of data for research purposes, 5) incorporate, optimize and validate emerging in situ assays that will generate complementary quantitative, high-content, high-throughput biomolecular data, 6) to discuss their proposed projects with existing TMCs and HIVE components before submitting applications, 7) reuse and adapt existing and widely-used data and metadata standards, ontologies, schemas, and formats, and to use common data elements, machine readable formats, structured reports and to minimize human data entry where possible, 8) use existing software packages and analysis methods, such as R-based or Python-based solutions, and 9) contact NIH Staff to discuss the alignment of their proposed work with the goals of this FOA and the HuBMAP Program.
DP: When will the demonstration projects (DPs) start?
The goal for these projects is to demonstrate the value of the datasets generated by the Consortium. Therefore, pending the availability of funds, demonstration projects are expected to start half-way through the program once sufficient data has been generated, and to complement existing Consortium projects - for example by analyzing tissues not yet part of the Consortium, comparing “normal” tissue with pathological tissue, or by testing biological hypotheses based on the preliminary evidence provided by the Consortium data. DPs that tie together the data of HuBMAP and complementary initiatives will be strongly encouraged.RFA Specific Questions RFA Specific Questions
HuBMAP: Plan for Enhancing Diverse Perspectives (PEDP)
For more information on the PEDP, please see the Frequently Asked Questions and the Key Elements and Examples below.
The NIH HuBMAP Program understands that diverse teams working together and capitalizing on innovative ideas and distinct perspectives outperform homogeneous teams. There are many benefits that flow from a diverse scientific workforce, including: fostering scientific innovation, enhancing global competitiveness, contributing to robust learning environments, improving the quality of the research, advancing the likelihood that underserved populations participate in, and benefit from research, and enhancing public trust.
HuBMAP is firmly committed to fostering diversity and inclusivity in the research community. Beginning in Fall 2021 most HuBMAP ROAs and FOAs will be requiring that applications include a Plan for Enhancing Diverse Perspectives (PEDP) in the proposed research. Examples of structures that promote diverse perspectives include but are not limited to:
• Participation of investigators from diverse backgrounds, including groups traditionally underrepresented in the biomedical, behavioral, and clinical research workforce (see NOT-OD-20-031), such as underrepresented racial and ethnic groups, those with disabilities, those from disadvantaged backgrounds, and women.
• Engagement with different types of institutions and organizations (e.g., research-intensive and research active, undergraduate-focused, minority-serving, community-based).
• Partnerships that may enhance geographic and regional diversity.
• Use of the project infrastructure (i.e., research and structure) to support career-enhancing research opportunities for diverse junior, early-, and mid-career researchers.
• Training and mentoring opportunities encouraging participation of students, postdoctoral researchers, and co-investigators from diverse backgrounds.
• Transdisciplinary collaborations that require unique expertise and/or solicit diverse perspectives to address research questions.
• Inclusion of community-based partners to ensure alignment of research goals and activities with community values.
When a PEDP is required, applications submitted without such a plan will be considered incomplete and will be withdrawn prior to peer review. Evaluation of the applicant’s PEDP will be made during the peer review stages as part of the scorable criteria and during programmatic reviews and will be used to inform funding decisions.
See these related resources for information about diversity and inclusion efforts around the NIH:
• Ending Structural Racism: The NIH UNITE Initiative
• NIH Office of Scientific Workforce Diversity
• Idea States
• Diversity in NIH Extramural Programs
HuBMAP PEDP: Frequently Asked Questions
I. General FAQs
1. What is a PEDP?
PEDP or “Plan for Enhancing Diverse Perspectives” strategies and relevant milestones should be integrated into the Research Plan section of the application. PEDP strategies aim to advance the scientific and technical merit of the proposed project through inclusivity. The PEDP strategies should also be summarized and submitted as a 1-page “Other Attachment” to be included in applications submitted in response to specified Research or Funding Opportunity Announcements. Please see the PEDP Overview and the Key Elements and Examples.
2. What does "diverse perspectives" mean for a research project? Broadly, diverse perspectives refer to the people WHO* do the research and the places WHERE** research is done, as well as WHO PARTICIPATES *** in the research as part of the study population.
*WHO: The inclusion and empowerment of investigators and trainees from a variety of backgrounds, including those traditionally underrepresented in the biomedical research workforce (see NOT-OD-20-031), and investigators from different scientific disciplines, at varying career stages, and with varied skills, experience, and expertise.
**WHERE: Participation of researchers from all relevant sectors, including diverse organizations and institutions (e.g., research intensive and research active, undergraduate, minority-serving, community-based etc.). Historically, largely well-resourced academic and research institutions have competed successfully for HuBMAP funding. The goal is to broaden the reach by supporting projects, partnerships, and collaborations at institutions and organizations that, to date, have not been part of HuBMAP Program-funded work. The expectation is that by broadening its support (e.g. geographically and/or to different institutions and organizations), the HuBMAP program will simultaneously advance the goals of the individual projects as well as the goals of the program.
***WHO PARTICIPATES: To realize the broadest benefits to human health impacting all segments of the population, The HuBMAP program is committed to promoting equity in research participation. To that end, maximum effort is encouraged to engage and recruit diverse participants for human studies. To make findings broadly relevant, it is expected that studies that use human tissues will collect and use specimens derived from varied ancestries. Any projects involving human participants or samples derived from humans should be collected in an ethically sound manner and consented appropriately. More information about human subjects can be found at Human Subjects Research - Home Page
3. Why is the PEDP included in HuBMAP Program grant applications?
It is widely accepted that diverse teams working together and capitalizing on innovative ideas and distinct perspectives outperform homogenous teams. Accordingly, the NIH’s commitment to diversity is well documented (NOT-OD-20-031). The inclusion of a PEDP represents explicit alignment of research activities, peer review, and research funding considerations with the HuBMAP Program’s commitment to advance the scientific and technical merit of HuBMAP Program research projects through expanded inclusivity.
4. What should be included in a PEDP?
Within the 1-page PEDP summary, applicant(s) are expected to show how enhancing diverse perspectives is supported throughout the application and how this strengthens the scientific and technical merit of the project (in terms of significance, investigator(s), innovation, approach, and environment), as appropriate. The PEDP will depend on the content and structure of the scientific aims, the expertise required, the environment, and the performance site(s). The PEDP strategies should include a timeline and milestones for relevant components that will be evaluated as part of the review. Within the research strategy, applicant(s) are expected to align their description with the strategies summarized in the PEDP. Please see the PEDP Key Elements and Examples below.
5. What guidance on the PEDP is available for applicants? For guidance and other materials please see the PEDP Overview and the Key Elements and Examples. Questions not covered in these FAQs can be directed to the HuBMAP mailbox.
Additional guidance and FAQs will be updated as needed.
1. Where in applications should the PEDP information be addressed?
The PEDP information should be included in the "Plan for Enhancing Diverse Perspectives" under “Other attachments” (see Section IV of FOA, 1-page limit) and where appropriate, within the research strategy section. The 1-page PEDP attachment should:
• include a summary of strategies of expanded inclusivity to advance the scientific and technical merit of the proposed project.
• outline how enhancing diverse perspectives is viewed and supported throughout the application.
• incorporate strategies relevant to each of the review criteria (significance, investigator(s), innovation, approach, and environment), as appropriate.
• include a timeline and milestones for relevant components that will be considered as part of the review.
Within the Research Strategy, applicant(s) should align their description with the PEDP strategies and milestones and are encouraged to refer to information included in the PEDP attachment. The content of the PEDP will depend on the content and structure of the scientific aims, the required expertise, the environment, and the performance site(s). Please see the PEDP Key Elements and Examples below.
2. Are there examples of the types of strategies that might be part of a PEDP?
The HuBMAP program anticipates that every PEDP will be unique and will depend on the content and structure of the scientific aims, the required expertise, the environment, and the performance site(s). Examples of strategies that advance inclusivity in research and may be part of a PEDP can include but are not limited to the list provided here.
3. Is there a PEDP template or example available?
No. A PEDP template or example is not available because the PEDP will depend on the content and structure of the scientific aims, required expertise, the environment, and performance site(s). Please see the PEDP Key Elements and Examples below.
4. Does a grant application need to include every strategy listed in the PEDP Key Elements and Examples? No. The details of the PEDP will depend on the content and structure of the scientific aims, the required expertise, the environment, and the performance site(s). Applicants are asked to explain how the proposed research project will benefit from the diverse perspectives described in the application. They are expected to provide a rationale for the inclusion of different PEDP strategies and how these strategies strengthen the research project.
5. Are there specific type(s) of diversity that are preferred?
No. HuBMAP encourages innovative approaches that support scientific excellence by fostering inclusivity and promoting culture change. The HuBMAP program has always placed strong emphasis on the inclusion of investigators representing diverse disciplines of science. The PEDP seeks to broaden this approach beyond scientific disciplines to include career stage, investigator background, partnerships, collaborations, etc. that advance the goals of the project. Please see the PEDP Key Elements and Examples below.
6. What makes a strong PEDP?
Reviewers will evaluate the PEDP based on the criteria specified in Section V of the FOA. Briefly, the PEDP should reflect careful consideration of how to maximize diverse perspectives within the research project and outline the benefits. It should also provide rationale for the selected types of PEDP strategies and include a timeline and milestones for relevant PEDP components.
7. Are foreign collaborations considered to enhance diverse perspectives?
While an emphasis on U.S.-based geographic diversity is encouraged, foreign collaborations may be considered to enhance geographic and regional diversity, if justified as described in III.5. Consistent with NIH policy, foreign components will be subject to additional review requirements (Please see NIH Grants Policy Statement Section 16).
8. If costs increase as a result of the PEDP, can funds be requested to support the PEDP?
Applicants may include a request for allowable costs associated with PEDP implementation (please see NIH Grants Policy Statement Section 7).
1. How will reviewers be instructed to evaluate the PEDP?
PEDP considerations will be included in each of the scored review criteria (Significance, Innovation, Investigators, Approach, and Environment). Reviewers are asked to consider the strengths and weaknesses associated with each of the review criteria and weigh them appropriately. Thus, the PEDP evaluation will contribute to the criterion scores and overall impact score of each application. It is expected that a PEDP judged by reviewers as insufficient, would result in poorer criterion score(s) and overall impact score.
2. What will happen to an application with its PEDP judged by reviewers as insufficient?
A PEDP judged by reviewers as insufficient may result in poorer criterion scores and overall impact score. The reviewers are instructed to evaluate all components of the application as reflected in Section V of the FOA or ROA. As such, peer reviewers will evaluate the PEDP as part of each of the scored review criteria, and in the overall impact score.
3. Is training on the PEDP available for reviewers?
Reviewers will be directed to the guidance materials available to applicants. In addition, review panels will be provided with opportunities to learn more about the PEDP ahead of any scheduled review meetings.
IV. Administrative Issues
1. Is a PEDP “Other Attachment” required?
Yes. Applications that fail to include the required PEDP “Other Attachment” will be considered incomplete and will be withdrawn prior to review.
2. Will the PEDP be considered in programmatic funding decisions?
Yes. The following will be considered in making programmatic 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, including the PEDP.
1. What post-award oversight of the PEDP will be expected?
As part of their required progress report, investigators will be asked for updates on the implementation of the PEDP in their annual NIH Research Performance Progress Report (RPPR) or Other Transaction Annual Reports. Investigators should describe progress in the PEDP based on the goals, timelines, and milestones outlined in the application and/or in response to the reviewers’ comments as well as on any additional elements recommended by the study section and/or program staff. If sufficient information is not provided in the progress report, program officials may request the additional information needed to assess satisfactory progress.
In cases where an investigator encounters challenges in meeting their PEDP objectives, Program Officers (POs) can request an interim progress report with clear explanation of the difficulties, as well as the actions taken to overcome them. In response, POs may suggest alternative approaches, request an interim progress report, or issue a no-cost extension, to delay the noncompeting renewal until the difficulties are resolved. Broadly speaking, failure to meet expectations agreed upon by the Recipient and the NIH/IC may result in Enforcement Actions as described in NIH Grants Policy Statement Section 8.5.2
PEDP Key Elements and Examples
A “Plan for Enhancing Diverse Perspectives” (PEDP) is a summary of strategies to advance the scientific and technical merit of the proposed project through inclusivity. Broadly, diverse perspectives refer to the people who do the research, the places where research is done, as well as the people who participate in the research as part of the study population. The PEDP is submitted as a 1-page “Other Attachment” to be included in grant applications submitted in response to specified Funding Opportunity Announcements. Within the Research Strategy, applicants should align their description with the PEDP strategies and specify milestones and are encouraged to refer to information included in the PEDP attachment. In the 1-page PEDP summary, applicants are expected to show how enhancing diverse perspectives is supported throughout the application and how this strengthens the scientific and technical merit of the project (in terms of significance, investigator(s), innovation, approach, and environment), as appropriate.
It is anticipated that every PEDP will be unique and will depend on the content and structure of the scientific aims, the required expertise, the environment, and the performance site(s). The HuBMAP Program encourages innovative and sustainable approaches that support scientific excellence by fostering inclusive environments and promoting culture change.
Key Elements to be included in a PEDP for a proposed research program:
• Summary of strategies (and their rationales) that advance the scientific and technical merit through expanded inclusivity
• Timeline and milestones for the PEDP
• Approaches to assessing progress towards meeting the PEDP defined goals
Examples of potential strategies that advance inclusivity in alignment with research goals can include, but are not limited to:
• Inclusion of personnel (MPIs, PIs, Co-Is, Consultants)
o from groups traditionally underrepresented in the biomedical, behavioral, and clinical research workforce (e.g. women, underrepresented racial and ethnic minorities, those with disabilities, and individuals from disadvantaged backgrounds).
o located within, or who have done training within, multiple geographic locations, especially those regions underrepresented in HuBMAP funding.
o representing different career stages.
o from different types of institutions and organizations (e.g. research intensive and research-active, undergraduate-focused, minority-serving, community-based, and industry).
o from varying scientific fields to contribute to transdisciplinary aspects of the proposed project (e. g. neuroscientists, computational biologists, engineering, mathematics, physicists, computer and data sciences, and bioethics).
• Training and mentoring opportunities to encourage participation of students, postdoctoral researchers, and co-investigators from diverse backgrounds (e.g., existing institution-based programs such as undergraduate research experience programs, or new individual opportunities for trainees, fellows, etc.).
• Activities to enhance recruitment of research participants from diverse groups, including those from under-represented backgrounds.
• Plans to use the project infrastructure (i.e., research and administrative structure) to support career-enhancing research opportunities for junior, early-, and mid-career researchers.
• Inclusion of community advisory boards or other relevant steering committees to inform research project design and/or dissemination of results.
• Publication plans that describe equitable processes to determine inclusive authorship and authorship order and ensure proper attribution. Opportunities promote visibility of junior faculty, post-docs, trainees, etc. by serving as first authors and/or presenting at national/international scientific meetings.
• Outreach to and recruitment of diverse trainees and investigators at regional and national scientific meetings.
• Partnerships with advocacy groups or professional societies to help recruit study participants for clinical research and/or to aid with dissemination of research results
. HuBMAP: Plan for Enhancing Diverse Perspectives (PEDP) HuBMAP: Plan for Enhancing Diverse Perspectives (PEDP)
This page last reviewed on January 28, 2022