Epigenomics

RFA-RM-08-017: Frequently Asked Questions

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1. How is this RFA related to the overall Roadmap Epigenomics Program?
2. What is meant by transformative research for the Epigenomics of Disease RFA?
3. What questions should I ask myself if I’m thinking about submitting an application?
4. Before I submit an application, should I contact NIH staff to determine whether any of the NIH Institutes may be interested in my project?
5. How does the content of an Epigenomics of Disease application differ from the content of a conventional R01 application?
6. How does the format of an Epigenomics of Disease application differ from the format of a conventional R01 application?
7. Do I need to include preliminary data in my Epigenomics of Disease application?
8. Should I include preliminary data, if I have any?
9. I am a new investigator. Can I apply for an Epigenomics of Disease award?
10. How can I explain what I want to do, if the research plan is limited to twelve pages and the approach section is limited to three pages?
11. I applied for another NIH “innovation” award. Can I submit the same project as an Epigenomics of Disease application?
12. Can I submit an Epigenomics of Disease application if I have a pending conventional R01 application that includes a similar aim?
13. Do I have to submit a letter of intent? What should be in it? How should I send it?
14. If I do not have room to include preliminary data, or to explain what I want to do in the experimental plan, can I put that information in an appendix, or submit it as an update?
15. Can I submit more than one application in response to this RFA?
16. Are there restrictions about particular model systems or cell types that may be proposed?
17. Are there any restrictions on proposals that involve human population studies?
18. Do I need to submit an informatics plan in my Epigenomics of Disease Application? What is the purpose?
19. Will the Epigenomics of Human Disease projects be integrated with other initiatives funded under the Roadmap Epigenomics Program, such as the Reference Epigenomic Mapping Centers (REMCs) and Epigenomics Data Coordinating Center (EDACC)? In what ways?
20. Why are data released so rapidly?
21. How would collaborations with Reference Epigenomics Mapping Center RFA investigators work in terms of budget?
22. What is the purpose of including a timeline in my Epigenomics of Disease application? How will my progress be evaluated after award?
23. Is there a minimum percent effort required?
24. How will Epigenomics of Disease applications be reviewed?
25. I want to know when my application will be reviewed. Who should I contact?
26. Will I have an opportunity to submit an update, before my application is reviewed?
27. Will the Epigenomics of Disease applications be reviewed by experts in my field?
28. After my application is reviewed, will I receive a summary statement?
29. If my Epigenomics of Disease application is not funded, will I have an opportunity to revise and resubmit it?
30. How many meetings will project PIs/co-PIs be required to attend each year?
31. Will these RFAs be reissued?
32. I am an NIH intramural investigator. Am I eligible to apply?
33. I am not a US citizen. Am I eligible to apply?
34. My institution is not in the US. Am I eligible to apply?
35. The budget for my application will be greater than $500,000 in direct costs. Do I require permission in advance?
36. What if I still have questions after reading the FAQs?

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1. How is this RFA related to the overall Roadmap Epigenomics Program?
The four Roadmap Epigenomics Program RFAs released in 2008 – Epigenomics Mapping Centers, Epigenomics Data Coordinating Center, Technology Development RFAs, and Discovery RFAs – provide the fundamental scientific data and tools to accelerate research aimed at understanding the epigenetic contributions to human disease. The purpose of this RFA on the Epigenomics of Disease is to begin to capitalize on these findings and support novel research that transforms our understanding of the epigenetic structure and mechanisms underlying specific diseases or disease-related processes, states, or conditions. Applicants should conduct global (epigenome-wide) mapping in diseased, aged, or environmentally compromised human cells or tissues, and in comparative “healthy” control cells or tissues. Applicants may also conduct follow-up targeted (epigenetic) analyses to begin to elucidate mechanisms of disease etiology. Follow-up studies, if proposed, should be based on results from the mapping analysis.

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2. What is meant by transformative research for the Epigenomics of Disease RFA?
Transformative is defined in this RFA as having a substantial impact on our understanding of the etiology, progression, or severity of a specific disease, or a disease-related process or condition, by creating a new paradigm or challenging an existing one. To determine whether your project has the potential to be transformative, consider the current state of the field of disease research which you are addressing. For example, knowledge of the epigenetics/epigenomics of cancer is much better developed than for most other diseases. In contrast, little is known about the epigenomic contributions to abnormal child development, aging, brain and psychiatric disorders, metabolic dysregulation, cardiovascular and respiratory disorders. Thus, a study that may transform the understanding of these diseases may not have the same impact in cancer research. The potential impact of the proposed research must be substantial with regard to the scientific community affected and state of understanding of the particular disease under study.

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3. What questions should I ask myself if I’m thinking about submitting an application?
Is what I want to do novel and exciting? Does the work have the potential to have a significant impact? Is what I want to do focused on testing a novel hypothesis, or solving a difficult problem?

If the focus is testing a hypothesis, would the results significantly alter the accepted model, and not just provide a minor variation or add incremental details? Would validating my hypothesis have a profound effect on the field? Based on the methodology that I am proposing and the effort that I would put into this project, is it likely that I will be able to conclusively validate or disprove my hypothesis by the end of the funding period?

If the focus is solving a technical problem, is my methodology significantly different from what has been attempted previously? Is the problem a major impediment to progress in the field? If I do solve the problem, will it have a profound effect on a lot of people?

Is my project likely to be of programmatic interest to one or more of the NIH institutes? Which Institutes would likely have an interest in this research?

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4. Before I submit an application, should I contact NIH staff to determine whether any of the NIH Institutes may be interested in my project?
The NIH strongly encourages applicants to contact Program staff prior to preparing an application in response to the RFA. All NIH Institutes and Centers participate in Roadmap programs, and will consider applications under this RFA. However, applications supported under this RFA will receive co-funding by a specific NIH Institute or Center and the Roadmap Common Fund. If you are an investigator planning to submit an application under the Epigenomics of Disease RFA, it is important that you contact program staff (see weblink in Section VII of the RFA and http://nihroadmap.nih.gov/epigenomics/grants.asp for list of program contacts) to determine if your project is likely to be responsive to the RFA and of high programmatic interest to one or more NIH Institutes or Centers. You should do this early in the preparation process. If you do submit an application under the Epigenomics of Disease RFA and it is not considered of high programmatic interest to any of the Institutes or Centers, your application is unlikely to be funded. If you are an institutional administrator, you may want to contact the financial/grants management contact listed in that section of the funding opportunity announcement.

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5. How does the content of an Epigenomics of Disease application differ from the content of a conventional R01 application? (See RFA-RM-08-017 for details)

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6. How does the format of an Epigenomics of Disease application differ from the format of a conventional R01 application?

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7. Do I need to include preliminary data in my Epigenomics of Disease application?
Preliminary data are not required, but may be included in your Epigenomics of Disease application. Reviewers will be focusing on the conceptual framework and the likely impact of the project as well as the feasibility of accomplishing the aims. Reviewers and NIH staff will evaluate your preliminary data (if any), your track record, and the logic of the experimental plan to determine the likelihood that what you are proposing to do will succeed. If you have no preliminary data, be sure that the logic of the experimental plan is sufficiently compelling to convince reviewers and staff of its feasibility.

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8. Should I include preliminary data, if I have any?
Yes, if your preliminary data will help you convince reviewers and staff of the feasibility. However, be aware that there is no Preliminary Studies section in an Epigenomics of Disease application. If you have pilot data, it should be VERY briefly summarized in the approach section of the research plan, which is limited to three pages. Also keep in mind that if your preliminary data are too extensive, it may be an indication that what your project is too “mature” for this RFA — or that what you are proposing to do is an extension of what you have already been doing, not something new, or will only make an incremental gain in knowledge about the disease you are studying.

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9. I am a new investigator. Can I apply for an Epigenomics of Disease award?
Yes. The NIH encourages applications from investigators at all levels of experience, including new investigators. Emphasis will be placed on the transformative nature of the ideas proposed and potential impact of the project. Reviewers will also evaluate your preliminary data (if any), your track record, and the feasibility of the experimental plan

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10. How can I explain what I want to do, if the research plan is limited to twelve pages and the approach section is limited to three pages?
It is best to forget everything that you have ever learned about what research plans should look like, especially for the R01 application. The Epigenomics of Disease instructions prompt you to answer specific questions. In the approach section, briefly describe what you want to do. You will not have room to describe every experiment in detail, so it is best to not try. Applicants are required to keep strictly to this page limit, and applications that do not conform will be returned without review.

Also, in your biosketch, be sure to include citations to publications documenting innovative and significant discoveries in the past, if you have any, no matter what field you were in when you made those discoveries.

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11. I applied for another NIH “innovation” award. Can I submit the same project as an Epigenomics of Disease application?
No, if your other application is pending review. NIH policy does not allow multiple submissions of essentially the same project. Therefore, funding for the same project may not be sought through multiple submissions to the Epigenomics of Disease initiative and any other award program that targets unusually innovative investigators or research (e.g., Pioneer Award, Young Innovator Award, EUREKA Award, Avant -Garde Award).

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12. Can I submit an Epigenomics of Disease application if I have a pending conventional R01 application that includes a similar aim?
Yes, since the scope, application format, and review criteria are very different for the Epigenomics of Disease and conventional R01 awards, such applications would not be considered multiple submissions for the same project. If both applications were funded, the overlap would have to be addressed, presumably by removing the overlapping aim from the non-Epigenomics award, and award levels adjusted accordingly.

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13. Do I have to submit a letter of intent? What should be in it? How should I send it?
We strongly recommend that you submit a letter of intent. It should include the information requested in the Epigenomics of Disease funding opportunity announcement, and where you recommend your application be assigned. If you have discussed the possibility of submitting an Epigenomics of Disease application with program staff at that institute, include the staff member’s name in your letter of intent.. In addition, we strongly recommend that you also include a brief description of your research project. The research description will help us determine whether your project is likely to be appropriate for the Epigenomics of Disease initiative and be of programmatic interest to one or more of the NIH institutes or centers.

Letters of intent do not need to be countersigned by institutional officials. They can be e-mailed, faxed, or sent as hard copy (e-mail is preferred). There is no need to send hard copy of a letter that has already been sent via e-mail or fax. All letters of intent should be sent to Dr. Brenda Weis, even if the application will be assigned to an institute other than NIAAA. Her e-mail address is weis@mail.nih.gov.

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14. If I do not have room to include preliminary data, or to explain what I want to do in the experimental plan, can I put that information in an appendix, or submit it as an update?
No. Appendices and updates are not allowed.

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15. Can I submit more than one application in response to this RFA?
Yes, as long as they are scientifically distinct.

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16. Are there restrictions about particular model systems or cell types that may be proposed?
Yes, The Epigenomics of Disease RFA is intended to advance our understanding of human disease etiology, and as such, applicants are required to work in human cells or tissues. However, we recognize that many human diseases, such as brain disorders, may be difficult or even impossible to study on a global scale in human systems because appropriate human cells or tissue are not available. In these instances, applicants may propose conducting the global epigenome-wide analysis in a mammalian animal model; however, they must provide a compelling justification why an equivalent human model is not available or appropriate for the proposed project. Determining whether it is appropriate for you to propose a project using a mammalian animal model, in lieu of using human cells or tissues, is something you should discuss with IC program staff, prior to submitting your application, as part of determining programmatic relevance for your project (as recommended in the RFA).

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17. Are there any restrictions on proposals that involve human population studies?
Yes. The RFA requires applicants to propose projects involving human cells and tissues, and applicants may propose to investigate epigenomes in existing (archived) or new human biospecimens that are collected as part of other ongoing funded human clinical or epidemiological studies of human disease. Proposals seeking to initiate new human epidemiological or clinical studies for the purpose of collecting biospecimens for epigenomic analysis are outside the scope of this funding announcement. However, the addition of an epigenome-wide mapping component, funded through this RFA, to an ongoing clinical or epidemiological study of human disease may be appropriate.

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18. Do I need to submit an informatics plan in my Epigenomics of Disease Application? What is the purpose?
Yes. The informatics plan will describe the process the applicant envisions for generating and formatting data in the “standard” format prescribed by the REMS and EDACC, and transferring the data to the National Center for Biotechnology Information (NCBI) for public release. The specifics of the informatics plan will vary depending on whether the applicant proposes to engage the Epigenomics Data Coordinating Center (EDACC) to assist with data formatting and transfer. Either way, the Epigenomics of Disease applications must identify key personnel with enough informatics expertise and capacity to communicate and work with the NCBI or EDACC to facilitate data formatting and ultimate transfer to the NCBI.

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19. Will the Epigenomics of Human Disease projects be integrated with other initiatives funded under the Roadmap Epigenomics Program, such as the Reference Epigenomic Mapping Centers (REMCs) and Epigenomics Data Coordinating Center (EDACC)? In what ways?
All initiatives of the Roadmap Epigenomics Program will be highly integrated. For example, the Reference Epigenomics Mapping Centers (REMCs) will focus on the global (epigenome-wide) mapping of normal cells and tissues. The Epigenomics of Disease RFA, by contrast, will focus on developing global (epigenome-wide) maps in diseased, aged, or environmentally compromised cells and tissues. The Epigenomics of Disease applicants are encouraged to form collaborative arrangements with the Reference Epigenome Mapping Centers (REMCs), to develop specific “reference” epigenome mapping data for their disease of interest, or to conduct epigenome-wide analyses of biospecimens.

The National Center for Biotechnology Information (NCBI) is creating a publicly accessible database for the Roadmap Epigenomics Program, and all data will ultimately be submitted to them. Epigenomics of Disease applicants should describe, in their informatics plan, how they envision the data they generate will be sent to the NCBI. Applicants may choose to utilize the Epigenomics Data Coordinating Center (EDACC) to assist with data formatting and transfer to NCBI.

Applicants who are considering establishing collaborative arrangements with the REMCs or EDACC, to assist with activities such as epigenome-wide analyses of biospecimens or data formatting, are encouraged to contact the program leads for these RFAs (listed below) to discuss timelines and logistics. Given the proposed timeline for selecting and awarding the REMCs and EDACC, there will be obvious time constraints for establishing formal collaborations with the REMCs or EDACC prior to the application due date for this RFA. It may be possible for applicants to discuss such arrangements with the REMC and EDACC awardees prior to submitting an application to this RFA, and then including a letter of intent to collaborate from the REMC or EDACC in their application. Alternatively, applicants may indicate their intent to establish a collaboration with an REMC or EDACC, to conduct specific activities described in their project, and then establish the formal arrangements after awards to this RFA are made.

RFA Program Leads for Roadmap Epigenomics Program:

• RFA-RM-07-013 - Reference Epigenome Mapping Centers (REMCs): Fred Tyson (NIEHS), Christine Colvis (NIDA)
• RFA-RM-07-014 - Epigenomics Data Analysis and Coordinating Center: Joni Rutter (NIDA), Kim McAllister (NIEHS)
• RFA-RM-07-015/016 - Discovery of Novel Epigenetic Marks in Mammalian Cells: Phil Smith and Olivier Blondel (NIDDK)
• RFA-RM-07-011/012 - Technology Development in Epigenetics: John Satterlee (NIDA), David Balshaw (NIEHS)

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20. Why are data released so rapidly?
The disease-related epigenome maps generated through this initiative are considered a community resource. As such, the data generated by the funded investigators must be made freely available as rapidly as possible, i.e. as soon as the data are verified. The specific data release policy for the Roadmap Epigenomics program will be established with the NIH and the participating funded investigators. Although mapping data are released, once verified, individual investigators are encouraged to publish using data gathered as part of this effort.

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21. How would collaborations with Reference Epigenomics Mapping Center RFA investigators work in terms of budget?
Epigenomics of Disease applicants are encouraged to form collaborative arrangements with the REMCs to generate “reference” epigenome-wide maps in normal “healthy” cells and tissues that may serve as comparative states for the disease under study. They may also engage in collaborative activities with the EDACC to assist with data formatting and transfer to NCBI. Any collaborative arrangements are likely to be subject to subcontract arrangements. Additional questions in this area should be directed to program and grants management staff listed in the specific Roadmap Epigenomics Program RFAs.

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22. What is the purpose of including a timeline in my Epigenomics of Disease application? How will my progress be evaluated after award?
Reviewers and program staff will utilize the timeline included in the application to evaluate the likelihood that the project will be completed during the funding period and to track progress during the award period.An external scientific panel will be assembled at the yearly all-hands meeting to evaluate the progress of the overall Roadmap Epigenomics Program and make recommendations for improvements.

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23. Is there a minimum percent effort required?
Although the instructions do not specify a minimum percent effort, a low percent effort may raise concerns about whether you or other essential personnel are devoting enough time and attention to the project to complete it in the time allotted.

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24. How will Epigenomics of Disease applications be reviewed?
After they are received, applications will be evaluated by NIH review and program staff for responsiveness to the RFA and compliance with the instructions as well as for relevance to the missions of NIH institutes and Centers. If an application is not in the specified format outlined in the Epigenomics of Disease RFA, includes prohibited information, or the project is not germane to the mission of any of the NIH Institutes or Centers, the application will be administratively withdrawn before review. Note that your application may be withdrawn because of lack of NIH Institute relevance, even if staff from one of the Institutes or Centers expressed tentative interest in the project before you submitted your application. If this situation occurs, it is because staff based their earlier opinion on the information that you supplied before submission, which did not accurately reflect the content of the application.

Applications will be reviewed in special study sections with other Epigenomics of Disease applications, not with conventional R01 applications. Reviewers will focus on innovation and the potential to be transformative and, if successful, whether the research will have a profound impact on our understanding of human disease processes. Risk will not be a factor in the evaluation, unless the reviewers are convinced that there are substantial flaws and there is little likelihood of success.

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25. I want to know when my application will be reviewed. Who should I contact?
If you have any questions about review, contact the scientific review administrator/officer (SRA or SRO) whose name appears on your eCommons screen.

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26. Will I have an opportunity to submit an update, before my application is reviewed?
No. Everything that you want reviewers to see must be included in the application.

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27. Will the Epigenomics of Disease applications be reviewed by experts in my field?
Every effort will be made to ensure appropriate reviewer expertise, however, it is likely that not all of the reviewers assigned to your application will be considered experts in your specific field. We anticipate that investigators will submit Epigenomics of Disease applications on a wide range of topics, representing the breadth of the participating NIH institutes’ interests. The reviewers will have general expertise that is relevant to your application, but the odds are low that all of the people who review your application will be experts in your field. It is extremely important to keep this in mind when you are writing your application. When you are describing what you want to do, avoid jargon, and use language that scientists in other fields can understand. You will also have to convince scientists in other fields that what you are proposing to do is exciting and exceptionally innovative, and that the proposed research will have a profound impact on a large number of people.

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28. After my application is reviewed, will I receive a summary statement?
You will receive information about the outcome of the review, but it will be much less detailed than a typical summary statement for a conventional R01 application.

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29. If my Epigenomics of Disease application is not funded, will I have an opportunity to revise and resubmit it?
No. However, you may be able to incorporate some elements of your Epigenomics of Disease application into a conventional R01 application. Likewise, if no NIH Institute or Center is interested in your project, or the Epigenomics of Disease initiative is not appropriate for what you want to do, ask the program director with whom you have discussed the possibility of submitting an Epigenomics of Disease application whether there are other NIH institutes or other funding opportunities that would be more appropriate. There is also valuable information about funding opportunities on each NIH institute’s Web site, and in the NIH Guide for Grants and Contracts.

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30. How many meetings will project PIs/co-PIs be required to attend each year?
Project PIs/co-PIs should budget for two face-to-face meetings each year. One will be an all-hands meeting for the entire cadre of Roadmap Epigenomic Program investigators.

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31. Will these RFAs be reissued?
We hope to reissue this RFA in the future, contingent on both the success of the program and the availability of funds.

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32. I am an NIH intramural investigator. Am I eligible to apply?
Yes. Please see special application instructions under Section IV.2. “Applications involving federal agencies” of the RFA.

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33. I am not a US citizen. Am I eligible to apply?
Yes.

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34. My institution is not in the US. Am I eligible to apply?
Qualified investigators at non-US (foreign) institutions are eligible to apply. As with other funding mechanisms, applications having substantial foreign involvement of non-US institutions should describe how the project presents special opportunities for furthering research programs through the use of unusual talent, resources, populations, or environmental conditions in other countries that are not readily available in the United States or that augment existing U.S. resources. Grants to non-domestic entities must comply with all policies as described in the RFA and in the NIH Grants Policy Statement (http://grants.nih.gov/grants/policy/nihgps_2003/).

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35. The budget for my application will be greater than $500,000 in direct costs. Do I require permission in advance?
No, however we strongly recommend that you contact program staff in advance to discuss your plans as well as the potential pitfalls of such a proposal. You should try to determine if the aims of your application are both fully responsive to the RFA and of significant programmatic interest. The budget should be commensurate with the research proposed.

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36. What if I still have questions after reading the FAQs?
You may call or email the Scientific/Research Contacts listed under Agency Contacts in Section VII in the specific RFA of interest.

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