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Frequently Asked Questions

This FAQs page addresses the questions NIH has received in response to RFA-RM-12-021, Evaluation of Multi ‘Omic Data in Understanding the Human Microbiome’s Role in Health and Disease (U54) and will be updated regularly. Send questions to lita.proctor@nih.gov An Applicant Information Webinar will be held January 8, 2013. Please see NIH Guide Notice for more information.

 

General Questions

  1. Is the competition limited to current Human Microbiome Project grantees?
  2. Are foreign institutions eligible?
  3. How are applications submitted?
  4. What are the page limits for specific sections of the application?
  5. When are letters of intent due?
  6. Can an institution submit more than one application?
  7. Can an investigator be listed on more than one application?
  8. Can an R01 application be converted into an application for this FOA?
  9. My institution has been affected by Super Storm Sandy. Can I submit my application late?
  10. Will there be other opportunities to ask questions about this FOA?
  11. What is a cooperative agreement?
  12. Can the applicants use electronic submission for the U54 grant applications?
  13. If my institution is not yet registered in the DUNS/System for Award (SAM) entities, will there be time to complete this before the receipt date?
  14. If the samples I am proposing to use are de-identified, is the study considered to be human subjects? Do I need to include a human subjects section in the application?
  15. How are applications submitted?

Questions specific to the requirements of this FOA

  1. Can cohorts be obtained through new recruitment of donors?
  2. Are the data release guidelines flexible?
  3. Will there be a distinct Data Coordination Center for this program?
  4. Can applicants propose novel technologies?
  5. How much analysis of the dataset can be included in the application?
  6. Can an application include more than one cohort (i.e., health or disease condition)?
  7. How should the proof of principle tests of the integrated datasets be conducted?
  8. How broad will the consents for the cohort studies need to be? Newly Updated!
  9. How do I organize and select the HMP Center structure?
  10. Will applications from previous HMP investigators be evaluated differently from those applications submitted by investigators without prior HMP support?
  11. What is the minimum number of ‘omics data types which should be collected from the proposed microbiome samples?
  12. What is a community resource project and how is this concept being applied in the HMP program and specifically for this FOA?
  13. What is the goal of the proof-of-principle test for the combined dataset?
  14. What is the purpose of the milestones and will the grantee be held to the milestones in the application?
  15. Can case/control studies be proposed in this FOA?
  16. Will only disease related cohort studies be considered in this FOA or will applications which study disease prevention be considered?
  17. No animal models are allowed in the application. Am I allowed to include preliminary data from animal models?
  18. The data release and sharing is discussed both as part of the Research Strategy and the Resource Sharing Plan sections. Where should I address this in my application?

 

Is the competition limited to current Human Microbiome Project grantees?

No. Participation in the first phase of the NIH Human Microbiome Project is not a requirement for eligibility in this FOA.

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Are foreign institutions eligible?

No. Applications from foreign institutions are not eligible, but applications from US-based institutions can contain foreign components (see the NIH GPS for definitions of these terms).

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How are applications submitted?

These applications should be submitted in paper form. Electronic submission is not available for this RFA.

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What are the page limits for specific sections of the application?

All page limitations described in the PHS 398 Application Guide and the Table of Page Limits must be followed, with the only exception that the Research Strategy is limited to 30 pages. Please also see Section IV. Application and Submission Information of the FOA for specific information on page limits.

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When are letters of intent due?

The letter of intent due date is January 8, 2013 but may be sent any time before or after that date.

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Can an institution submit more than one application?

Yes. Applicant organizations may submit more than one application, provided that each application is scientifically distinct.

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Can an investigator be listed on more than one application?

Yes. An individual investigator can be listed as key personnel on as many applications as s/he wants, provided that each application is scientifically distinct.

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Can an R01 application be converted into an application for this FOA?

If the RO1 is new or revised, it could be converted to a U54 by including all of the requirements of the FOA. The main difference from the RO1 is that the U54 is a mechanism for a cooperative agreement in which NIH program staff have substantial involvement in the research. The applicant is advised to review the requirements of the FOA and evaluate whether these requirements have been met in their current R01 application.

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My institution has been affected by Super Storm Sandy. Can I submit my application late?

NIH has issued Guide Notices on this topic NOT-OD-13-006 and additional Notices may be issued in the future. Applicants should closely follow the NIH Guide Notices on this topic.

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Will there be other opportunities to ask questions about this FOA?

NIH staff will update this FAQs site with answers to questions we receive about the FOA. In addition, NIH will hold an Applicant Information Webinar on January 8, 2013 at 2 PM (Eastern) for prospective applicants. The answers to questions posed during the webinar will also be posted on the FAQs page and the webinar slides will be posted. A Notice will be published in the NIH Guide with instructions on how to participate in this webinar.

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What is a cooperative agreement?

A cooperative agreement is a support mechanism developed by NIH and used when there will be substantial Federal scientific or programmatic involvement. Substantial involvement means that, after award, NIH staff will assist, guide, coordinate, or participate in project activities.

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Can the applicants use electronic submission for the U54 grant applications?

No, these U54 applications must be submitted on paper. Therefore, deadline for receipt of these paper applications is 5 PM (eastern) February 8, 2013. No extensions to the deadline will be given.

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If my institution is not yet registered in the DUNS/System for Award (SAM) entities, will there be time to complete this before the receipt date?

This process usually takes at least a month, so it is unlikely you will be fully registered by the receipt date (http://grants.nih.gov/grants/electronicreceipt/preparing_grantsgov_reg.htm). Incomplete DUNS/SAM registration is not considered a valid reason for the NIH to accept a late application.

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If the samples I am proposing to use are de-identified, is the study considered to be human subjects? Do I need to include a human subjects section in the application?
Even if the samples are de-identified, you must include a human subjects in the application. To include information on the de-identification process, confidentiality, and access to the key that deciphers any de-identifying codes, see: http://grants.nih.gov/grants/policy/hs/ and the human subjects section of the PHS398 instructions.

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How are applications submitted?

These applications should be submitted in paper form. Electronic submission is not available for this RFA. The applications are must be received (not sent or postmarked) by 5pm Eastern Time. There are no exceptions and applicants are not eligible for continuous submission.

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Can cohorts be obtained through new recruitment of donors?

Yes. Applicants must describe an existing or readily accessible set or collection of donors/samples from a human cohort study. Because of the 3-year period of this initiative, utilization of an existing broadly consented cohort which allows for broad sharing of the microbiome and host data is strongly encouraged. Recruitment of new patient samples is allowed, as long as the applicant can describe a credible timeline for the project which meets the objectives of the FOA within the 3-year funding period.

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Are the data release guidelines flexible?

The HMP strongly endorses rapid release of HMP-related data and materials. The quality of the data release plan will be a criterion in the review of the application. NIH staff will also evaluate the Data Sharing and Release Plans and negotiate details of release of data and materials prior to making awards.

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Will there be a distinct Data Coordination Center for this program?

No.

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Can applicants propose novel technologies?

It is not a priority for this FOA for applicants to propose novel or experimental technologies in the application as there is little or no scale up time and the applicants must be able to generate the proposed integrated dataset within 3 years.

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How much analysis of the dataset can be included in the application?

The primary objective of the FOA is to produce an integrated dataset of multiple microbiome properties and relevant host data. The applicant will have to demonstrate in the application that he/she can meet this objective within the three years of the program before planning to conduct an analysis of the integrated dataset.

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Can an application include more than one cohort (i.e., health or disease condition)?

Yes. The choice of one or more health or disease condition(s) and cohort(s) is up to the applicant. However, the choices of cohort and condition must be based on addressing the main requirements of the FOA. Please refer to the Rationale section under Research Strategy for further information on the criteria for selection of cohort and health or disease condition.

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How should the proof of principle tests of the integrated datasets be conducted?

The goal of the proof of principle tests is to evaluate whether the integrated datasets can be queried by the broader community. The applicants can choose any approach for carrying out the proof of principle tests as long as the approach includes input and feedback from the broader research community.

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How broad will the consents for the cohort studies need to be?

In addition to reviewing the Human Subjects section under the Research Plan in the FOA for information about consents for the cohort studies, prospective applicants are strongly encouraged to review the Schloissnig et al. 2013 study here and the Gymrek et al. 2013 study here. Findings from these two recent studies suggest that microbiome sequence information and human sequence information may be identifiable to the individual. This potential for risk should be considered in the development of consents for this FOA.

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How do I organize and select the HMP Center structure?

The applicant can select any type of Center structure that will best address the goals of the FOA. Regardless of the proposed structure, the applicant must present a clear organization of the different Components and a rationale for this structure. There should also be inclusion of clear governance and management strategies. The Center may include members from more than one institution. Please see Section IV. Application and Submission Information of the FOA for specific information on application organization.

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Will applications from previous HMP investigators be evaluated differently from those applications submitted by investigators without prior HMP support?

No. All applications will be evaluated with the same criteria by the review panel and no distinction will be made between those applications from previous HMP investigators and those submitted from other investigators.

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What is the minimum number of ‘omics data types which should be collected from the proposed microbiome samples?

As noted under 'Purpose' in the FOA, at a minimum, taxonomic data should be collected from the microbiome samples and at least 3 of the other ‘omics data types from the microbiome such as (but not limited to) metagenomics, metatranscriptomics, metaproteomics, and metabolomics.

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What is a community resource project and how is this concept being applied in the HMP program and specifically for this FOA?

A community resource project is a research activity which results in rapid and broad data and research resource sharing in a user-friendly, accessible format with the larger research community. The HMP program builds community resources by insuring that 1) the subject consents permit broad data sharing, 2) the data are deposited in public or easily accessible databases and 3) a clear procedure is available for the data, even if deposited in controlled access databases, to be accessible to qualified researchers. In addition and more specifically to this FOA, a community resource will also be created by insuring that 1) the multiple data types generated from the microbiome and the cohort are integrated into one combined dataset and 2) proof-of-principle tests of the combined dataset will verify its usability by the larger research community.

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What is the goal of the proof-of-principle test for the combined dataset?

As the combined dataset is intended as a major community resource for the broader research community, the proof-of-principle tests are intended to be an evaluation of the usability of the combined dataset. Factors which can go into the evaluation of the usability of the dataset include but are not limited to: 1) how accessible the combined dataset is, 2) if stored in different databases, how easily can the community locate the different data types which make up the dataset and 3) whether the dataset can be easily queried by interested users outside the research consortium.

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What is the purpose of the milestones and will the grantee be held to the milestones in the application?

The milestones in the application serve two purposes. They indicate to NIH program staff and to the reviewers how well organized the proposed plan is for completing the objectives of the FOA. They will also serve as guides towards progress for NIH program staff and will be used as a tool for evaluating progress during the grant project period. However, milestones for the project will be renegotiated with the grantee before the award.

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Can case/control studies be proposed in this FOA?

Yes

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Will only disease related cohort studies be considered in this FOA or will applications which study disease prevention be considered?

All applications will be considered in this FOA as long as they meet the requirements of the FOA. There is no specific focus in disease or on a specific disease or body site in this FOA.

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No animal models are allowed in the application. Am I allowed to include preliminary data from animal models?

Yes, preliminary data from animal models is allowed. However, the proposed microbiome data to be collected in the application must be from a human body site(s), it cannot be from animal models.

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The data release and sharing is discussed both as part of the Research Strategy and the Resource Sharing Plan sections. Where should I address this in my application?

The basic outline and milestones of data release should be covered in the Research Strategy. The quality of the data release plan is a criterion that influences the Overall Impact Score of the application. Include any information that is necessary for reviewers to evaluate the quality of the data release plan. The details should be addressed in the Resource Sharing Plan. These details are not part of the Overall Impact Score, although they are reviewed by the reviewers and Program Staff before awards are made. It is important to remember that the Resource Sharing Plan should also address the sharing of resources such as clones and organisms.

 

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