Frequently Asked Questions about ENCODE RFAs

RFA-HG-16-002, RFA-HG-16-003, RFA-HG-16-004, RFA-HG-16-005, RFA-HG-16-006

General Questions
RFA-HG-16-002 Mapping
RFA-HG-16-003 Characterization
RFA-HG-16-004 Computational
RFA-HG-16-005 Data Coordinating Center
RFA-HG-16-006 Data Analysis Center

General Questions

Can I apply to any of these RFAs if I have not previously been involved in ENCODE?

Yes. All RFAs are open competitions and NHGRI is particularly interested in bringing new expertise and ideas to the ENCODE Project.

Can I apply to more than one RFA?

Yes. Applicants are free to apply to multiple RFAs. However, to encourage participation from a broad representation of the research community, when making funding decisions, NHGRI intends to consider whether an applicant will be funded as a PD/PI through other ENCODE RFAs and may choose to limit awards from multiple RFAs. Funding will be considered in the context of the all of the Selection Criteria, including merit as determined by peer review.

How does a UM1 application compare to a U54 application?

Like a U54, a UM1 receives one overall score, but unlike a U54, a UM1 allows for multiple Research Strategy Subsections.

May an application submitted from a domestic institution include a subcontract to a PI at a foreign institution?

Yes, for all 5 ENCODE RFAs.

Are the funds available listed in each RFA total or direct costs?

These are all total costs.

RFA-HG-16-002 Mapping

Experimental Assays:

How many different assays can I propose?

To encourage highly-focused research projects and streamline data management, applicants are strongly encouraged to propose the use of only one biochemical assay (e.g., ChIP-seq, RNA-seq, and variations thereof). An additional 1-2 assay(s) will be allowed; however if more than one assay is being proposed, applicants should provide a justification for how centralizing data production within one group, compared with data generation by other groups within the consortium, will result in production efficiencies or other synergistic benefits.

Can I propose to study sequence-specific transcription factors and/or RNA binding proteins in a wide range of cells?

No. The RFA calls for mapping binding sites for factor that have not previously been studied in ENCODE only in a small (2-5) number of cell types/tissues. Both the specific biological samples proposed as well as the study of more than two samples should be well-justified in terms of identifying binding motifs.

Is the study of chromatin remodelers limited to only tagged factors?

No, factor specific-antibodies are permitted for mapping of chromatin remodelers as well as histone modifications.

Can I propose to use factor-specific antibodies as affinity reagents to map binding sites of sequence-specific transcription factors or RNA binding proteins?

In order to avoid the need for costly and limiting factor-specific affinity reagents for ChIP-seq, CLIP-seq, RIP-seq or related assays, the only affinity-based projects being encouraged are those using epitope-tagged factors using standard affinity reagents against those tags. Applicants who wish to propose the use of factor-specific antibodies, despite not being encouraged, must provide a strong justification that addresses the above concerns. Alternative, non-affinity-based assays may also be considered if their ability to map factor binding sites genome wide at high specificity and sensitivity can be demonstrated.

What scale is sought for studying sequence-specific transcription factors and/or RNA binding proteins?

Applicants should propose to maximize the number of unique sequence-specific transcription factors and/or RNA binding proteins studied to the extent technically feasible.

I don't see the functional element(s) I'd like to propose listed in the RFA. Can I propose something not specifically mentioned in the RFA?

Applicants proposing to discover elements that were not listed among NHGRI's highest priorities in the Research Objectives should justify their importance to the community. At least two specific questions must be addressed: acknowledging that biochemical activities are often a proxy for function, what is the evidence that the proposed biological activity is associated with actual biological function, for example in gene regulation? Second, how will the proposed work scale to be able to assay the biochemical activity, with high specificity and sensitivity, and cost-effectively, over the entire genome in multiple cell types? Applicants are strongly encouraged to contact NHGRI to discuss such a proposal.

May I include in my application plans for technology development?

Incremental technology improvements will play an important role in increasing the efficiency and quality and decreasing the cost of identifying candidate functional elements. NHGRI encourages applicants to include plans for such technology development activities in their applications; however, these should be focused exclusively on the assays proposed for data generation. The plans for technology improvement should be well described and the cost of the proposed technology development should be justified in terms of resulting reduction in production costs and/or increased data quality. Projects requiring substantial technology development to achieve production of high-quality high-throughput data will not be considered responsive to this RFA.

Can I propose assays that validate or characterize the candidate functional elements that are identified by other components of my project?

No, validation or characterization of candidate functional elements is outside the scope of this RFA. Proposed assays are expected to have already been demonstrated to generate data that have been mechanistically associated with gene regulatory activities. Applicants wishing to conduct such experiments should consider applying to RFA-HG-16-003.

Biological Samples:

Must a proposal for a production-level assay necessarily be coupled to a source of biological samples? Is sample sharing with the consortium required?

Yes to both questions. All applications submitted in response to this RFA must propose specific biological samples to be studied and they should be justified in terms of their potential for new discovery. To the extent possible, all groups funded through this initiative will conduct experiments on biological samples that will be used in common by all the Mapping Centers. Therefore, all Mapping Centers are expected to acquire samples in sufficient quantities to be assayed by all of the other groups funded through this initiative so that the range of assays can be applied to all samples, and are expected to be willing and able to share with other groups. Once awards are made, the funded Mapping Centers will work together and with NHGRI, in consultation with the rest of the ENCODE Consortium, to prioritize shared samples to be studied across all assays and groups, and to develop a process for obtaining additional samples from collaborations with the broader research community. It is likely that only some of the samples proposed by each group will be studied.

How do applicants determine the amount of sample sufficient for sharing with the consortium?

Since applicants will not know in advance what assays will be funded, the quantity of available samples and applicability to widely used assays should be addressed in general terms. Once awards are issued and decisions are made about which common samples will be used and an assessment can be made about what the experimental requirements are, awardees will likely be asked to re-budget in order to have sufficient funds to provide the necessary samples to all Mapping Centers.

What fraction of assays can be carried out with disease tissues? Must a proposal include disease-relevant samples?

Applicants may, but are not required to, include plans to study samples that are disease relevant and should provide a strong justification for their use in terms of discovery of new candidate functional elements. Disease-relevant samples may be specialized cells of high relevance to a disease from unaffected individuals, if not previously studied in ENCODE, and from affected individuals. Applicants may propose to devote up to 25% of their data production effort to disease-relevant samples from affected individuals. Data from these sources should simultaneously help build the catalog of functional elements, inform about differences between normal and affected samples, and support the long term goal of developing a general strategy to apply these approaches to disease.

Can I propose to use biological samples requiring that data generated on them be submitted to controlled access databases, e.g., dbGAP?

All human biological samples used in the mapping centers need to be obtained with consents explicitly allowing for unrestricted data access. Exceptions may be granted by NHGRI for studies employing new methods being applied across a relatively small set of common samples previously used within ENCODE (for which significant amounts of ENCODE data already exist). Applicants proposing samples to be considered as an exception to having explicit consent for unrestricted data access should justify the use of those samples in their applications. NHGRI will not grant exceptions prior to funding of awards and decision made about biological samples that will be used by the funded groups.

Can I map functional elements in the rat genome?

No. This RFA is limited to studies in the human and mouse genomes.

Administrative Details:

Should applications to the Mapping RFA include a specific aims page?

Yes, a specific aims page is required for UM1 applications for Mapping and Characterization centers.

If I submit an application with multiple PIs, can our collective effort add up to 3 calendar months/year?

No. The effective management of a production project requires a significant commitment by the PI. For an application proposing a single PI, that PI is expected to devote at least 3 calendar months annually to the project. If multiple PIs are proposed, the lead PI is still expected to commit at least 3 calendar months annually and the other(s) should devote sufficient time to serve his/her proposed role.

I am submitting a Multiple PD/PI (MPI) application. The Multiple PD/PI Leadership Plan and the Management Plan section appear to have overlap. How should I complete them?

There is some overlap between what is required in the Multiple PD/PI Leadership Plan and the Management Plan section, when the application is a multi-PI (MPI) application. It would be acceptable to put all of the required information from both sections in the Management Plan section, and for the Multiple PD/PI Leadership Plan to provide a one line statement that all of the required information is in the Management Plan section. The requirement remains in effect for the applicant to address all points of the Multiple PD/PI Leadership Plan.

Does the Research Strategy Section need to have separate sections on Significance, Innovation, and Approach in addition to the five sub-sections: Overall Goals, Experimental Assay, Selection of Biological Samples, Data Management Plan and Project Management Plan?

No. The instructions in the RFA supersede what is in the standard SF424 (R&R) Application Guide. You should divide the research strategy section into the 5 subsections. You can address significance, innovation and approach in the Overall Goals section, and expand on those points in the subsequent sections, as relevant, but they aren't required sections.

RFA-HG-16-003 Characterization

Is ongoing technology development allowed as part of this RFA, or are we supposed to have the technologies up and running from Day 1?

Individual assays should be up and running at the start of the project. The overall approach, combining sets of assays, could be novel and develop over time.

Are cell based phenotypes sufficient for functional characterization?

Applicants should propose what they think is the appropriate level of characterization. Applicants should consider the continuum from molecular to organismal phenotypes, from high throughput to low throughput assays, and based on the tradeoffs, could chose more than one assay.

Can I start with GENCODE elements, such as non-coding RNA, as predictions to test for my center?

If an applicant was proposing to characterize non-coding RNA, then yes. If an applicant was only identifying the ~20k protein coding genes and them studying them, then no. Projects that primarily test the function of changes in protein coding sequences are not within the scope of this RFA, as such approaches are relatively well developed relative to characterization of non-coding elements.

May applicants propose to study natural genetic variation, or is it only appropriate to study engineered variants?

Applicants are welcome to study natural genetic variation, and these variants could be associated with disease or other traits, or they could be variation of unknown significance.

Do I have to propose to use existing ENCODE data or analyses to identify functional elements for characterization?

Yes. Applications must use existing ENCODE mapping data or analyses as part of the process to identify candidate functional elements.

May I propose to use other existing data, in addition to ENCODE data, to identify functional elements for testing?

Yes. Projects that combine ENCODE data with other relevant data are welcome. This other data could be orthogonal, such as GWAS, or closely related, such as epigenomic/transcriptomic data from additional cell fates and cell states.

May I propose to generate additional mapping data to identify functional elements for testing?

Applications that propose extensive mapping efforts to identify candidate functional elements are not within scope and would be non-responsive.

Why is it suggested to use 1-2 biological systems, and 1-2 main assays?

These are guidelines, and it is for the applicant to propose what they think is the best scientific plan, and to justify that plan. At least one system and assay are required to describe and to evaluate the work. Additional systems and assays could add important additional comparisons. However, if an application has too many systems and/or assays, reviewers could judge it to be overly ambitious or unfocused.

What genomes may be studied?

Applicants must propose to study candidate functional elements derived from the human and/or mouse genomes. However, applicants are welcome to propose characterizing these human and mouse elements in assays using other organisms (such as fish and flies) if they think that is a sound scientific approach to accomplish their goals.

Can I propose to use biological samples requiring that data generated on them be submitted to controlled access databases, e.g., dbGAP?

No. All human biological samples used in the characterization centers need to be obtained with consents explicitly allowing for unrestricted data access.

Why are reviewers and applicants asked to comment on the potential of the approach to be generalizable to other disease and biological process?

A long-term goal for NHGRI is to support work to understand genome function, and its role in biology and disease. However, as NHGRI is not focused on any particular diseases or biological systems, we are especially interested in developing approaches that could be broadly applied to other diseases and systems.

25% of capacity is to be reserved for comparing common samples. Why? How will this work?

Applicants are asked to propose their best plans for characterizing functional elements. NHGRI would also like to learn about the relative strengths and weaknesses of the different approaches, to inform future work. The funded centers will work with NHGRI staff to identify common elements that can be tested across systems and assays (to the extent that this is scientifically practical) to assess the generalizability of these approaches.

Does the Research Strategy Section need to have separate sections on Significance, Innovation, and Approach in addition to the two sub-sections: Overall Research, and Management Plan?

No. The instructions in the RFA supersede what is in the standard SF424 (R&R) Application Guide. You should divide the research strategy section into the 2 subsections. You can address significance, innovation and approach in the Overall Research section, and expand on those points in the subsequent sections, as relevant, but they aren't required sections.

Should applications to the characterization RFA include specific aims and a specific aims page?

Yes, a specific aims page is required for UM1 applications for mapping and characterization centers.

If I submit an application with multiple PIs, can our collective effort add up to 2.4 calendar months/year?

Yes. For single PI applications, the PD/PI funded under this FOA is expected to devote at least 2.4 person months annually to the project. If multi-PDs/PIs are proposed, then each PD/PI is expected to commit sufficient time to serve his/her proposed role, with a minimum aggregate PD/PI effort of 2.4 calendar months.

I am submitting a Multiple PD/PI (MPI) application. The Multiple PD/PI Leadership Plan and the Management Plan section appear to have overlap. How should I complete them?

RFA-HG-16-004 Computational

What is the format for U01 applications?

The U01 activity code is the cooperative agreement analog of the R01 research project. This RFA uses the standard limit of 12 pages for research strategy, and a specific aims page.

Do I have to propose to use existing ENCODE data as part of my project?

Yes. The primary goal of this RFA is to develop and apply new computational analysis methods to ENCODE data, with the goal of improving and interpreting the catalogs of candidate functional elements that the ENCODE Project has produced. Applications that do not use existing ENCODE data would be considered non-responsive to this RFA.

May I propose to compute on existing data from sources other than ENCODE, in addition to ENCODE data?

Yes, applicants must make use of existing ENCODE data, but use of additional data from sources outside of the ENCODE Project is encouraged.

Will this RFA fund generation of new data?

Applications should focus on the generation of new computational or analytical approaches, not on data generation. Limited data generation for the purposes of validating or testing approaches is permitted, but should not represent a substantial fraction of the cost or effort of a proposal. Devoting on the order of 10% of the cost of a proposal towards well-justified experimental validation of computational approaches would be acceptable.

I would like to focus on a specific disease system. Is this appropriate for this RFA?

This RFA seeks to support approaches that can be applied broadly by a broad range of researchers. If the approaches being developed will be generalizable and applicable across a range of disease systems, then the application may be appropriate for this RFA.

NHGRI emphasizes unrestricted data access in the Mapping (HG-16-002) and Characterization (HG-16-003) RFAs. Does all of the data utilized in my proposal need to be consented for unrestricted access?

No. Computational research projects need not rely entirely on unrestricted access data. For example, it is expected that projects incorporating results of GWAS studies may need to utilize data available through dbGaP or other sources with controlled access.

What is meant by 'enhancing the utility of the ENCODE data for the community'?

Applicants should propose projects that will result in the development of new analytical methods, computational tools, and/or software that:

make innovative use of ENCODE data
will be made freely available to the research community in readily usable formats
are applicable across a range of diseases or biological or experimental systems

RFA-HG-16-005 Data Coordinating Center

Can I apply to be both the Data Coordinating Center (DCC) and the Data Analysis Center (DAC)?

Yes, but any applicant planning to do so is strongly encouraged to discuss such plans with NHGRI. Applicants must submit separate applications to RFA-HG-16-005 and RFA-HG-16-006.

To encourage participation from a broad representation of the research community, when making funding decisions, NHGRI intends to consider whether an applicant will be funded as a PD/PI through other ENCODE RFAs and may choose to limit awards from multiple RFAs. Funding will be considered in the context of the all of the Selection Criteria, including merit as determined by peer review.

How do you envision the DCC importing community data? Would a researcher who is contributing data, but not funded by ENCODE, have access to view preliminary ENCODE data? Does this mean conferring "partial" membership of ENCODE to these data contributors?

This is a new activity, and NHGRI is asking applicants to propose their own ideas. NHGRI is interested in sharing data from outside the consortium with the community, possibly using the ENCODE portal. Data contributors would not become consortium members nor have access to preliminary ENCODE data.

Should applicants describe a plan, and request funds, for both a yearly consortium meeting and a yearly ENCODE Community Users meeting?

Yes.

Do I have to take over the current ENCODE Portal or can I propose a new one?

No, an applicant may propose a new portal, but should describe plans for providing uninterrupted access to the existing data and other information available through this portal.

If I submit an application with multiple PIs, can our collective effort add up to 3 calendar months/year?

No. The effective management of the ENCODE Data Coordinating Center requires a significant commitment by the PI. For an application proposing a single PI, that PI is expected to devote at least 3 calendar months annually to the project. If multiple PIs are proposed, the lead PI is still expected to commit at least calendar months annually and the other(s) should devote sufficient time to serve his/her proposed role.

RFA-HG-16-006 Data Analysis Center

May a DAC applicant propose to integrate, calibrate and normalize ENCODE datasets with other large datasets, such as GTEx, 1000 Genomes, and TCGA, in order to facilitate integrative analysis?

This work would be in scope and is permitted, but it is not required of the DAC. Scientific and programmatic priorities will need to be balanced with costs.

Can I apply to be both the Data Coordinating Center (DCC) and the Data Analysis Center (DAC)?

Yes, but any applicant planning to do so is strongly encouraged to discuss such plans with NHGRI. Applicants must submit separate applications to RFA-HG-16-005 and RFA-HG-16-006.

Does the DAC do all of the analysis of ENCODE data?

No. The DAC is the lead for coordinating integrative analysis, and will perform at least some of the integrative analysis. The ENCODE Analysis Working Group (AWG) and sub-groups serve as DAC-led forums to coordinate this work. However, mapping and characterization centers will perform some analysis of their own data, computational analysis projects will be funded to perform particular analyses described in their applications, and the DCC will perform data processing and quality assessment for the major data types.

May foreign institutions apply?

Yes (for this ENCODE RFA only).

If I submit an application with multiple PIs, can our collective effort add up to 3 calendar months/year?

No. Effective management will require a significant commitment by the Program Director(s)/Principal Investigator(s). For an application proposing a single PD/PI, that PD/PI is expected to devote at least 3 calendar months annually to the project. If multi-PDs/PIs are proposed, then one PD/PI is expected to commit at least 3 calendar months annually and the other(s) should devote sufficient time to serve his/her proposed role.

Last updated: March 17, 2016