Frequently Asked Questions for Centers for Common Disease Genomics (UM1)

Frequently Asked Questions for Centers for Common Disease Genomics (UM1)

(RFA-HG-15-001)

• Questions about the Goals of the RFA
• Questions about Application Format
• Questions about Eligibility and Funding

Questions about the Goals of the RFA

Do we need to be a genome center in order to apply?

The RFA asks for applications from groups that will have a wide range of capabilities. These are described in the Research Objectives (Section 1) under Scientific Goals and Objectives (e.g., selecting, creatively designing and carrying out comprehensive common disease studies; analyzing the data; identifying appropriate, well-justified samples), and the Foundational Goals and Objectives, (e.g., innovating to optimize cost and quality and expand to novel applications such as non-standard samples; improvement of genome sequence assemblies; evaluating, adopting, optimizing and integrating new genome sequencing platforms and data types; developing data handling and analysis platforms compatible with advances in DNA sequencing and computer hardware and software).   Any applicant that can demonstrate that these goals and objectives can be met is encouraged to apply.

Applicants are expected to include detailed plans for genome sequencing in their applications. They may propose to subcontract out some, or even most, of their genome sequencing (see below). However, both the scientific and the foundational goals must still be addressed. This is almost certain to require a close connection with a genome sequencing group (either at the same institution, or in collaboration).  Please keep in mind that, as part of the overall research consortium, both the scientific and the foundational goals and objectives will be active topics of ongoing collaborative consortium discussion, which will be important to achieving the goal of improving the state-of-the-art in application of sequencing to common disease.

If a subcontract is proposed for genome sequencing, the capabilities of the sequence data generator should be described. In addition, you will need to demonstrate to reviewers that you understand the project design, detailed technical aspects of how the sequencing platforms perform, and implications of that for data quality, data analysis, and cost.  All applicants, whether performing sequencing in-house or contracting out, will also need to demonstrate to reviewers that they will be able to take advantage of evolving sequencing technologies in an optimal timeframe to meet the research objectives with the available funds.

The Scientific and Foundational Goals and Objectives detailed in the Research Objectives section are reflected closely in Section IV.2: Research Strategy and Section V.1 Review Criteria. 

We have been studying and characterizing a cohort (or case/control study) in common human disease that we believe would be ideal for this. May we apply?

A connection to a particular study cohort has the potential to be a strength in an application to this RFA (collaborations, knowledge of the disease biology, access to samples, etc.). However, a major objective of this program has to do with understanding how best to approach the genomics of the range of common human diseases; individual disease studies are considered as examples. Accordingly, applications must demonstrate the ability to address the genomics of common disease in general, in addition to the capability to investigate individual examples. Please note that the RFA asks applicants to identify samples/projects sufficient for at least the initial year of genome sequencing, and up to 40% of overall capacity over the four years; the remainder of projects/samples will be selected by NHGRI based on a number of factors, which will include representation of a range of underlying genomic architectures.

This RFA is not intended to fund stand-alone applications that are based only on a single set of samples or a single study, and that do not address the more general scientific and foundational objectives. If you are involved in a particular study, but decide not to submit an application to this RFA, you may have questions about how to get samples considered for inclusion for genome sequencing within this program.  NHGRI is interested in any information on sample sets and we encourage you to contact the Program Officer listed in the RFA.

We would like to propose a clinical component. Is this consistent with the intent of the RFA?

This RFA is not intended to support clinical studies. For example, research involving return of results, collecting new samples, re-consenting or re-testing research participants or following them over time, will not be funded under this RFA. Applications that request funding for these activities may be unresponsive.  However, applications may propose projects that will work on sample sets that will be used in studies that do have a clinical component, funded by other means.

The RFA heavily emphasizes whole genome sequencing. May we propose whole exome sequencing? 

Whole exome sequencing may be proposed only with caution; it must be very well justified, and contribute towards "comprehensiveness" of studies.

We are aware that WES data are currently less expensive to produce and easier to analyze than WGS data. However, this RFA heavily emphasizes WGS, with full awareness of its current potential shortcomings, in order to advance the long-term state of the art in analysis of whole genome sequence in the context of common disease, particularly with regard to the ability to access disease-associated variants in noncoding regions.This is one of the "Foundational" aims of the program.

How much data generation may I propose that goes beyond genome sequencing? How far does the notion of "comprehensiveness" extend with regard to the objective of characterizing putative common disease variants? 

The RFA does not specify the extent of data generation other than genome sequencing that is allowed. However, applicants should consider that the Scientific and Foundational objectives discussed in the RFA must be satisfied, and those will require applications whose major focus is on genome sequence data and analysis in order to identify variants underlying common human diseases; generation of other data types may restrict capacity available for genome sequencing. Should applicants propose generation of other types of high-throughput data(produced on genome sequencing platforms) they should be a well-justified component, efficient to obtain, and should be directly tied to and complement specific genome sequencing projects, towards the objective of "comprehensiveness" as set out in the RFA.

Applicants have the option to request $200,000 total costs per year to propose one-year "pilot collaborations" with other investigators (not awardees of this RFA). Pilot efforts may extend a study even further beyond the realm of genome sequencing, but still must be well-justified as being contiguous or well integrated with a genome sequencing project or projects.Please note that we will seek reviewer comments on any proposed "pilot collaborations", but these comments will not factor in to the review score.

We expect that these efforts will provide examples for future discussion within the program about the usefulness of different data types or analyses in characterizing variants underlying common disease, and how (and how much) these activities benefit from being integrated.

Is there an ELSI research component in this FOA?

No, the FOA does not include an ELSI research component. However, there are two relevant points:       

• These proposals need to consider overall ethical, legal and social policies in sample selection, data use and data release. A link to current NIH policy is included in the RFA.
          
• It is possible, or even likely, that this program, on its own or in interaction with changing technological and societal factors, will raise issues over time that will illuminate or benefit from consideration of ELSI topics. A proposed CCDG effort that has a connection to ELSI research funded under other mechanisms could be of interest.  

What products are grantees expected to share?

Individuals are required to comply with the instructions for the Resource Sharing Plans provided in the SF424 (R&R) Application Guide, with the modifications noted in the RFA. 

We expect program grantees to share: 

• Data. The release of sequence and accompanying phenotype and metadata to dbGaP must be consistent with the NIH Genomic Data Sharing Policy (See: http://gds.nih.gov). The plan should also describe how informed consent will be designed and obtained in order to:
   
  • 1) Allow sharing of sequence and associated metadata in dbGaP for general biomedical research rather than for narrowly defined fields.
  • 2) Maximize the ability to share sequence and phenotype information within research consortia.
  • 3) Allow public release with easy access of non-identifiable information that can be derived from genome sequences and accompanying metadata.
     
• Any tools, methods, etc. developed as part of this research.
• NHGRI intends to engage the program to release any value-added products developed as part of the program, including e.g., common controls, and more generally, knowledge about how to use genome sequencing to inform common disease, including the limits of this approach. 

Will there be other components of this program?

Yes. Applicants and applications should consider that the overall program will include several CCDG grantees and several CMG awardees. In addition, NHGRI recently received approval for concepts for a Coordinating Center and for Analysis Satellites. NHGRI will manage all components together as a research consortium. We will enlist a set of outside scientific consultants to help us with the management of the program. Every grantee should be prepared to work together collaboratively on common challenges and to share information and ideas in order to increase the success of the entire program. 

(Please be aware that we will not be able to answer detailed questions about the new concepts until such time as FOAs are published. The written concept proposals and an archived recording of the Council discussion are available through links at http://www.genome.gov/27560312/february-2015-nachgr-agenda-and-documents/.)

Finally, the CCDG program will involve collaborations with outside investigators including those funded by other NIH Institutes (often these include investigators engaged in cohort or other disease studies). CCDG grantees should be prepared to work collaboratively with these communities as well.

Questions about Application Format

The Research Strategy section outlines how to apply, but it does not explicitly mention whether the application should include Specific Aims. The application form provides for a single one-page Specific Aims section. This will appear in the application just before the Research Strategy. 

Questions about Eligibility and Funding

What types of applications is the RFA inviting? How will applications be reviewed?  How will funding decisions be made?

This RFA is an open competition seeking new applications only; renewal applications are not allowed.  All applications will be reviewed by an independent panel of outside experts and evaluated against criteria stated in the RFA.  Then the applications will be subject to a second level review - including review of a proposed overall funding plan the National Advisory Council for Human Genome Research.  The funding criteria are also stated in the RFA.  

What is the budget cap for an application?

An application may request up to$40 M total costs (direct costs plus F&A) in any year. Applicants may expect that budgets will be negotiated prior to making funding decisions.

May I (or my institution) apply to this RFA and also RFA-HG-15-002 (Centers for Mendelian Genomics)?

Yes, applying to both RFAs is an option. However, awarding two large awards to one institution may become a factor in funding decisions, under the general consideration of achieving overall program balance.

The RFA asks that the PI commit a specific minimum amount of time and effort to the proposed work. However, we will propose a center with multiple PI's and very experienced key investigators. Can the PI's individually commit less than the stated minimum?

Reviewers will be asked (see Review Criteria within the RFA) to evaluate the Management Plan section of the proposal carefully to ensure that adequate effort and organization is proposed. Depending on the size and complexity of what is proposed, the level of effort that is appropriate may actually be deemed to be higher than stated as a minimum in the RFA.  .  At least one of the named PI's must commit at least the stated minimum level of effort, and applications should justify why that person is the best-suited for the role.  

Is it required that I identify additional resources to complement studies funded with this RFA? 

No. This is encouraged but not required in the application; NHGRI does intend to encourage this further over the full term of the program. The word "resources" is interpreted broadly here, and can include (but is not limited to) direct collaborations, in-kind resources (for example, genome sequencing capacity), internal or external funds, equipment, or other resources. The main point is that these should demonstrably increase the chances of attaining the scientific objectives of the program (e.g., comprehensiveness of studies), and be directly aligned with obtaining those objectives.  Identifying additional resources that can enhance the chances for success of the proposed effort may be considered in review in the normal sense that it may contribute to the "Environment" criterion. In addition, NHGRI intends to provide incentive to successful awardees to identify additional resources that would contribute to success of studies over the course of the grant term.

Please note that a Notice has been published in order to clarify the RFA on this point:    

Notice of Clarification of Language in RFA-HG-15-001"Centers for Common Disease Genomics (UM1)" (NOT-HG-15-020)

Will the funds be equally divided?

They may or may not be, depending on the outcome of the review and funding decisions based on factors including those listed in the RFA section entitled, Review and Selection Process. At a more general level,  the objectives of the RFA call for groups operating at significant scale in order to efficiently undertake comprehensive projects, so it is reasonable to expect that requested budgets will be substantial.

Will this RFA fund sample collection activities?

No, this RFA will not fund sample collection. However, funds may be requested to cover reasonable costs for transfer of samples to a CCDG. 

Will this RFA fund genotyping?

Applicants may propose limited genotyping activities if they are scientifically justified to further the genome sequencing studies. For example, genotyping may be required for quality assessment of samples, or as a component of validation of results, especially if a project depends on uniquely valuable samples that have not previously been genotyped.  Stand-alone genotyping studies will not be supported.           

May I propose to use existing equipment for the proposed center? Will new equipment be funded?

You may propose to use existing or new equipment, or a combination of both. Equipment purchases will be funded within the overall budget of the award. Note that equipment amortization should be included in the overall cost of sequence production.

Will this FOA be renewed after the four-year funding period?

This is currently unknown. Essentially all large NHGRI programs are currently based on the outcomes of strategic planning meetings held about a year in advance of any consideration of renewal. 

Posted: February 11. 2015