Opportunity Information: Apply for RFA HG 09 014
Apply for RFA HG 09 014
- The National Institutes of Health in the health sector is offering a public funding opportunity titled "Comparing Design Approaches for Sequencing Disease Associated Regions found in Genome Wide Association Studies (U01)" and is now available to receive applicants.
- Interested and eligible applicants and submit their applications by referencing the CFDA number(s): 93.172 Human Genome Research.
- This funding opportunity was created on Oct 6, 2009 and posted on Oct 6, 2009.
- Applicants must submit their applications by Dec 11, 2009. (Agency may still review applications by suitable applicants for the remaining/unused allocated funding in 2026.)
- The funding agency has allocated a total of $750,000.00 to eligible and selected applicants.
- Each selected applicant is eligible to receive up to $150,000.00 in funding.
- Eligible applicants include: Native American tribal organizations (other than Federally recognized tribal governments) Small businesses Private institutions of higher education City or township governments Others (see text field entitled Additional Information on Eligibility for clarification) State governments Nonprofits that do not have a 501(c)(3) status with the IRS, other than institutions of higher education Public and State controlled institutions of higher education Nonprofits having a 501(c)(3) status with the IRS, other than institutions of higher education County governments Native American tribal governments (Federally recognized) Special district governments For profit organizations other than small businesses.
- Other Eligible Applicants include the following Alaska Native and Native Hawaiian Serving Institutions Eligible Agencies of the Federal Government Hispanic serving Institutions Historically Black Colleges and Universities (HBCUs) Indian/Native American Tribal Governments (Other than Federally Recognized) Non domestic (non U.S.) Entities (Foreign Organizations) Regional Organizations Tribally Controlled Colleges and Universities (TCCUs) U.S. Territory or Possession.
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Opportunity Summary:
This grant opportunity, titled "Comparing Design Approaches for Sequencing Disease Associated Regions found in Genome Wide Association Studies (U01)" (Funding Opportunity Number RFA-HG-09-014), is an NIH National Human Genome Research Institute (NHGRI) initiative aimed at improving how researchers design sequencing studies that follow up on genome-wide association study (GWAS) results. GWAS projects have already flagged many genomic regions linked to common diseases and traits, but those regions typically contain many correlated variants, making it hard to pinpoint which specific changes in DNA actually contribute to risk. The central idea behind this program is to take well-established GWAS signals and perform more complete sequencing of the implicated regions across large numbers of samples, producing high-quality reference datasets that the broader research community can use to compare and test different sequencing study designs.
A key focus of the announcement is the uncertainty around which sequencing and sampling strategies work best under different scientific conditions. Follow-up sequencing can be done in several ways, such as targeting only protein-coding exons, sequencing entire gene bodies including introns and regulatory elements, or capturing broader surrounding regions that may contain functional non-coding variants. Similarly, researchers can choose to sequence individuals at the extremes of a phenotype distribution (for example, very early onset cases or unusually high trait values), or they can sample across the full distribution to better represent population-level variation. Because it is not well understood when one approach outperforms another, NHGRI proposes generating standardized, deeply characterized datasets from multiple disease-associated loci and cohorts so that methods and design choices can be evaluated on real, comparable data rather than simulations alone.
The program is structured as a cooperative agreement (U01), which generally means awardees are expected to work closely with NIH and other partners rather than operating entirely independently. Applicants are expected to come from GWAS investigator groups that already have well-replicated disease or trait associations and can nominate specific association regions for sequencing. They must also be able to provide access to an adequate number of samples drawn from completed GWAS cohorts, along with the accompanying genotype data, phenotype measurements, and exposure or environmental data where available. In other words, the funded projects are not starting new GWAS collections from scratch; they are leveraging existing cohorts that already have rich data and strong statistical signals.
An important operational feature is that the large-scale sequencing itself is not expected to be performed by the applicant laboratories. Sequencing capacity is to be provided through NHGRI large-scale sequencing centers, using a broad sequencing design intended to encompass multiple narrower strategies. This is meant to ensure consistency, depth, and comparability across projects and regions. Funding for analysis of the resulting sequence data is provided through the Genes, Environment, and Health Initiative (GEI), and the funded GWAS groups are expected to work as part of a consortium with the sequencing centers and analysis teams. Consortium activities include jointly developing the broad sequencing strategy, analyzing the data for each selected study, and then systematically evaluating how different design choices (region selection, sampling frame, analytical approach) affect the ability to identify the most strongly associated variants and narrow down candidate causal variants.
From an administrative standpoint, the opportunity is categorized as a discretionary health research funding program under NIH, with a CFDA listing of 93.172 (Human Genome Research). The estimated total funding described is $750,000, with an award ceiling of $150,000, and there is no cost-sharing or matching requirement. The original posting date was October 6, 2009, with an original and final closing date of December 11, 2009, and an archive date of January 11, 2010, meaning it was a time-limited call rather than an ongoing program announcement.
Eligibility is broad and includes many common applicant types: public and private institutions of higher education, nonprofits (including both 501(c)(3) and certain non-501(c)(3) entities), small businesses and other for-profit organizations (with some distinctions), and multiple levels of government (state, county, city/township, special districts). The announcement also explicitly notes additional eligible applicants such as Alaska Native and Native Hawaiian Serving Institutions, Hispanic-serving institutions, Historically Black Colleges and Universities, tribally controlled colleges and universities, tribal governments (both federally recognized and other than federally recognized), U.S. territories or possessions, and even non-U.S. entities (foreign organizations) and regional organizations. Practically, though, the most competitive applicants would be groups that already control or can access large, well-phenotyped GWAS datasets with replicated associations and can coordinate sample sharing and data governance suitable for consortium-based sequencing and analysis.
Overall, this FOA is less about discovering new GWAS hits and more about building the empirical foundation for best practices in post-GWAS sequencing. The expected products are complete sequence datasets for selected GWAS regions in large cohorts, along with analyses that let researchers compare design tradeoffs in a realistic setting. The longer-term payoff is meant to be methodological clarity for the field: clearer guidance on when targeted exon sequencing is sufficient versus when broader region sequencing is necessary, how different phenotype-based sampling strategies influence power and interpretability, and how to most efficiently move from broad association signals to a smaller, more credible set of candidate variants for downstream functional and clinical studies.
Frequently Asked Questions (FAQs)
What is the name of this grant opportunity?
The opportunity is titled "Comparing Design Approaches for Sequencing Disease Associated Regions found in Genome Wide Association Studies (U01)."
What is the Funding Opportunity Number (FON)?
The Funding Opportunity Number is RFA-HG-09-014.
Which NIH institute is sponsoring this opportunity?
This is an NIH National Human Genome Research Institute (NHGRI) initiative.
What type of award mechanism is being used?
The program uses a cooperative agreement mechanism (U01), which means funded groups are expected to work closely with NIH and other partners as part of a coordinated effort.
What is the main purpose of the program?
The purpose is to improve how researchers design sequencing studies that follow up on genome-wide association study (GWAS) results by generating high-quality reference datasets from well-established GWAS signals.
Why is follow-up sequencing needed after GWAS?
GWAS often identifies genomic regions associated with common diseases and traits, but those regions typically contain many correlated variants. This makes it difficult to pinpoint which specific DNA changes contribute to risk. Follow-up sequencing aims to more completely characterize variation in the implicated regions.
What specific problem is this initiative trying to address?
A central issue is uncertainty about which sequencing and sampling strategies work best under different scientific conditions. The initiative is designed to create standardized datasets that allow design choices to be evaluated using real, comparable data rather than simulations alone.
Is this funding meant to support new GWAS discovery projects?
No. The focus is not on discovering new GWAS hits. It is focused on building an empirical foundation for best practices in post-GWAS sequencing by sequencing well-replicated, already-established GWAS association regions.
What kinds of sequencing design approaches are being compared?
The announcement discusses multiple region-selection strategies, including targeting only protein-coding exons, sequencing entire gene bodies (including introns and regulatory elements), or capturing broader surrounding regions that may contain functional non-coding variants.
What sampling strategies does the FOA highlight?
It highlights strategies such as sequencing individuals at the extremes of a phenotype distribution (for example, very early onset cases or unusually high trait values) versus sampling across the full phenotype distribution to represent population-level variation.
What are the expected outputs or deliverables of the program?
Expected products include complete sequence datasets for selected GWAS regions in large cohorts and analyses that allow systematic comparison of design tradeoffs (region selection, sampling frame, and analytical approach) to help narrow down candidate causal variants.
Who is expected to apply?
Applicants are expected to come from GWAS investigator groups that already have well-replicated disease or trait associations and can nominate specific association regions for sequencing.
Do applicants need to already have GWAS cohorts and data available?
Yes. Applicants must be able to provide access to an adequate number of samples drawn from completed GWAS cohorts, along with accompanying genotype data, phenotype measurements, and exposure or environmental data where available.
Are applicants expected to collect new cohorts or start new GWAS sample collections?
No. The projects are expected to leverage existing cohorts from completed GWAS efforts rather than starting new GWAS collections from scratch.
Will the applicant lab conduct the large-scale sequencing?
No. Large-scale sequencing is not expected to be performed by applicant laboratories. Sequencing capacity is intended to be provided through NHGRI large-scale sequencing centers.
Why does the FOA use NHGRI large-scale sequencing centers?
The intent is to promote consistency, sequencing depth, and comparability across projects and regions by using centralized large-scale sequencing capacity and a broad sequencing design.
What is meant by a "broad sequencing design" in this program?
The sequencing design is described as broad enough to encompass multiple narrower strategies, enabling the community to compare different design approaches using the same underlying sequence data resource.
How is analysis of the resulting sequence data supported?
Funding for analysis of the resulting sequence data is provided through the Genes, Environment, and Health Initiative (GEI).
Is participation in a consortium required?
Yes. Funded GWAS groups are expected to work as part of a consortium with the NHGRI sequencing centers and analysis teams.
What kinds of activities are expected within the consortium?
Consortium activities include jointly developing the broad sequencing strategy, analyzing data for each selected study, and systematically evaluating how design choices affect the ability to identify the most strongly associated variants and narrow candidate causal variants.
What federal assistance listing (CFDA) is associated with this opportunity?
The CFDA listing is 93.172 (Human Genome Research).
How much total funding is estimated for this FOA?
The estimated total funding described is $750,000.
What is the award ceiling per award?
The award ceiling is $150,000.
Is cost sharing or matching required?
No. There is no cost-sharing or matching requirement described.
When was this funding opportunity originally posted?
The original posting date was October 6, 2009.
What were the application closing dates?
The original and final closing date was December 11, 2009.
Is this opportunity still active?
No. The archive date is January 11, 2010, and the closing date was December 11, 2009, indicating this was a time-limited call rather than an ongoing program announcement.
What types of organizations are eligible to apply?
Eligibility is broad and includes public and private institutions of higher education, nonprofits (including 501(c)(3) and certain non-501(c)(3) entities), small businesses and other for-profit organizations (with some distinctions), and various levels of government (state, county, city/township, and special districts).
Are minority-serving institutions and tribal entities eligible?
Yes. The FOA explicitly notes eligibility for organizations such as Alaska Native and Native Hawaiian Serving Institutions, Hispanic-serving institutions, Historically Black Colleges and Universities, tribally controlled colleges and universities, and tribal governments (both federally recognized and other than federally recognized).
Are U.S. territories or possessions eligible to apply?
Yes. U.S. territories or possessions are listed as eligible applicants.
Are foreign organizations eligible to apply?
Yes. The announcement notes that non-U.S. entities (foreign organizations) and regional organizations are eligible.
What would make an application practically competitive, based on the FOA description?
While eligibility is broad, the FOA indicates that the most competitive applicants would be groups that control or can access large, well-phenotyped GWAS datasets with replicated associations and can coordinate sample access, data sharing, and governance suitable for consortium-based sequencing and analysis.
What kinds of data are applicants expected to have available?
Applicants are expected to provide access to samples from completed GWAS cohorts and to have associated genotype data, phenotype measurements, and exposure or environmental data where available.
What is the long-term impact the FOA is aiming for?
The longer-term payoff is methodological clarity for post-GWAS sequencing, including guidance on when exon-only sequencing may be sufficient versus when broader regional sequencing is needed, how phenotype-based sampling affects power and interpretation, and how to move from broad association signals to a smaller set of credible candidate variants for downstream studies.
Does the FOA indicate which diseases or traits are covered?
It does not specify particular diseases or traits in the provided description; instead, it focuses on using well-established, replicated GWAS signals and sequencing the associated regions.
What is the role of "reference datasets" in this program?
The program aims to produce high-quality reference datasets from multiple disease-associated loci and cohorts so the broader research community can compare and test sequencing study designs using real datasets.
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