Research and Development for Genome Reference Representations (GRR) (U01 Clinical Trial Not Allowed) | RFA HG 19 003

Opportunity Information: Apply for RFA HG 19 003

The National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), offered this funding opportunity to push the human genome reference forward into a true next-generation, pangenome-based resource. The main goal is to support research and development that produces practical genome reference representations that can capture essentially all human genomic variation, especially as the community generates more and more high-quality genome assemblies from diverse populations. Rather than relying on a single linear reference sequence, the opportunity centers on building representations that can handle many alternative sequences and variants at once, with the long-term aim of making population-scale genomic analysis more accurate, more inclusive, and more scalable.

A key scientific and technical focus is the idea of the pangenome as a graph. The general concept of graph-based genome references is already widely discussed in genomics, but NHGRI emphasized that major work still remained to make these ideas usable in day-to-day research and analysis. That includes refining how the reference is represented, how variation is encoded, how coordinate systems and annotations work in a non-linear framework, and how researchers can compute on these references efficiently. In plain terms, the FOA is looking for methods and implementations that do not just look good in theory, but actually perform well when used with large datasets and real analytical workflows.

The solicitation strongly prioritizes software development and practical implementation. NHGRI is looking for tools that demonstrate efficiency and scalability, including strong computational speed and the ability to work as the number of genomes and variants grows. Ease of use and the likelihood of broad adoption are also central: the software should be usable by the wider genomics community, not only by a small set of specialists. The expectation is that funded projects will help create a workable foundation for open science in genome referencing and analysis, enabling downstream tool builders and researchers to adopt the new reference models without prohibitive technical barriers.

Because NHGRI expects this area to become core infrastructure for genomics, the FOA is structured to fund multiple cooperative agreement projects that collectively help set benchmarks and standards. That means the program is not only about producing individual tools; it is also about shaping shared community expectations around performance, interoperability, data structures, specifications, and evaluation. By supporting several projects at once, NHGRI aims to accelerate convergence toward approaches that can serve as dependable building blocks for the field, rather than a fragmented ecosystem of incompatible formats and one-off implementations.

Open science is a primary requirement throughout. The opportunity calls for open-source tools, open standards, and openly available specifications, along with robust software engineering practices. The intention is that these products can be widely integrated across the broader genomics community and can support outside contributions, including from developers and researchers not directly funded under the award. At the same time, the FOA notes that robust design should allow the core work to serve as a foundation for independent implementations that may need stronger privacy and security controls. In other words, the default expectation is openness, but the architecture should not prevent privacy-preserving or security-enhanced use cases from being built on top of the core ideas.

Administratively, the opportunity is a discretionary NIH funding program under a cooperative agreement mechanism (U01), meaning NHGRI anticipates substantial programmatic involvement compared with a standard research grant. It is explicitly "Clinical Trial Not Allowed," signaling that the work should focus on computational methods, representations, and software infrastructure rather than prospective clinical interventions or trial activities. The funding opportunity is identified as RFA HG 19 003, associated with CFDA 93.172, and was created on January 30, 2019, with an original closing date of April 2, 2019.

Eligibility is broad and includes many types of domestic U.S. organizations and governments, such as public and private institutions of higher education, nonprofits (with or without 501(c)(3) status), for-profit organizations (other than small businesses as well as small businesses), and multiple levels of government (state, county, city/township, special districts), plus independent school districts and public housing authorities/Indian housing authorities. It also includes federally recognized Native American tribal governments and other Native American tribal organizations. Beyond the typical NIH applicant pool, the FOA explicitly highlights additional eligible applicants such as Alaska Native and Native Hawaiian Serving Institutions, Asian American Native American Pacific Islander Serving Institutions (AANAPISIs), Hispanic-serving Institutions, Historically Black Colleges and Universities (HBCUs), Tribally Controlled Colleges and Universities (TCCUs), faith-based or community-based organizations, regional organizations, U.S. territories or possessions, eligible federal agencies, and even non-U.S. entities (foreign organizations). The overall message is that NHGRI wanted wide participation to help ensure the next reference representation is both technically strong and broadly useful across communities and settings.

• The National Institutes of Health in the health sector is offering a public funding opportunity titled "Research and Development for Genome Reference Representations (GRR) (U01 Clinical Trial Not Allowed)" and is now available to receive applicants.
• Interested and eligible applicants and submit their applications by referencing the CFDA number(s): 93.172.
• This funding opportunity was created on 2019-01-30.
• Applicants must submit their applications by 2019-04-02. (Agency may still review applications by suitable applicants for the remaining/unused allocated funding in 2026.)
• Eligible applicants include: State governments, County governments, City or township governments, Special district governments, Independent school districts, Public and State controlled institutions of higher education, Native American tribal governments (Federally recognized), Public housing authorities/Indian housing authorities, Native American tribal organizations (other than Federally recognized tribal governments), Nonprofits having a 501 (c) (3) status with the IRS, other than institutions of higher education, Nonprofits that do not have a 501 (c) (3) status with the IRS, other than institutions of higher education, Private institutions of higher education, For-profit organizations other than small businesses, Small businesses, Others.

Apply for RFA HG 19 003

[Watch] Creating a grant proposal using the step-by-step wizard inside the applicant portal: