Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Mouse (UM1) | Apply Online

Frequently Asked Questions (FAQs)

What is this funding opportunity?

This opportunity is the NIH program titled "Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Mouse (UM1)" (RFA HG 16 002). It supports large, coordinated research projects designed to improve and extend ENCODE reference catalogs of functional genomic elements in humans and in mouse (Mus musculus).

Which agency is offering this program?

The program is offered under HHS-NIH (the U.S. Department of Health and Human Services, National Institutes of Health).

What is ENCODE and why does it matter?

ENCODE is a major effort that has produced widely used maps of genomic regions that appear to carry biological function, including regulatory sequences and other elements that influence when and where genes are active. These maps are foundational for basic genome biology, for building experimental and computational tools, and for interpreting genetic signals found in disease association studies.

What is the main purpose of this FOA?

The core purpose is to fund projects that can run state-of-the-art, high-throughput, and cost-effective data generation pipelines to identify and map additional candidate functional elements across the human and mouse genomes. The deliverable emphasis is on expanding a community-facing reference catalog that can be broadly used by other researchers.

What kinds of projects does NIH appear to be seeking?

Based on the description, NIH is looking for groups that can generate large volumes of standardized genomic data efficiently and reproducibly using modern experimental assays and processing workflows suitable for consortium-wide integration. The focus is on scalable, consistent, reference-grade dataset production rather than small standalone projects.

Is this opportunity focused only on generating new data?

No. While generating new datasets is central, the FOA stresses generating data in a scalable and consistent way so it can be merged into an expanded ENCODE reference catalog. That implies an emphasis on standardization, reproducibility, and interoperability with existing ENCODE resources.

Does the FOA include disease-relevant research?

Yes. The announcement explicitly encourages mapping candidate functional elements in biological samples relevant to particular diseases. This is framed as both a way to expand the catalog into under-profiled contexts (cell types, tissues, or conditions) and to improve the field's ability to interpret disease studies by identifying which functional annotations are most informative for disease mechanisms.

If disease relevance is encouraged, is the deliverable still a general reference resource?

Yes. Even with disease-relevant samples encouraged, the program is described as being centered on broadly useful maps of genomic function in both human and mouse, intended to be integrated into community reference catalogs.

What organisms are covered by this funding opportunity?

The FOA targets both human and mouse (Mus musculus) functional genomics mapping.

What funding mechanism is used?

Awards are made as a cooperative agreement (UM1).

What does a UM1 cooperative agreement generally imply for applicants and awardees?

In general terms, a UM1 cooperative agreement indicates a tightly coordinated NIH-led program structure rather than a fully independent investigator-driven award. The description indicates that awardees are expected to operate as part of a coordinated program with shared standards, collaborative planning, common data and metadata expectations, and regular coordination with other sites and NIH program staff.

Will awardees be part of the ENCODE Consortium?

Yes. The FOA states that funded teams will participate in the ENCODE Consortium.

What kinds of consortium expectations are described?

The opportunity describes expectations consistent with consortium participation, including shared standards, harmonized protocols, rigorous quality control, rapid data release practices, and integration with existing ENCODE resources so outputs are immediately interoperable with what has already been produced.

What is meant by "reference catalogs of functional genomic elements" in this context?

In the context provided, these catalogs are structured maps of candidate functional DNA regions, including regulatory sequences and other genomic elements that influence gene activity. The goal is to expand and improve the completeness and utility of these catalogs for the research community.

Why is NIH emphasizing that existing ENCODE catalogs are incomplete?

The description indicates NIH believes important gaps remain in current catalogs and that a major goal of the FOA is to close those gaps by generating additional high-quality datasets at scale.

What does "high-throughput" and "cost-effective" mean for the types of work proposed?

Based on the wording, projects are expected to run pipelines capable of producing large volumes of genomic data efficiently, using modern assays and processing workflows that are scalable and reproducible enough to support a consortium-wide, reference-building effort.

Who is eligible to apply?

Eligibility is described as broad and includes: federal, state, local, and tribal government entities; public and private institutions of higher education; nonprofit organizations (including 501(c)(3) and non-501(c)(3)); for-profit organizations (other than small businesses); and small businesses. The listing notes that additional eligibility details may appear in the full announcement text.

Are small businesses eligible?

Yes. Small businesses are listed as eligible.

Are for-profit organizations eligible?

Yes. For-profit organizations are listed as eligible, with the listing specifying "for-profit organizations (other than small businesses)" as an eligible category, and small businesses also listed separately as eligible.

What is the CFDA number for this opportunity?

The listing includes CFDA number 93.172 (and it is also listed with 93.172 in the source).

What is the program category?

The opportunity is listed in the health research category.

When was this opportunity posted?

The public listing states it was posted and created on January 15, 2016.

What is the application deadline?

The listing shows an original and current closing date of March 21, 2016.

Does the listing provide an award ceiling or the expected number of awards?

No. The public listing does not provide an award ceiling or an expected number of awards.

What scale of project does this FOA seem to support?

While no dollar amounts or counts are provided in the listing, the UM1 cooperative agreement mechanism and consortium setting are described as indicating multi-component, resource-building projects intended to produce broadly shared datasets and reference-grade outputs rather than small, standalone studies.

What is meant by "standardized genomic data" in this FOA?

From the description, "standardized" refers to data produced with consistent methods, metadata, and quality control so that datasets can be integrated across multiple sites and merged into an expanded ENCODE reference catalog.

How does this FOA connect basic genome biology with human health research?

The FOA highlights that disease-relevant mapping can both expand ENCODE catalogs into important biological contexts and improve interpretation of disease association studies by revealing which functional annotations best inform disease mechanisms, while still delivering broadly useful reference maps.

What is the central takeaway for prospective applicants?

This FOA is best understood as a call for teams capable of producing high-volume, high-quality, standardized functional genomics datasets in human and mouse, potentially including disease-relevant samples, and willing to work as active ENCODE Consortium participants to deliver integrated reference resources for the wider biomedical research community.