ARRA: Administrative Supplements

National Human Genome Research Institute

National Institutes of Health
U.S. Department of Health and Human Services

Administrative Supplements to NHGRI Grants and Cooperative Agreements Under the American Recovery and Reinvestment Act

The American Recovery and Reinvestment Act (ARRA) was enacted to help stimulate the U.S. economy, and includes additional support of biomedical and behavioral research as one approach to doing so. Additional information on the ARRA and related NIH opportunities is available through the Office of Extramural Research (Grant Funding Opportunities Supported by the American Recovery & Reinvestment Act of 2009 (ARRA)).

Under the ARRA, NIH and NHGRI are authorized to provide researchers supplementary funds that can be used to accelerate the tempo of scientific research on active grants and, at the same time, can promote job creation and retention. This document details NHGRI processes and procedures with respect to administrative supplement requests that can be submitted in response to the ARRA.

The NHGRI will accept administrative supplements in response to:

The following information describes how NHGRI will implement the program of administrative supplements under the ARRA.

Areas of Scientific Priority for ARRA Funding:

NHGRI will accept supplement requests from any current grantee in response to any of the notices and announcements listed above. However, the following scientific areas are considered of particularly high interest by NHGRI to achieve the goals of the ARRA, which are to create or retain jobs and to accelerate science. Requests that address the following areas will be given priority for funding (note that these are not listed in priority order):

Job Retention and Creation: A major objective of the ARRA is to provide funding to create or retain jobs. Therefore, NHGRI's priorities will include providing supplements for the retention of post-doctoral trainees, particularly senior-level post-docs in their last or next-to-last year who have been adversely affected by the lack of employment opportunities due to the current economic circumstances and who therefore wish to continue in their current position and who have agreement from their mentor to do so. Requests for supplements to existing training grants to restore slots that have been programmatically cut below Council-approved levels, as well as for post-docs on research awards will be considered. Requests for funds needed to continue to employ research technicians (job retention) should be made as requests for supplements to research projects.

NHGRI will also consider requests for supplements for ARRA funds to support summer research experiences for students and science educators, to promote diversity in health-related research, or to promote re-entry into biomedical and behavioral research careers. Supplement requests should provide information about how support will be provided for such individuals after the termination of ARRA funding.

Accelerating Science

Additional information concerning requests for supplements for the development and application of statistical and computational data analysis methods.

NHGRI is interested in providing support continue to the development of analytical methods and software. NHGRI will also accept requests for support to test the methods being developed on large sets of data of relevance to the Institute's mission. Appropriate topics include, but are not limited, to the following:

1. Processing sequence and genotype data: Methods need to be improved to assess the quality of sequence data, to assemble complete de novo genomes or complex regions, to align resequencing data to reference sequences, to call SNPs and structural variants, to combine data across samples, to integrate various types of variation data, to impute untyped variants, and to characterize RNA transcripts.

2. Comparative genomics: Methods need to be improved to compare the genomes of multiple species, to find functional genomic elements, and to study genome organization.

3. Sequence analysis of metagenomic samples: Methods need to be improved to assemble complete or partial genomic sequences in mixed samples from individual people to compare microbial communities across time, body sites, individuals, and disease states, and to make inferences about community composition, processes, and function.

4. Population genetic analysis: Methods need to be developed to elucidate mutation and recombination rates, natural selection, and population history and structure.

5. Analysis of genome-wide association studies (GWAS): Methods need to be improved to relate genetic variation and environmental exposures to phenotypes in studies of diseases and other traits, and to design studies to follow up on GWAS results.

6. Integration with functional genomic datasets: Methods need to be developed to integrate sequence data with expression, epigenetic, related genomic, phenotypic, and environmental datasets; to map variants affecting these processes; and to help identify which genes and variants affect biological processes or causally contribute to disease risk or other traits.

7. Statistical issues: Methods need to be improved to design studies and assess the statistical significance of findings, including sampling, artifacts, and properties such as LD.

8. Small molecule chemical biology: Methods need to be improved to analyze small molecule chemical biology data, including integrating multiple assays and developing ontologies.

9. Software development: Applicants are encouraged to write robust, modular software for the methods being developed, including good documentation.

Additional information concerning requests for supplements to ENCODE and modENCODE.

The value of these two research projects could be greatly enhanced by added efforts targeted to increasing the breadth, depth, quality and utility of the data. To accomplish the ARRA goals of accelerating science and creating or retaining jobs, NHGRI is interested in applications for two-year projects that address the following issues:

1. Expanding production efforts to create a more comprehensive and higher quality catalog of functional elements by increasing the throughput of existing approaches, or increasing the number of cell states being analyzed by all currently employed assays, or introducing new assays that will detect one or more new types of sequence-based functional elements across the entire human, worm or fly genome. Any new method proposed must be capable of being applied in an efficient, cost-effective and high-throughput manner to the entire genome and of identifying a new set of functional elements not available from the current experimental approaches used for the respective projects.

2. Expanding the significance of the human ENCODE Project by conducting parallel studies of the mouse genome that will allow direct comparison to human data. Efforts to identify functional elements in the mouse genome must employ efficient, cost-effective and high-throughput methods to generate a focused set of data from mouse tissues, stem cells, and developmental stages that can be directly compared to human data already produced by the ENCODE Project. Supplement requests to study functional elements in mouse are limited to $750,000 in total costs per year for projects that can be completed in two years;

3. Expanding efforts to experimentally validate the biological function of the elements that have been defined biochemically in the ENCODE or modENCODE Projects using high-throughput means. Supplement requests for biological validation are limited to work on the functional elements already defined by the ENCODE/modENCODE Projects. The request must describe and justify how the elements will be chosen for validation;

4. Generating and validating a large number of widely available high-grade antibodies against human proteins or protein modifications that can be used to identify new functional elements within the ENCODE and/or modENCODE Projects;

5. Enhancing bioinformatics support for data analysis and submission, particularly in the modENCODE Project.

Additional information concerning requests for supplements to population genomics awards.

Supplements that would promote the overall goals of the three NHGRI collaborative programs in the area of population genomics — eMERGE, GENEVA, and PAGE — are of interest to NHGRI. Investigators supported by these programs are encouraged to work together to propose collaborative, program-wide, innovative research including, but not limited to:

1. Addition of cutting-edge genomic technologies such as targeted or exome sequencing, transcriptome sequencing, assessment of structural variation, and measurement of DNA methylation and histone modification to identify novel genetic or epigenetic variants that may account for some of the remaining unexplained heritability from genome-wide association and candidate gene studies or otherwise help to clarify genetic influences on health and disease.

2. Addition of currently available technologies such as additional SNP genotyping, rare variant-specific genotyping, or measurement of ancestry informative markers.

3. Extension of analysis and informatics support for investigation of additional phenotypes; gene-environment interactions; or informative subphenotypes such as early onset or rapidly progressive disease, extreme phenotypic values, mild or subclinical disease, or highly resistant (such as disease-free despite strong environmental exposures) or highly sensitive (disease present despite absent conventional risk factors) individuals.

4. Addition of populations of recent African ancestry for investigation of consistency of genome-wide associations across populations or identification of rare sequence variants or lower levels of linkage disequilibrium.

Additional information about the enhancement of Model Organism Databases.

The model organism databases (MODs) funded by NHGRI provide an essential resource to their respective research communities linking the genome sequence to the biology. Multiple barriers exist for the wider utility of these MODs both within their communities and by a broader research community. The two-year timespan for ARRA funding provides an opportunity for NHGRI-funded MODs to develop new resources to promote better utility of these resources. Projects funded under ARRA funding should represent unique opportunities to add new features to improve a MOD and not merely an expansion of existing capacity. Supplement requests might include development of robust generic model organism database (GMOD) software modules similar to the software developed under RFA HG-02-002 or projects to integrate model organism data with existing resources for human genetic and genomic data to maximize the use of models organism as models for human biology and disease. Any supplement request must demonstrate how the proposed project will increase the utility of a MOD to a wider research community.

Additional information concerning requests for supplements to ELSI awards.

The NHGRI Ethical, Legal and Social Implications (ELSI) Research Program expects to fund a limited number of ARRA supplement requests. The program is especially interested in requests that will promote job creation and retention. Individuals interested in submitting supplement requests are strongly encouraged to contact their ELSI Program Official prior to preparing a supplement request. While the program welcomes supplement requests, please note that priority in allocating ARRA funds will, in most cases, be given to new ELSI grants submitted under the ARRA Challenge Grant FOA: RFA-OD-09-003

Additional Information about Administrative Supplement Requests to NHGRI under ARRA.

Communication between the Program Director and the awardee early in the development of a supplement request is strongly encouraged. Please send an e-mail to the Program Director listed on your Notice of Award succinctly describing the proposed supplement request. A telephone call may then be arranged, if necessary.

Supplement requests must meet the following criteria:

1 For supplements to Research Project Grants, the requested budget must be in line with the work being proposed. Although there is no maximum dollar limit on the request, in general, NIH expects that administrative supplements will not exceed $100,000 direct costs or 50 percent of the amount of the parent grant, whichever is lower. Awardees considering larger requests are encouraged to contact the appropriate Program Director to discuss the proposed request.

For supplements to Research Career Development Awards, requests are limited to $50,000 direct costs for Research Development Support costs. Requests for an additional year of support for Transition Career awards (K99 and K22) may also be submitted.

For supplements for summer research experiences the following dollar limits apply: (1) up to $4,000 direct costs for high school students; (2) up to $6,000 direct costs for undergraduate students; (3) up to $18,0000 for science educators.

Receipt Dates for Requests for Administrative Supplements:

Administrative supplements in response to the ARRA may be submitted by the following receipt dates: April 30, 2009; June 30, 2009; and December 1, 2009. If funds are available, NHGRI may elect to accept additional requests in 2010.

How to Apply

Compliance with the ARRA will be greatly facilitated and easily documented if requests are made in standardized request formats. . Applicants should follow the format detailed in NOT-OD-09-056 under the section titled "Preparing an Administrative Supplement Request."

To be considered for an administrative supplement, the written request must be submitted directly to NHGRI, not to the Division of Receipt and Referral, NIH Center for Scientific Review. Requests must be signed by the authorized institutional official and applicants are strongly encouraged to submit the requests electronically as an e-mail attachment in PDF format. In doing so, the signature of the institutional official must be clearly visible.

Electronic Submissions:

Awardees are strongly encouraged to submit requests for administrative supplements by e-mail to: with a cc: to the NHGRI Program Director and Grants Management Specialist listed on the original Notice of Award. The Subject Line should state "ARRA Administrative Supplement & the Grant Number [of the parent grant]."

Send Hard-copy Submissions to:

Cheryl Chick
Chief Grants Management Officer
Grants Administration Branch, DER
National Human Genome Research Institute, NIH
5635 Fishers Lane, Ste. 4076, MSC 9306
Bethesda, MD 20892-9306
Courier services should use:
Rockville, Maryland 20852

A hard copy should NOT be sent if the application was e-mailed to NHGRI's ARRA Mailbox

Review of Administrative Supplement Requests by NHGRI:

Administrative supplement requests will be reviewed internally by NHGRI program staff; in some instances, program staff may consult outside experts.

The following factors will be considered in the review:

Funding Decisions

For FY 2009: Administrative supplement requests will be reviewed within six weeks of each receipt deadline, with notification of award as soon as possible thereafter, and no later than September 30, 2009. Administrative supplement applications received by December 1, 2009 will be reviewed by the end of February 2010 with notification of award no later than May 1, 2010.

Terms of the Award and Reporting

In addition to the standard NIH terms of award, all funding provided under the ARRA will be subject to the HHS Standard Terms and Conditions for American Recovery and Reinvestment Act of 2009 (ARRA). ARRA-related reporting requirements will be incorporated as a special term of award.

It is very important that applicants understand that projects awarded under the ARRA are subject to additional reporting requirements. Investigators are strongly encouraged to review these standard requirements, which are detailed at: Standard Terms and Conditions for ARRA Awards.

NHGRI Grants Management will also include the following special term of award:

The PI is responsible for informing NHGRI within 30 days if s/he receives an administrative supplement(s) from any other IC with budgetary and/or scientific overlap.


For scientific inquiries, awardees should contact the Program Director listed on the most recent Notice of Award for the parent grant. For fiscal inquiries, awardees should contact the Grants Management Specialist listed on the most recent Notice of Award. Before telephoning the NHGRI, awardees are strongly encouraged to send an e-mail to the appropriate staff member succinctly describing the nature of the inquiry; a telephone call can then be subsequently arranged if necessary.

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Last Reviewed: October 1, 2012