Notice of Availability of Administrative Supplements for the Addition of Standard Measures to Population-Based Genomic Research: The PhenX Toolkit

Notice Number: NOT-HG-11-001

Update: The following update relating to this announcement has been issued:

• January 21, 2011 - See Notice NOT-HG-11-009 Notice of Amendment and Re-issuance of Administrative Supplements for the Addition of Standard Measures to Population-based Genomic Research: The PhenX Toolkit.

Release Date: October 8, 2010
Receipt Date: December 3, 2010
Earliest Anticipated Start Date: March, 2011

National Human Genome Research Institute (NHGRI)
Office of Behavioral and Social Sciences Research (OBSSR)

The National Human Genome Research Institute (NHGRI) along with the Office of Behavioral and Social Sciences Research (OBSSR) announces an Administrative Supplement Program to promote the inclusion of standard phenotypic and environmental exposure measures selected from the PhenX Toolkit (www.phenxtoolkit.org) into existing population-based genomic studies supported by the NIH. The goals of this supplement program are to evaluate the usefulness of PhenX measures and to stimulate their uptake into population studies to enhance genomic research. The inclusion of measures from the PhenX Toolkit will enable researchers to broaden the scope of their studies, examine additional genetic and environmental factors contributing to human health and disease, and combine their studies with other investigators using the same measures to increase power and efficiency of genomic discovery.

Genome-wide association (GWA) studies have identified hundreds of associations between genetic variants and complex human diseases, and for some diseases, such as diabetes and Crohn’s disease, pooling of multiple GWA studies by meta-analysis has led to the discovery of new gene associations. However, most GWA studies have had relatively few phenotypic and exposure measures in common. Harmonizing data across studies that have used disparate measures to collect similar information is difficult and time consuming. Development and adoption of standard phenotypic and exposure measures could facilitate the creation of larger, more comprehensive datasets with a variety of phenotype and exposure data for cross-study analysis, thus increasing statistical power and the ability to detect associations of modest effect sizes and gene-gene and gene-environment interactions.

Recognizing the need for standard phenotypic and exposure measures, particularly as related to GWA studies, NHGRI initiated the PhenX Toolkit in 2006 through RFA-HG-00-006, High-Priority Phenotype and Exposure Measures for Cross-Study Analysis in Genome-Wide Association Studies. The goal of this three-year program was to identify and catalogue 15 high-quality, well-established, and broadly applicable measures for each of 21 research domains for use in GWA studies and other large-scale genomic research. A PhenX domain is a topic area with a unifying theme such as Demographics, Anthropometrics, Neurology, Cancer, or Social Environments. PhenX measures are selected by Working Groups of domain experts using a consensus process and are made available to the scientific community via the PhenX Toolkit (www.phenxtoolkit.org).

Although PhenX is on track to meet its three-year goal of producing 15 measures in each of 21 domains, many of the domains have been released relatively recently and experience has not been sufficient to gauge the impact of the Toolkit nor potential needs for its continuation. NHGRI has been urged to catalyze adoption of PhenX measures in ongoing genomic studies to obtain timely and needed feedback on the value of the resource including gaps in measures, ease of use, and overall usefulness of the PhenX Toolkit for the research community.

This Notice announces the availability of administrative supplements to existing NIH-funded projects to support the incorporation of a minimum of 8-10 PhenX measures into existing population-based genomic research studies that aim to identify the genetic and environmental factors that contribute to health and the development of complex disease. Principal Investigators (PIs) are strongly encouraged to select PhenX measures that are broadly related to a variety of complex traits (e.g., substance use, physical activity, height, weight, etc.) and not just measures related to the primary phenotypes being evaluated in the parent study. Individual-level phenotypic and exposure data collected using PhenX measures, along with previously generated genetic data, will be made available to the broader research community through the National Center for Biotechnology Information's Database of Genotypes and Phenotypes (dbGaP).

PIs should budget for themselves and a data analyst to travel to the Washington, DC area shortly after award for a grantee meeting where they will work together with NHGRI and the PhenX Toolkit grantee, RTI International, to decide upon metrics that will allow a thorough evaluation of the functionality and utility of the PhenX Toolkit, agree upon common approaches for describing and analyzing data collected using the PhenX measures, and identify potential cross-study analyses that can be conducted by the entire set or subsets of PIs. RTI will serve as a facilitator, and if desired, a collaborator in effective incorporation and use of PhenX measures. At a second grantee meeting near the end of the supplement period, PIs will be expected to report findings from analyses of both individual projects and cross-study collaborations and to provide feedback to NHGRI based on the agreed-upon metrics.

A total of $1M is anticipated to be provided in Fiscal Year 2011 to support 6-10 supplements for a project duration of one year.

Administrative supplements are limited to $100,000 in direct costs.

This announcement is for supplements to NIH grants meeting the selection criteria outlined in the section titled "Selection." The grant must have at least one year remaining at the time the award is made.

To be eligible, the PI must be able to demonstrate that the PhenX measures can be administered to participants within the first three months of the award to ensure that data collection and analysis will be completed by the end of the supplement period. Studies should include at least 1,000 participants with previously generated genotype data whom have been adequately consented for sharing of both genomic and phenotypic data with the broader research community for a variety of research purposes. Priority will be given to studies with higher numbers of participants.

To be eligible, the parent grant must be active, and the research proposed in the supplement must be accomplished within the competitive segment. The proposed supplement must be within the general scope of the peer-reviewed activities and aims approved within the parent grant.

IMPORTANT: The research proposed by the NIH grantee in the supplement application must be within the original scope of the NIH-supported grant project. The funding mechanism being used to support this program, administrative supplements, can be used to cover cost increases that are associated with achieving certain new research objectives as long as they are within the original scope of the project. Any cost increases need to result from making modifications to the project in order to take advantage of opportunities that would increase the value of the project consistent with its originally approved objectives and purposes.

To be considered for an administrative supplement, the request must be signed by the Authorized Organizational Representative/Signing Official (AOR/SO), and must describe the need for additional funding and the categorical costs.

Submit (1) one original, hard copy of the request packet (with original signatures of the authorized business official) and (2) an electronic copy of the submitted supplement request as a single email attachment in PDF format to the contact listed below:

Ms. Monika Christman
Lead Grants Management Specialist
Grants Administration Branch
National Human Genome Research Institute
5635 Fishers Lane, Suite 3058, MSC 9307
Bethesda, MD 20892-9307
Rockville, MD 20852 (express/courier)
TEL: 301-435-7860
Email: [email protected]

Requests should be submitted on the PHS398 Application Guide forms (font size and other formatting rules apply as designated in the instructions), as indicated below. Include only the following elements:

Cover Letter which cites this Notice, and the following information:

• Project Director/Principal Investigator (PD/PI) name
• Parent grant number and title
• Amount of the requested supplement
• Name and title of the institutional official, and
• Phone, email, and address information for both the PD/PI and institutional official.
• The cover letter must be signed by the authorized organizational representative/institutional official.

PHS 398 Form Page 1 (Face page)

• The title of the project should be the title of the parent award.
• This Notice should be cited in Box 2, and the yes box should be checked.
• The Principal Investigator (PI) must be the same as the PI on the parent award. For Multiple PI parent awards, the Contact PI must be the PI listed on the supplement request, and the supplement cannot change the Multiple PI team.
• The remaining items on the face page should be filled out in accordance with the PHS 398 application instructions.

PHS 398 Form Page 2

• Note: The project summary is that of the administrative supplement, not the parent grant.

A brief proposal describing the project, including:

• Scope of the overall project and the anticipated contribution of the requested supplement (not to exceed five pages).
  • Provide a brief description of the scope of the overall project on which the supplemental request is based.
  • This section should include a description of the supplement's specific aims, including research design and methods and data analysis. Describe the relationship of the supplement request to the parent grant.
• Budget for the supplement with a justification that details the items requested, including Facilities and Administrative costs.
• Biographical Sketch for all new key personnel (those who are additions on the supplemental project
• Human Subjects documentation (if applicable).
  • Include a current Human Subjects/IRB approval letter, if available. Otherwise, this will be required at the time of funding. All appropriate IRB approvals must be in place prior to a supplement award being made.
  • Any differences in the involvement or use of human subjects or specimens between the administrative supplement activity and the parent grant should be noted.
  • When appropriate, details should be provided on the protection of human subjects and inclusion of women, children, and minorities. Additional guidance on Human Subjects Research is provided under Part II of the PHS 398 instructions.
• PHS 398 Checklist Form

Administrative supplement requests will be reviewed administratively by NIH Staff. Selection factors will include the following:

• Relevance of the proposed activities to the parent grant
• Adequate progress of the parent grant appropriate to the current stage of the project
• Appropriate and well-described plan to accomplish the goals within the timeframe proposed including a plan demonstrating that the PhenX measures can be administered to study participants within the first three months of award to ensure that data collection and analysis can be completed within one year
• Appropriateness of the selected measures for the study population
• Population diversity, particularly in regard to children and minority populations with important health disparities
• Public health importance of the traits being studied
• Availability of high-quality genotyping data (approximately >2,000 variants) in at least 1,000 participants although higher numbers of participants will be given priority
• Institutional certification to share individual phenotype and genotype data through dbGaP
• Expertise of the research team proposed to conduct and achieve the goals the supplemental study.

Inquiries and discussion of plans for responding to this Notice are strongly encouraged.

1. Scientific/Research Contacts:

Heather A. Junkins, MS
Scientific Program Analyst, Office of Population Genomics
NHGRI
5635 Fishers Lane, Suite 3058, MSC 9307
Bethesda, MD 20892-9307
Rockville, MD 20852 (express/courier)
TEL: (301) 402-0343
Email: [email protected]

Erin M. Ramos, PhD MPH
Epidemiologist, Office of Population Genomics
NHGRI
5635 Fishers Lane, Suite 3058, MSC 9307
Bethesda, MD 20892-9307
Rockville, MD 20852 (express/courier)
TEL: (301) 451-3706
Email: [email protected]

2. Financial or Grants Management Contacts:

Ms. Monika Christman
Lead Grants Management Specialist
Grants Administration Branch
National Human Genome Research Institute
5635 Fishers Lane, Suite 3058, MSC 9307
Bethesda, MD 20892-9307
Rockville, MD 20852 (express/courier)
TEL: 301-435-7860
Email: [email protected]