EXPIRED
GENETIC ARCHITECTURE, BIOLOGICAL VARIATION, AND COMPLEX PHENOTYPES PA NUMBER: PA-02-110 Release Date: May 29, 2002 Expiration Date: June 5, 2005 National Institute of General Medical Sciences (NIGMS) (http://www.nigms.nih.gov/) National Human Genome Research Institute (http://www.nhgri.nih.gov/) National Institute on Aging (http://www.nia.nih.gov/) National Institute on Alcohol Abuse and Alcoholism (http://www.niaaa.nih.gov/) National Institute of Mental Health (http://www.nimh.nih.gov/) National Institute of Diabetes and Digestive and Kidney Diseases (http://www.niddk.nih.gov/) National Institute on Drug Abuse (http://www.nida.nih.gov/) National Institute of Environmental Health Sciences (http://www.niehs.nih.gov/) National Institute of Neurological Disorders and Stroke (http://www.ninds.nih.gov/) THIS PA CONTAINS THE FOLLOWING INFORMATION o Purpose of the PA o Research Objectives o Mechanism(s) of Support o Eligible Institutions o Individuals Eligible to Become Principal Investigators o Where to send Inquiries o Submitting an Application o Peer Review Process o Review Criteria o Award Criteria o Required Federal Citations PURPOSE OF THE PA This announcement updates the 1998 Program Announcement PA-98-078, Genetic Architecture of Complex Phenotypes. The program announcement is to solicit applications for new studies on genetic variation and the architecture of complex phenotypes. It restates the interest of several components of the National Institutes of Health in studies of the underlying causes and architecture of complex phenotypes, including human diseases. It is motivated by the amount and complexity of biological data that are being generated and by the understanding that complex phenotypes involve many genetic components that evolve in a variety of environments. RESEARCH OBJECTIVES Complex phenotypes are those that exhibit familial clustering, which may mean that there is some genetic component, but that do not occur in Mendelian proportions in pedigrees. Complex phenotypes may be continuous in distribution, like height or blood pressure, or they may be dichotomous, like affected and not affected. The complexity arises from the fact one cannot accurately predict the expression of the phenotype from knowledge of the individual effects of individual factors considered alone, no matter how well understood each separate component may be. The past few decades of biological research using largely a reductionist approach have yielded vast amounts of data. In addition, genome sequencing projects, as well as structural and functional genomics initiatives, are producing data far more rapidly than scientists can analyze them and understand their implications to biology and to health. As overwhelming as the current data are, they are only the beginning. Protein structures, DNA sequences, and gene expression patterns vary among individuals, among species, among populations within a species, and across environments. It will soon be possible to utilize information on thousands of variable genetic sites to investigate the relationships among genotypes, phenotypes, and environments. The term genetic architecture refers to the full range of genetic effects on a trait, however, when studying variation on such a large scale, it is especially important to consider the context or environments in which genetic variation arises, is selected, and is maintained. Genetic architecture is less a fixed property of the phenotype than a characteristic of a phenotype in a particular population. Genetic architecture is a moving target that changes according to gene and genotype frequencies, distributions of environmental factors, and such biological properties as age and sex. Studies of variation or genetic architecture may employ a variety of conceptual approaches. A researcher may consider the combinatorial effects of many variable sites, whether the scale is within a gene or across a genome. Comparative genomics, where the goal is to identify patterns of variation among genomes, is also a productive way of identifying attributes of variation, such as which genomic regions are rapidly evolving. Another approach is to study variation related to biological levels of organization, such as DNA sequence, protein structure, metabolic pathways, cell dynamics, individual phenotype, and population characteristics. The following are typical of research areas targeted by this initiative: Biological Variation Studies of genetic architecture have historically focused on associations of genotype and phenotype (e.g., between DNA markers and a disease). However, an organism is a unique consequence of both genes and environment and is created by complex interactions of multiple events and forces. How genes are expressed depends on their cellular, developmental, physiological, and environmental context. This initiative encourages research on biological variation and interactions, such as: o Variation in basic biological systems, including sequences, structures, and pathways that direct metabolism and development o Variation in these systems within individuals, among individuals, among populations, and among species with the goal of learning how these complex systems interact and evolve o Determination of the extent to which genetic architecture is shared across populations and among species o Effects of admixture, population history, recombination, mutation, population structure, selection, and drift on the organization of variation o Collection and analysis of both new and existing data o Tools and models for identifying and measuring important contextual features o Measuring the impact of context on biological data. Evolution of Genome Properties An emerging area of research focuses on how properties of genomes arise in evolutionary history. Such research has important consequences for understanding genome organization and for interpreting data on genetic and phenotypic variation. Such research could include the evolution of haplotypes, selection for genetic interactions, and the evolution of recombination and methylation patterns. Extensions to Other Organisms Many organisms have been studied for their value in agriculture or ecology. Thus, there is considerable information about the population structure, natural history, and genetics of these systems. It will be valuable to take advantage of this wealth of information to study variation in the natural settings in which it evolved. Bioinformatics The study of biological variation depends heavily on rich data sets, researchers need the ability to access many kinds of information (e.g., DNA sequence, protein structure, development, natural history, and phenotype) in organisms from different habitats, from different populations, or from different species. This initiative supports development of tools to help researchers use data from many databases to address research questions. Improved Dynamic Modeling and Statistical Methods Mathematical approaches to studying biological variation have changed little in several decades. There is a need to develop new dynamic models to illuminate how systems interact and evolve. Just as important, it is critical to study the nature of biological and mathematical assumptions of models and statistics. Tools for analyzing and interpreting data on the architecture of complex phenotypes should be developed in the context of real biological information. Areas of particular interest for this initiative include the following: o Implications and appropriate uses of different sampling strategies o Analytical tools to discover patterns of genotypic variation and their roles in conferring phenotype o Incorporation of data from new technologies o Development of robust methods that are compatible with real data (missing or incomplete data, typing errors, experimental errors) o Development of mathematical models based on empirical information which includes such biological realities as epistasis, recombination, mutation, protein structure, cell biology, metabolic pathways, development, population history, and evolution. MECHANISM(S) OF SUPPORT This Program Announcement will use the National Institutes of Health (NIH) research project grant (R01). As an applicant, you will be solely responsible for planning, directing, and executing the proposed project. This PA uses just-in-time concepts. It also uses the modular as well as the non-modular budgeting formats (see http://grants.nih.gov/grants/funding/modular/modular.htm). Specifically, if you are submitting an application with direct costs in each year of $250,000 or less, use the modular format. Otherwise follow the instructions for non- modular research grant applications. ELIGIBLE INSTITUTIONS You may submit (an) application(s) if your institution has any of the following characteristics: o For-profit or non-profit organizations o Public or private institutions, such as universities, colleges, hospitals, and laboratories o Units of State and local governments o Eligible agencies of the Federal government o Domestic or foreign institutions INDIVIDUALS ELIGIBLE TO BECOME PRINCIPAL INVESTIGATORS Any individual with the skills, knowledge, and resources necessary to carry out the proposed research is invited to work with his or her institution to develop an application for support. Individuals from underrepresented racial and ethnic groups as well as individuals with disabilities are always encouraged to apply for NIH programs. WHERE TO SEND INQUIRIES We encourage your inquiries concerning this PA and welcome the opportunity to answer questions from potential applicants. Inquiries may fall into two areas: scientific/research, and financial or grants management issues: o Direct your questions about scientific/research issues to: Irene Anne Eckstrand, Ph.D. Division of Genetics and Developmental Biology National Institute of General Medical Sciences 45 Center Drive, MSC 6200 Bethesda, MD 20892-6200 Telephone: (301) 594-0943 Fax: (301) 480-2228 Email: Irene_Eckstrand@nih.gov Lisa D. Brooks, Ph.D. National Human Genome Research Inst National Institutes of Health 31 Center Drive, 31/B2B07 Bethesda, MD 20892-2033 Telephone: (301) 435-5544 Fax: (301) 480-2770 Email: lisa_brooks@nih.gov Winifred K. Rossi, M.A. Genetic Epidemiology and Translational Research National Institute on Aging 7201 Wisconsin Avenue, Suite 3E327 Bethesda, Maryland 20892-9205 Telephone: (301) 496-3836 Fax: (301) 402-1784 Email: wr33a@nih.gov Lisa A. Neuhold, Ph.D. Division of Basic Research National Institute on Alcohol Abuse and Alcoholism 6000 Executive Boulevard, Suite 402 Bethesda, MD 20892-7003 [for express mail, use Rockville, MD 20852] Telephone: (301) 594-6228 Fax: (301) 594-0673 Email: lneuhold@willco.niaaa.nih.gov Steven O. Moldin, Ph.D. Genetics Research Branch Division of Neuroscience & Basic Behavioral Science National Institute of Mental Health 6001 Executive Blvd., Room 7189, MSC 9643 Bethesda, MD 20892-9643 Telephone: (301) 443-2037 Fax: (301) 443-9890 Email: smoldin@mail.nih.gov Robert W. Karp, Ph.D. Division of Digestive Diseases and Nutrition National Institute of Diabetes and Digestive and Kidney Diseases 6707 Democracy Boulevard, Room 671, MSC 5450 Bethesda, MD 20892-5450 (For FedEx and UPS, use Bethesda, MD 20817) Telephone: (301) 451-8875 Fax: (301) 480-8300 Email: karpr@extra.niddk.nih.gov Jonathan D. Pollock, Ph.D. Chief Genetics and Molecular Neurobiology Research Branch National Institute on Drug Abuse 6001 Executive Blvd, Rm. 4274 Bethesda, MD 20892 Telephone: (301) 435-1309 Fax: (301) 594-6043 Email: jp183r@nih.gov Jose M. Velazquez, Ph.D. Division of Extramural Research and Training National Institute of Environmental Health Sciences 111 Alexander Drive Research Triangle Park, NC 27709 Telephone: (919) 541-4998 Fax: (919) 316-4606 Email: Velazqu1@niehs.nih.gov Katrina Gwinn-Hardy, M.D. Neurogenetics National Institute of Neurological Diseases and Stroke 6100 Executive Blvd, Room 2142 MSC 9525 Bethesda, MD 20892 Telephone: (301) 496-5745 Fax: (301) 402-1501 Email: gwinnk@ninds.nih.gov o Direct your questions about financial or grants management matters to: Marcia Cohn Grants Management Office National Institute of General Medical Sciences 45 Center Drive, MSC 6200 Bethesda, MD 20892-6200 Telephone: (301) 594-3918 Fax: (301) 480-1969 Email: cohnm@nigms.nih.gov Jean Cahill Grants Administration Branch National Human Genome Research Institute Building 31, Room B2B34 Bethesda, MD 20892-2031 Telephone: (301) 402-0733 Fax: (301) 402-1951 Email: jean_cahill@nih.gov Linda Whipp Grants and Contracts Management Office National Institute on Aging Gateway Building, Room 2N212 7201 Wisconsin Avenue, MSC 9205 Telephone: (301) 496-1472 Fax: (301) 402-3672 Email: whippl@nia.nih.gov Judy Simons Grants Management Office National Institute on Alcohol Abuse and Alcoholism 6000 Executive Boulevard, Suite 504 Bethesda, MD 20892-7003 [for express mail, use Rockville, MD 20852] Telephone: (301) 443-2434 Fax: (301) 443-3891 Email: jsimons@willco.niaaa.nih.gov Diana S. Trunnell Grants Management Branch National Institute of Mental Health 6001 Executive Blvd., Room 6115, MSC 9605 Bethesda, MD 20892-9605 Telephone: (301) 443-2805 Fax: (301) 443-6885 Email: Diana_Trunnell@nih.gov Donna Huggins Grants Management Branch National Institute of Diabetes and Digestive and Kidney Diseases 6707 Democracy Blvd., Room 711 MSC 5456 Bethesda, MD 20892-5456 (For Express Mail Use Zip Code 20817) Telephone: (301) 594-8848 Fax: (301) 480-3504 Email: Hugginsd@extra.niddk.nih.gov Gary Fleming, J.D., M.A. Grants Management Branch Office of Planning and Resource Management National Institute on Drug Abuse/NIH 6001 Executive Boulevard, Room 3131, MSC 9541 Bethesda, MD 20892-9541 Telephone: (301) 443-6710 Fax: (301) 594-6847 Email: gf6s@nih.gov Carolyn Winters Grants Management Specialist Division of Extramural Research and Training National Institute of Environmental Health Sciences 111 Alexander Drive Research Triangle Park, NC 27709 Telephone: (919) 541-7823 Fax: (919) 541-2860 Email: winters@niehs.nih.gov Kathleen Howe Grants Management Branch National Institute of Neurological Disorders and Stroke 6001 Executive Blvd, Room 3290 MSC 9537 Bethesda, MD 20892 Telephone: (301) 496-9231 Fax: (301) 402-0219 Email: kh52x@nih.gov SUBMITTING AN APPLICATION Applications must be prepared using the PHS 398 research grant application instructions and forms (rev. 5/2001). The PHS 398 is available at http://grants.nih.gov/grants/funding/phs398/phs398.html in an interactive format. For further assistance contact GrantsInfo, Telephone (301) 710-0267, Email: GrantsInfo@nih.gov. APPLICATION RECEIPT DATES: Applications submitted in response to this program announcement will be accepted at the standard application deadlines, which are available at http://grants.nih.gov/grants/dates.htm. Application deadlines are also indicated in the PHS 398 application kit. SPECIFIC INSTRUCTIONS FOR MODULAR GRANT APPLICATIONS: Applications requesting up to $250,000 per year in direct costs must be submitted in a modular grant format. The modular grant format simplifies the preparation of the budget in these applications by limiting the level of budgetary detail. Applicants request direct costs in $25,000 modules. Section C of the research grant application instructions for the PHS 398 (rev. 5/2001) at http://grants.nih.gov/grants/funding/phs398/phs398.html includes step-by-step guidance for preparing modular grants. Additional information on modular grants is available at http://grants.nih.gov/grants/funding/modular/modular.htm. SPECIFIC INSTRUCTIONS FOR APPLICATIONS REQUESTING $500,000 OR MORE PER YEAR: Applications requesting $500,000 or more in direct costs for any year must include a cover letter identifying the NIH staff member within one of NIH institutes or centers who has agreed to accept assignment of the application. Applicants requesting more than $500,000 must carry out the following steps: 1) Contact the IC program staff at least 6 weeks before submitting the application, i.e., as you are developing plans for the study, 2) Obtain agreement from the IC staff that the IC will accept your application for consideration for award, and 3) Identify, in a cover letter sent with the application, the staff member and IC who agreed to accept assignment of the application. This policy applies to all investigator-initiated new (type 1), competing continuation (type 2), competing supplement, or any amended or revised version of these grant application types. Additional information on this policy is available in the NIH Guide for Grants and Contracts, October 19, 2001 at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-02-004.html. SENDING AN APPLICATION TO THE NIH: Submit a signed, typewritten original of the application, including the checklist, and five signed photocopies in one package to: Center for Scientific Review National Institutes of Health 6701 Rockledge Drive, Room 1040, MSC 7710 Bethesda, MD 20892-7710 Bethesda, MD 20817 (for express/courier service) APPLICATION PROCESSING: Applications must be received by or mailed before the receipt dates described at http://grants.nih.gov/grants/funding/submissionschedule.htm. The CSR will not accept any application in response to this PA that is essentially the same as one currently pending initial review unless the applicant withdraws the pending application. The CSR will not accept any application that is essentially the same as one already reviewed. This does not preclude the submission of a substantial revision of an application already reviewed, but such application must include an Introduction addressing the previous critique. PEER REVIEW PROCESS Applications submitted for this PA will be assigned on the basis of established PHS referral guidelines. An appropriate scientific review group convened in accordance with the standard NIH peer review procedures (http://www.csr.nih.gov/refrev.htm) will evaluate applications for scientific and technical merit. As part of the initial merit review, all applications will: o Receive a written critique o Undergo a selection process in which only those applications deemed to have the highest scientific merit, generally the top half of applications under review, will be discussed and assigned a priority score o Receive a second level review by the appropriate national advisory council or board REVIEW CRITERIA The goals of NIH-supported research are to advance our understanding of biological systems, improve the control of disease, and enhance health. In the written comments, reviewers will be asked to discuss the following aspects of your application in order to judge the likelihood that the proposed research will have a substantial impact on the pursuit of these goals: o Significance o Approach o Innovation o Investigator o Environment The scientific review group will address and consider each of these criteria in assigning your application"s overall score, weighting them as appropriate for each application. Your application does not need to be strong in all categories to be judged likely to have major scientific impact and thus deserve a high priority score. For example, you may propose to carry out important work that by its nature is not innovative but is essential to move a field forward. (1) SIGNIFICANCE: Does your study address an important problem? If the aims of your application are achieved, how do they advance scientific knowledge? What will be the effect of these studies on the concepts or methods that drive this field? (2) APPROACH: Are the conceptual framework, design, methods, and analyses adequately developed, well integrated, and appropriate to the aims of the project? Do you acknowledge potential problem areas and consider alternative tactics? (3) INNOVATION: Does your project employ novel concepts, approaches or methods? Are the aims original and innovative? Does your project challenge existing paradigms or develop new methodologies or technologies? (4) INVESTIGATOR: Are you appropriately trained and well suited to carry out this work? Is the work proposed appropriate to your experience level as the principal investigator and to that of other researchers (if any)? (5) ENVIRONMENT: Does the scientific environment in which your work will be done contribute to the probability of success? Do the proposed experiments take advantage of unique features of the scientific environment or employ useful collaborative arrangements? Is there evidence of institutional support? ADDITIONAL REVIEW CRITERIA: In addition to the above criteria, your application will also be reviewed with respect to the following: PROTECTIONS: The adequacy of the proposed protection for humans, animals, or the environment, to the extent they may be adversely affected by the project proposed in the application. INCLUSION: The adequacy of plans to include subjects from both genders, all racial and ethnic groups (and subgroups), and children as appropriate for the scientific goals of the research. Plans for the recruitment and retention of subjects will also be evaluated. (See Inclusion Criteria included in the section on Federal Citations, below) DATA SHARING: The adequacy of the proposed plan to share data. BUDGET: The reasonableness of the proposed budget and the requested period of support in relation to the proposed research. AWARD CRITERIA Applications submitted in response to a PA will compete for available funds with all other recommended applications. The following will be considered in making funding decisions: o Scientific merit (as determined by peer review) o Availability of funds o Programmatic priorities. REQUIRED FEDERAL CITATIONS INCLUSION OF WOMEN AND MINORITIES IN RESEARCH INVOLVING HUMAN SUBJECTS It is the policy of the NIH that women and members of minority groups and their sub-populations must be included in all NIH-supported biomedical and behavioral research projects involving human subjects, unless a clear and compelling rationale and justification are provided indicating that inclusion is inappropriate with respect to the health of the subjects or the purpose of the research. This policy results from the NIH Revitalization Act of 1993 (Section 492B of Public Law 103-43). All investigators proposing research involving human subjects should read the UPDATED "NIH Guidelines for Inclusion of Women and Minorities as Subjects in Clinical Research," published in the NIH Guide for Grants and Contracts on August 2, 2000 (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-00-048.html), a complete copy of the updated Guidelines are available at http://grants.nih.gov/grants/funding/women_min/guidelines_update.htm: The revisions relate to NIH defined Phase III clinical trials and require: a) all applications or proposals and/or protocols to provide a description of plans to conduct analyses, as appropriate, to address differences by sex/gender and/or racial/ethnic groups, including subgroups if applicable, and b) all investigators to report accrual, and to conduct and report analyses, as appropriate, by sex/gender and/or racial/ethnic group differences. INCLUSION OF CHILDREN AS PARTICIPANTS IN RESEARCH INVOLVING HUMAN SUBJECTS It is the policy of NIH that children (i.e., individuals under the age of 21) must be included in all human subjects research, conducted or supported by the NIH, unless there are scientific and ethical reasons not to include them. This policy applies to all initial (Type 1) applications submitted for receipt dates after October 1, 1998. All investigators proposing research involving human subjects should read the "NIH Policy and Guidelines" on the inclusion of children as participants in research involving human subjects that is available at http://grants.nih.gov/grants/funding/children/children.htm. REQUIRED EDUCATION ON THE PROTECTION OF HUMAN SUBJECT PARTICIPANTS: NIH policy requires education on the protection of human subject participants for all investigators submitting NIH proposals for research involving human subjects. You will find this policy announcement in the NIH Guide for Grants and Contracts Announcement, dated June 5, 2000, at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-00-039.html. HUMAN EMBRYONIC STEM CELLS (hESC): Criteria for federal funding of research on hESCs can be found at http://grants.nih.gov/grants/stem_cells.htm and at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-02-005.html. Only research using hESC lines that are registered in the NIH Human Embryonic Stem Cell Registry will be eligible for Federal funding (see http://escr.nih.gov). It is the responsibility of the applicant to provide the official NIH identifier(s)for the hESC line(s)to be used in the proposed research. Applications that do not provide this information will be returned without review. PUBLIC ACCESS TO RESEARCH DATA THROUGH THE FREEDOM OF INFORMATION ACT The Office of Management and Budget (OMB) Circular A-110 has been revised to provide public access to research data through the Freedom of Information Act (FOIA) under some circumstances. Data that are (1) first produced in a project that is supported in whole or in part with Federal funds and (2) cited publicly and officially by a Federal agency in support of an action that has the force and effect of law (i.e., a regulation) may be accessed through FOIA. It is important for applicants to understand the basic scope of this amendment. NIH has provided guidance at http://grants.nih.gov/grants/policy/a110/a110_guidance_dec1999.htm Applicants may wish to place data collected under this RFA (PA) in a public archive, which can provide protections for the data and manage the distribution for an indefinite period of time. If so, the application should include a description of the archiving plan in the study design and include information about this in the budget justification section of the application. In addition, applicants should think about how to structure informed consent statements and other human subjects procedures given the potential for wider use of data collected under this award. URLS IN NIH GRANT APPLICATIONS OR APPENDICES All applications and proposals for NIH funding must be self-contained within specified page limitations. Unless otherwise specified in an NIH solicitation, internet addresses (URLs) should not be used to provide information necessary to the review because reviewers are under no obligation to view the Internet sites. Reviewers are cautioned that their anonymity may be compromised when they directly access an Internet site. HEALTHY PEOPLE 2010 The Public Health Service (PHS) is committed to achieving the health promotion and disease prevention objectives of "Healthy People 2010," a PHS led national activity for setting priority areas. This Program Announcement (PA), Genetic Architecture, Biological Variation, and Complex Phenotypes, is related to one or more of the priority areas. Potential applicants may obtain a copy of "Healthy People 2010" at http://www.health.gov/healthypeople/. AUTHORITY AND REGULATIONS This program is described in the Catalog of Federal Domestic Assistance No. 93.862, 93.847, 93.848, 93.242, 93.172, 93.279, 93.849 and 93.853 and is not subject to the intergovernmental review requirements of Executive Order 12372 or Health Systems Agency review. Awards are made under authorization of sections 301 and 405 of the Public Health Service Act as amended (42 USC 241 and 284) and administered under NIH grants policies described at http://grants.nih.gov/grants/policy/policy.htm and under Federal Regulations 42 CFR 52 and 45 CFR Parts 74 and 92. The PHS strongly encourages all grant and contract recipients to provide a smoke-free workplace and promote the non-use of all tobacco products. In addition, Public Law 103-227, the Pro-Children Act of 1994, prohibits smoking in certain facilities (or in some cases, and portion of a facility) in which regular or routine education, library, day care, health care or early childhood development services are provided to children. This is consistent with the PHS mission to protect and advance the physical and mental health of the American people.
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