GENE DISCOVERY FOR CRANIOFACIAL DISORDERS RELEASE DATE: May 9, 2002 RFA: DE-03-001 PARTICIPATING INSTITUTES AND CENTERS (ICs): National Institute of Dental and Craniofacial Research (NIDCR) (http://www.nidr.nih.gov/) National Eye Institute (NEI) (http://www.nei.nih.gov/) LETTER OF INTENT RECEIPT DATE: June 30, 2002 APPLICATION RECEIPT DATE: July 30, 2002 THIS RFA CONTAINS THE FOLLOWING INFORMATION o Purpose of this RFA o Research Objectives o Mechanisms of Support o Funds Available o Eligible Institutions o Individuals Eligible to become Principal Investigators o Where to Send Inquiries o Letter of Intent o Submitting an Application o Peer Review Process o Review Criteria o Receipt and Review Schedule o Award Criteria o Required Federal Citations: PURPOSE OF THIS RFA The National Institute of Dental and Craniofacial Research (NIDCR) and the National Eye Institute (NEI) invite applications aimed at fostering creative approaches for the discovery of genes that cause or modify susceptibility to craniofacial, dental, oral, and ocular disorders. The applications may be for individual research projects (R01) or for exploratory/developmental grants (R21). This Request for Applications (RFA) encourages research projects focused on identifying genes that cause craniofacial disorders, modifier genes that influence risk, and environmental conditions that alter gene expression and modify susceptibility in diverse genetic backgrounds. Advances in genetic studies will reveal the molecular networks that regulate the formation of craniofacial, dental, and ocular tissues and thus, shed light on pathogenic mechanisms leading to structural defects and disorders. These advances will provide a basis for gene-based diagnostic criteria, improved genetic counseling, and they will provide insights for developing novel prevention and therapeutic strategies. Collaborative projects involving interdisciplinary teams of investigators are strongly encouraged. RESEARCH OBJECTIVES Background Birth defects affect 5% of all infants born in the United States, and three-quarters of these involve the head, face and oral tissues. This means that in the United States there is a child born every 5 minutes with a craniofacial defect. While there are several hundred disorders affecting the face, skull, jaw, eyes and teeth, by far the most common craniofacial defect is isolated, or non-syndromic cleft lip with or without cleft palate (CL/P) that affects more than one child per 1000 births. Other hereditary syndromes such as ectodermal dysplasias are marked by the absence of all or most teeth in children and adults, while Rieger"s syndrome is associated with significant ocular and tooth anomalies. The social and economic costs of craniofacial disorders are enormous and they place a disproportionately high burden on particular population subgroups. During the past decade, there has been significant progress in identifying the genetic basis of many rare craniofacial and ophthalmologic disorders that are strongly influenced by single genes (i.e., hypohidrotic ectodermal dysplasia, dentinogenesis imperfecta II, Papillon-Lefevre syndrome, Apert syndrome, aniredia, and congenital fibrosis of the extraocular muscles). Progress has been substantially slower for the more common craniofacial disorders that are complex disorders influenced by multiple genes interacting with each other and with environmental factors. The search for susceptibility loci for complex craniofacial disorders such as non-syndromic cleft lip with or without cleft palate (CL/P) has often yielded weak linkages and inconsistent results. This may be due in part, to the limitations of current linkage strategies as well as our lack of understanding of the role of genetic polymorphisms in response to environmental factors. Genetic analysis may also be hampered by the use of disease categories that combine phenotypes of different severity that may represent genetically heterogeneous defects. Identification of susceptibility genes for craniofacial disorders will permit studies of the molecular pathways leading to these disorders and will enhance our understanding of individual risk, clinical phenotype, and variation in response to environmental factors. The current initiative is the result of recommendations from several prior NIDCR-supported conferences focused on craniofacial disorders and genetics. These meetings highlighted the major scientific opportunities created by the wealth of genomic information from the Human, Mouse and other Genome Projects for the discovery of genes involved in craniofacial disorders. These meetings include the Workshop on the Prevention of Craniofacial Anomalies, held in September 1999, the NIDCR Genetics Workgroup held in November 1999, and a series of three NIDCR-sponsored World Health Organization meetings "International Collaborative Research on Craniofacial Anomalies" held in 2000-2001. Scope Applications submitted in response to this announcement should focus on discovery of genes causing or contributing to craniofacial, oral, dental, and ocular disorders. A partial list of disorders of interest to NIDCR is available in Appendix 5 of the Report of the NIDCR Genetics Workgroup http://www.nidr.nih.gov/about/strat-plan/Genetics_Rpt.pdf). These include common disorders such as orofacial clefting and hypodontia/tooth agenesis as well as a broad spectrum of less common disorders such as amelogenesis and dentinogenesis imperfecta, Sjögren"s syndrome, Treacher-Collins syndrome, Papillon-Lefevre syndrome, and many others. The types of research that would be encouraged by the proposed initiative include: o Discovery of genes involved in single-gene or polygenic disorders that affect dental, oral, ocular and craniofacial tissues throughout the lifespan. o Genotype-phenotype analysis including correlations of specific allelic variants in primary or modifier genes and their clinical phenotype. o Studies focused on distinguishing heterogeneous genetic subgroups that show similar clinical presentations. o Research strategies for gene discovery for craniofacial disorders may include traditional linkage analysis, case-control association studies, linkage disequilibrium mapping, candidate gene analyses, positional cloning techniques, SNP variant analyses, gene expression profiling and proteomics using microarray and other high-throughput technologies. o Studies in model organisms(e.g., mouse, rat, zebrafish, chick, and fruit fly) for identifying and validating candidate and modifier genes, and for analyzing molecular mechanisms that underlie genetic disorders are encouraged as research indicates that key molecules involved in facial specification and assembly are evolutionarily conserved. o Backcross strategies such as speed congenics for mapping susceptibility loci and evaluating modifier genes that influence penetrance and expressivity. High-throughput human and mouse genotyping services are available to applicants through the Center for Inherited Disease Research (CIDR). Since NIDCR and NEI are NIH Institutes that participate in the support of CIDR, research projects funded under this initiative are eligible to apply for no-cost genotyping services at CIDR through a competitive peer review process by a chartered CIDR Access Committee (CAC). Detailed information and deadlines for applications to CIDR are available at http://www.cidr.jhmi.edu. Applicants are also advised of the availability of global gene expression profiles during early stages of human craniofacial, oral and dental development. These resource tools are available through the Craniofacial and Oral Gene Expression Network (COGENE) a NIDCR- supported consortium, and can be accessed at the web site http://hg.wustl.edu/COGENE. This initiative encourages multidisciplinary approaches involving geneticists, molecular biologists, dental and medical clinicians, epidemiologists, ophthalmologists, optometrists, bioinformaticians, and researchers in other disciplines in order to enhance gene discovery research. Applicants are strongly encouraged to develop comprehensive operational diagnostic criteria that include state-of-the-art diagnostic methodologies such as imaging techniques in order to refine diagnostic classifications. Diagnostic criteria for many rare craniofacial disorders are highly variable and this hampers attempts to combine data across samples and to replicate findings. Analysis of genetic and environmental etiologies for complex traits such as orofacial clefting, will benefit from the application of sophisticated methodologies that permit phenotypic subgroups to be distinguished and classification schema to be developed. MECHANISMS OF SUPPORT This RFA will use NIH R01 (investigator-initiated research project grant) and the R21 (exploratory/developmental research grant) award mechanisms. As an applicant you will be solely responsible for planning, directing, and executing the proposed project. This RFA is a one-time solicitation. Future unsolicited, competing-continuation applications based on this project will compete with all investigator- initiated applications and will be reviewed according to the customary peer review procedures. The anticipated award date is February 01, 2003. This RFA uses just-in-time concepts. It also uses the modular budgeting format. (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. R21 Applications. R21 proposals should have the potential for truly groundbreaking impact. Use of this mechanism by investigators experienced in orofacial disorders who wish to explore new genetic approaches to address basic and applied research questions is encouraged. Investigators with expertise in fields other than orofacial disorders who wish to establish new research programs on the genetics of these disorders is also encouraged. Applicants are encouraged to contact program staff for advice about choosing the appropriate grant mechanism. FUNDS AVAILABLE The NIDCR intends to commit approximately $2,500,000 and the NEI intends to commit approximately $1,500,000 in FY 2003 to fund 10 to 16 new grants in response to this RFA. An R01 applicant may request a project period of up to 4 years and a budget for direct costs of up to $250,000 per year. An R21 applicant may request a project period of up to 2 years and a budget for direct costs of up to $125,000 per year. Because the nature and scope of the proposed research will vary from application to application, it is anticipated that the size and duration of each award will also vary. Although the financial plans of the ICs provide support for this program, awards pursuant to this RFA are contingent upon the availability of funds and the receipt of a sufficient number of meritorious applications. At this time, it is not known if this RFA will be reissued. 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 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 their institution to develop an application for support. Individuals from under-represented racial and ethnic groups as well as individuals with disabilities are always encouraged to apply for NIH programs. SPECIAL REQUIREMENTS Plan for Dissemination of Data and Biomaterials Rapid sharing of data and biomaterials is strongly encouraged. Applications are required to contain a detailed plan for the timely dissemination of data and biomaterials generated through the grant, in agreement with PHS policy (NIH Grants Policy Statement at http://grants.nih.gov/grants/guide/notice-files/not96-184.html. Sharing of data and biomaterials is essential to foster rapid progress in genetic studies of craniofacial disorders. The information to be shared is expected to include pedigree structures and all clinical and diagnostic data, which should be stripped of personal identifiers and placed in publicly accessible databases. Applicants may also propose to share biomaterials such as DNA samples and cell lines. The Initial Review Group will evaluate the proposed sharing plan and comment on its adequacy as an administrative note in the summary statement. The adequacy of the sharing plan will be considered by NIH staff in determining whether the grant shall be awarded. The sharing plan as approved, after negotiation with the applicant when necessary, will be a condition of the award. Evaluation of renewal applications will include an assessment of the effectiveness of data and biomaterial release. WHERE TO SEND INQUIRIES We encourage inquiries concerning this RFA and welcome the opportunity to answer questions from potential applicants. Inquiries may fall into three areas: scientific/research, peer review, and financial or grants management issues: o Direct your questions about scientific/research issues to: Rochelle K. Small, Ph.D. Director, Developmental Biology and Mammalian Genetics Division of Basic and Translational Sciences National Institute of Dental and Craniofacial Research National Institutes of Health 45 Center Drive, Room 4AN-44F Bethesda, MD 20892-6402 Telephone: (301) 594-9898 FAX: (301) 480-8318 Email: Rochelle.Small@nih.gov Ellen Liberman, Ph.D. National Eye Institute Executive Plaza South, Suite 350 6120 Executive Blvd., MSC 7164 Bethesda, MD 20892-7164 Phone: (301) 451-2020 Fax: (301) 502-0528 Email: ellenliberman@nei.nih.gov o Direct your questions about peer review issues to: H. George Hausch, Ph.D. Acting Director, Division of Extramural Activities National Institute of Dental and Craniofacial Research National Institutes of Health 45 Center Drive, Room 4AN-44F Bethesda, MD 20892-6402 Telephone: (301) 594-2904 FAX: (301) 480-8303 Email: George.Hausch@nih.gov Direct your questions about financial or grants management matters to: Mr. Kevin Crist Grants Management Branch Division of Extramural Activities National Institute of Dental and Craniofacial Research 45 Center Drive, Room 4AN-44F Bethesda, MD 20892-6402 Telephone: (301) 594-4800 Fax: (301) 402-1517 Email: Kevin.Crist@nih.gov Mr. William W. Darby Grants Management Branch Division of Extramural Research National Eye Institute 6120 Executive Blvd., Suite 350 Bethesda, MD 20892-7164 Telephone: (301) 451-2020 Fax: (301) 496-9997 Email: wwd@nei.nih.gov LETTER OF INTENT Prospective applicants are asked to submit a letter of intent that includes the following information: o Descriptive title of the proposed research o Name, address, and telephone number of the Principal Investigator o Names of other key personnel o Participating institutions o Number and Title of this RFA Although a letter of intent is not required, is not binding, and does not enter into the review of a subsequent application, the information that it contains allows NIDCR staff to estimate the potential review workload and plan the review. The letter of intent is to be sent by the date listed at the beginning of this document. The letter of intent should be sent to: H. George Hausch, Ph.D. Acting Director, Division of Extramural Activities National Institute of Dental and Craniofacial Research National Institutes of Health 45 Center Drive, Room 4AN-44F Bethesda, MD 20892-6402 Telephone: (301) 594-2904 FAX: (301) 480-8303 Email: George.Hausch@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) 435-0714, Email: GrantsInfo@nih.gov. 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. USING THE RFA LABEL: The RFA label available in the PHS 398 (rev. 5/2001) application form must be affixed to the bottom of the face page of the application. Type the RFA number on the label. Failure to use this label could result in delayed processing of the application such that it may not reach the review committee in time for review. In addition, the RFA title and number must be typed on line 2 of the face page of the application form and the YES box must be marked. The RFA label is also available at: http://grants.nih.gov/grants/funding/phs398/label-bk.pdf. SENDING AN APPLICATION TO THE NIH: Submit a signed, typewritten original of the application, including the Checklist, and three 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) At the time of submission, two additional copies of the application must be sent to: Dr. H. George Hausch Division of Extramural Activities National Institute of Dental and Craniofacial Research 45 Center Drive, Room 4AN-44F Bethesda, MD 20892-6402 APPLICATION PROCESSING: Applications must be received by July 30, 2002. If an application is received after that date, it will be returned to the applicant without review. The Center for Scientific Review (CSR) will not accept any application in response to this RFA 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 substantial revisions of applications already reviewed, but such applications must include an Introduction addressing the previous critique. PEER REVIEW PROCESS Upon receipt, applications will be reviewed for completeness by the CSR and responsiveness by NIDCR and NEI. Incomplete applications will be returned to the applicant without further consideration. And, if the application is not responsive to the RFA, CSR staff may contact the applicant to determine whether to return the application to the applicant or submit it for review in competition with unsolicited applications at the next appropriate NIH review cycle. Applications that are complete and responsive to the RFA will be evaluated for scientific and technical merit by an appropriate peer review group convened by the NIDCR in accordance with the review criteria stated below. As part of the initial merit review, all applications will: o Receive a written critique o Undergo a process in which only those applications deemed to have the highest scientific merit, generally the top half of the applications under review, will be discussed and assigned a priority score o Receive a second level review by the National Advisory Councils of either NIDCR or NEI. 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: o 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. o 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) o SHARING PLAN: The adequacy of the proposed plan to make all data and biological materials collected and produced as a result of the proposed research accessible in a timely manner to the biomedical research community. o BUDGET: The reasonableness of the proposed budget and the requested period of support in relation to the proposed research. o OTHER REVIEW CRITERIA: R21 applications only: Does this project have the potential for groundbreaking impact? If successful, will this project achieve at least one of the following goals: 1) generate pilot data to assess the feasibility of a novel avenue of investigation, 2) involve high risk experiments that could lead to a breakthrough in a particular field, or 3) demonstrate the feasibility of new technologies that could have major impact in a specific area. RECEIPT AND REVIEW SCHEDULE Letter of Intent Receipt Date: June 30, 2002 Application Receipt Date: July 30, 2002 Peer Review Date: Fall 2003 Council Review: January 2003 Earliest Anticipated Start Date: February 1, 2003 AWARD CRITERIA Award criteria that will be used to make award decisions include: o Scientific merit (as determined by peer review) o Availability of funds o Programmatic priorities o Adequacy of proposed sharing plan REQUIRED FEDERAL CITATIONS INCLUSION OF WOMEN AND MINORITIES IN CLINICAL RESEARCH: 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 clinical research projects unless a clear and compelling justification is 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 clinical research should read the AMENDMENT "NIH Guidelines for Inclusion of Women and Minorities as Subjects in Clinical Research - Amended, October, 2001," published in the NIH Guide for Grants and Contracts on October 9, 2001 (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-02-001.html), a complete copy of the updated Guidelines are available at http://grants.nih.gov/grants/funding/women_min/guidelines_amended_10_2001.htm. The amended policy incorporates: the use of an NIH definition of clinical research, updated racial and ethnic categories in compliance with the new OMB standards, clarification of language governing NIH-defined Phase III clinical trials consistent with the new PHS Form 398, and updated roles and responsibilities of NIH staff and the extramural community. The policy continues to require for all NIH- defined Phase III clinical trials that: a) all applications or proposals and/or protocols must 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) investigators must report annual accrual and progress in conducting analyses, as appropriate, by sex/gender and/or racial/ethnic group differences. INCLUSION OF CHILDREN AS PARTICIPANTS IN RESEARCH INVOLVING HUMAN SUBJECTS: The NIH maintains a policy 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 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. Furthermore, we caution reviewers 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 RFA 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. 93.173 (NIDCR) and No. 93.867 (NEI) 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 recipients to provide a smoke- free workplace and discourage the 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, any 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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