TOOLS FOR GENETIC AND GENOMIC STUDIES IN EMERGING MODEL ORGANISMS 

RELEASE DATE: July 28, 2004

PA NUMBER:  PA-04-135 - September 29, 2007 (Reissued as PA-07-457)

September 17, 2007 - Expiration Date adjusted to accommodate recent changes 
to standing  submission deadlines, per NOT-OD-07-093.

May 10, 2006 (NOT-GM-06-010) - See this notice for Changes in 
Program Announcement PA-04-135: Tools for Genetic and Genomic 
Studies in Emerging Model Organisms 

EXPIRATION DATE: November 2, 2007, unless reissued (September 28, 2007 per PA-07-457)

(January 8, 2008 per NOT-OD-07-093)

Department of Health and Human Services (DHHS)

PARTICIPATING ORGANIZATION:  
National Institutes of Health (NIH)
(http://www.nih.gov)

COMPONENT OF PARTICIPATING ORGANIZATION:
National Institute of General Medical Sciences (NIGMS)
(http://www.nigms.nih.gov) 

CATALOG OF FEDERAL DOMESTIC ASSISTANCE NUMBER(S):  93.859

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 Special Requirements 
o Where to Send Inquiries
o Submitting an Application
o Supplementary Instructions
o Peer Review Process
o Review Criteria
o Award Criteria
o Required Federal Citations

PURPOSE OF THIS PA  

This Program Announcement (PA) is to encourage investigator-initiated 
applications for research designed to generate genetic tools and genomic 
resources that will enable researchers to exploit the full potential of novel 
or developing model systems for comparative and functional genomic studies. 
The typical model organism to be considered should have a publicly available 
draft of the genomic DNA sequence with a minimum of 5X coverage. In addition, 
it should have at least one of the following characteristics: (1) shows 
promise as, or is, a model for basic biological or behavioral mechanisms; (2) 
occupies an important evolutionary niche that may yield novel insights in 
comparative studies; or (3) has potential as, or is, a model for 
developmental or disease processes. Applicants are expected to ensure that 
reagents, technologies, and resources developed under this initiative are 
made widely available to the research community.  

This PA is not intended to encourage genome sequencing projects or studies of 
model organisms for which there are well-established databases and other 
genome-related resources – e.g. mouse, Drosophila, C. elegans, S. cerevisiae. 
In general, resources to study organisms that fit primarily within the 
mission of another NIH Institute or Center, such as, pathogenic 
microorganisms, are not encouraged through this PA.

RESEARCH OBJECTIVES

The advent of the genomic era has been a boon for the investigation of a 
growing number of model organisms. Completion of DNA sequencing of each 
genome presents opportunities for novel insights into genomic function, the 
regulation of gene expression, and evolutionary processes. Yet, the large 
scale of many sequencing projects and the sheer volume of sequence data 
create a considerable challenge for the individual investigator as well as 
consortia of researchers to obtain the resources and tools required to make 
maximal use of genomic information for comparative or functional studies. 

The major goal of this PA is to support research that will enhance the 
usefulness of DNA sequence information for newly emerging or developing model 
organisms for which there are limited genomic resources. Objectives to be 
addressed in applications submitted in response to this PA include, but are 
not limited to, the following:

o Improvements in tools for mining of data for genomes having unique 
composition or structure
o Improved database management and integration with other databases 
(Requests for the maintenance of databases alone are not encouraged.)
o Generation of comprehensive cDNA libraries 
o Development of microarray reagents and/or services
o Improved methods for linking expression arrays with standard phenotypes or 
with specific biological or behavioral outcomes 
o Development of novel approaches for mutagenesis and for rapid 
identification and characterization of point mutations
o Development of novel transposable element-based techniques for the 
generation of knockouts or other mutations 
o Improvements in gene transfer technology and in vectors for genomic 
manipulation 
o Generation of sets of gene knockouts or knock-downs

MECHANISM(S) OF SUPPORT 

This PA will use the National Institutes of Health (NIH) research resource
grant (R24) mechanism.  Responsibility for the planning, direction, and
execution of the proposed project will be solely that of the applicant.  The
total project period for an application submitted in response to this PA may
not exceed four years. A maximum of $250,000 direct costs (exclusive of 
subcontractual indirect costs) per year will be provided.

This PA uses just-in-time concepts. It uses the non-modular budgeting format. 
Follow the instructions for non-modular budget research grant applications.  
This program does not require cost sharing as defined in the current NIH 
Grants Policy Statement at 
http://grants.nih.gov/grants/policy/nihgps_2003/NIHGPS_Part2.htm.  

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/organizations

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 underrepresented racial 
and ethnic groups as well as individuals with disabilities are always 
encouraged to apply for NIH programs.   

SPECIAL REQUIREMENTS 

The NIH is interested in ensuring that the research resources (constructs, 
reagents, cell lines, software tools, expression data, methods, etc.) 
developed through this PA become readily available to the research community 
for further research, development, and application, in the expectation that 
this will lead to products and knowledge of benefit to the public.  At the 
same time, NIH recognizes the rights of grantees to elect and retain title to 
subject inventions developed under federal funding under the provision of the 
Bayh-Dole Act.

This PA has two special requirements regarding research resources produced in 
proposed projects:

(1) Applicants are required to include in their applications a specific plan 
by which they will share research resources with the wider scientific 
community. A reasonable time frame for periodic deposition of mutants, 
reagents, and data should be specified in the application. 

(2) Applicants are required to include a plan addressing if, or how, they 
will exercise their intellectual property rights while making available to 
the broader scientific community patentable research resources.  The plan 
should address the following questions:

o Will material transfers be made with no more restrictive terms than in the 
Simple Letter Material Transfer Agreement or the Uniform Biological 
Material Transfer Agreement?
o Will there be reach-through requirements on materials transferred?
o Should any intellectual property arise that requires a patent, will the 
technology remain widely available to the research community?

Both the sharing and intellectual property plans should, at a minimum, 
address these elements in a clear and concise manner.  Applicants are 
encouraged to inform and/or confer with their institutional offices of 
technology transfer to develop plans for addressing these requirements.
 
Applicants are reminded that the grantee institution is required to disclose 
each subject invention to NIH within two months after the inventor discloses 
it in writing to grantee institutional personnel responsible for patent 
matters.  The awarding Institute reserves the right to monitor awardee 
activity in this area to ascertain if patents or patent applications are 
adversely affecting the goals of this PA.

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:

Anthony Carter, Ph.D.
Division of Genetics and Developmental Biology
National Institute of General Medical Sciences
Building 45, Room 2AS-25R, MSC 6200
Bethesda, MD 20892-6200
Telephone: 301-594-0943
FAX: 301-480-2228
Email: CarterA@nigms.nih.gov

o   Direct inquiries about financial or grants management matters to:

Ms. Marcia Cohn
Grants Administration Branch
National Institute of General Medical Sciences
Building 45, Room 2AN50E, MSC 6200
Bethesda, MD 20892-6200
Telephone: 301-594-3918
FAX: 301-480-2554
Email: cohnm@nigms.nih.gov

SUBMITTING AN APPLICATION

Applications must be prepared using the PHS 398 research grant application 
instructions and forms (rev. 5/2001). Applications must have a Dun and 
Bradstreet (D&B) Data Universal Numbering System (DUNS) number as the 
Universal Identifier when applying for Federal grants or cooperative 
agreements. The DUNS number can be obtained by calling (866) 705-5711 or 
through the web site at http://www.dunandbradstreet.com/. The DUNS number 
should be entered on line 11 of the face page of the PHS 398 form. 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.

The title and number of this program announcement must be typed on line 2 of 
the face page of the application form and the YES box must be checked.

SUPPLEMENTARY INSTRUCTIONS 

APPLICATION CONTENTS: In the Background section, the applicant should include 
a description of existing publicly available resources for the model organism 
being studied. The applicant should define how the proposal will enhance 
available resources and provide evidence of research community consultation 
and consensus regarding the potential value of the resource.

In a brief section following the research plan, the applicant must describe 
plans to share research resources and to exercise intellectual property 
rights (see SPECIAL REQUIREMENTS).  

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.

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 mailed on or 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 unfunded version of an application 
already reviewed, but such application must include an Introduction 
addressing the previous critique.  

Although there is no immediate acknowledgement of the receipt of an 
application, applicants are generally notified of the review and funding 
assignment within 8 weeks.

PEER REVIEW PROCESS

Applications submitted for this PA will be assigned on the basis of 
established PHS referral guidelines.  Appropriate scientific review groups 
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 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 written critique
o Receive a second level review by the National Advisory General Medical 
Sciences Council.  

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 evaluate application in 
order to judge the likelihood that the proposed research will have a 
substantial impact on the pursuit of these goals.  The scientific review 
group will address and consider each of the following criteria in assigning 
the application’s overall score, weighting them as appropriate for each 
application.

o Significance 
o Approach 
o Innovation
o Investigator
o Environment
  
The 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, an investigator may propose to carry out important work 
that by its nature is not innovative but is essential to move a field 
forward.

SIGNIFICANCE: Does the proposed resource or technology development address an 
important problem or need? If the aims of the application are achieved, how 
will scientific knowledge be advanced? What will be the effect of this 
project on the concepts or methods that drive the field? Will this project 
enhance the usefulness of the model organism being studied?

APPROACH: Are the conceptual framework, design, methods, and analyses 
adequately developed, well-integrated, and appropriate to the aims of the 
project? Does the applicant acknowledge potential problem areas and consider 
alternative tactics?

INNOVATION: Does the project employ novel concepts, approaches or methods? 

INVESTIGATOR: Is the investigator appropriately trained and well suited to 
carry out this work? Is the work proposed appropriate to the experience level 
of the principal investigator and other researchers (if any)?

ENVIRONMENT: Does the scientific environment in which the 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 CRITERION: In addition to the above criteria, the following 
item will be considered in the determination of scientific merit and the 
priority score:

CARE AND USE OF VERTEBRATE ANIMALS IN RESEARCH: If vertebrate animals are to 
be used in the project, the five items described under Section f of the PHS 
398 research grant application instructions (rev. 5/2001) will be assessed.  

ADDITIONAL REVIEW CONSIDERATIONS 

DATA SHARING:  Reviewers will evaluate the reasonableness of the data sharing 
plan. However, reviewers will not factor the proposed data sharing plan into 
the determination of scientific merit or priority score. 

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 of the proposed project as determined by peer review
o Availability of funds 
o Relevance to program priorities

REQUIRED FEDERAL CITATIONS 

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 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.   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 PA 
is related to one or more of the priority areas. Potential applicants may 
obtain a copy of "Healthy People 2010" at http://www.healthypeople.gov/.

AUTHORITY AND REGULATIONS: This program is described in the Catalog of 
Federal Domestic Assistance at http://www.cfda.gov/ and is not subject 
to the intergovernmental review requirements of Executive Order 12372 
or Health Systems Agency review.  Awards are made under the 
authorization of Sections 301 and 405 of the Public Health Service Act 
as amended (42 USC 241 and 284) and under Federal Regulations 42 CFR 52 
and 45 CFR Parts 74 and 92. All awards are subject to the terms and 
conditions, cost principles, and other considerations described in the 
NIH Grants Policy Statement.  The NIH Grants Policy Statement can be 
found at http://grants.nih.gov/grants/policy/policy.htm. 
 
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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