GENE EXPRESSION STUDIES IN ARTHRITIS AND MUSCULOSKELETAL AND SKIN 
DISEASES
 
RELEASE DATE:  December 4, 2002
 
RFA:  AR-03-007
 
National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
 (http://www.niams.nih.gov/)
 
LETTER OF INTENT RECEIPT DATE:  February 17, 2003

APPLICATION RECEIPT DATE:  March 17, 2003
 
THIS RFA CONTAINS THE FOLLOWING INFORMATION

o Purpose of this RFA
o Research Objectives
o Mechanism(s) of Support 
o Funds Available
o Eligible Institutions
o Individuals Eligible to Become Principal Investigators
o Special Requirements
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 

This solicitation is intended to facilitate the use of comprehensive 
gene expression analysis technology in basic and clinical research 
relevant to arthritis and musculoskeletal and skin diseases. The NIAMS 
invites two types of applications. First, Principal Investigators who 
are currently supported by research project grants from the NIAMS are 
invited to submit competing supplement applications, proposing the 
expansion of the scope of the projects to include use of comprehensive 
gene expression analysis technology. Second, scientists with 
established expertise in arthritis or musculoskeletal or skin diseases 
are invited to propose new projects in which comprehensive gene 
expression analysis technology is a major and essential component, and 
in which new insights are likely to be obtained that would not arise 
from the use of conventional analytical techniques.
 
RESEARCH OBJECTIVES

Background and Rationale

In recent years, a variety of techniques have been developed that allow 
for the assessment of messenger RNA levels for very large numbers of 
genes in a single procedure. The most commonly used tools are high-
density arrays of hybridization probes, which have been produced using 
either synthetic oligonucleotides or cloned DNA fragments. High-
throughput sequencing of concatenated DNA fragments has also shown 
promise. The adoption of these techniques has presented a number of 
challenges, both technical and conceptual. Technical problems include 
the specialized and costly nature of the required equipment, the 
substantial degree of skill and experience required to make use of the 
techniques, the limited availability of standardized probe collections, 
and the bioinformatic problems of analyzing very large datasets.  
Conceptually, it has been difficult to frame rigorous hypotheses and 
models that integrate the enormous amount of detail obtained in these 
experiments with broader questions in biology and medicine. This 
solicitation is intended to focus available resources on those 
applications of gene expression analysis that hold the most immediate 
promise of contributing to rigorous investigations in areas within the 
NIAMS mission.

Objectives and Scope

Proposed research must support the NIAMS mission as detailed in the
NIAMS World Wide Web home page, which can be found at 
http://www.niams.nih.gov/rtac/funding/faq.htm. In brief, the NIAMS 
supports research in: rheumatic diseases; cartilage biology and 
diseases; bone biology and diseases (e.g., osteoporosis, Paget's 
disease); skin biology and skin diseases; autoimmune diseases (e.g., 
lupus, rheumatoid arthritis); connective tissue diseases; 
musculoskeletal diseases (e.g., osteoarthritis); musculoskeletal 
imaging; injuries and disorders of the musculoskeletal system; muscle 
biology and diseases (e.g., muscular dystrophy); exercise physiology 
and musculoskeletal fitness; sports injuries; occupational diseases and 
injuries; and orthopaedic and bioengineering topics.

Applications will be accepted across the spectrum of biological models 
and diseases within the NIAMS mission. The primary objective of this 
initiative is to focus resources on specific biological and medical 
problems for which the immediate application of comprehensive gene 
expression analysis technology has the potential to yield significant 
new insights. For example, characterizing gene knockout or transgenic 
mouse strains, in which genetic variation from controls is limited and 
known, should produce manageable datasets, and may indicate the 
downstream targets of inactivated or introduced genes. In more complex 
situations, computational approaches such as hierarchical clustering 
can group genes into subsets showing coordinated expression patterns, 
presumably reflecting related functions. However, such an approach must 
be firmly grounded in established biology.  

A second objective is to direct support to groups that are in the best 
position to make use of comprehensive gene expression analysis 
technology at this time. These are likely to be groups with access to 
necessary equipment, and with substantial previous experience in the 
use of the technology. Alternatively, investigators may establish 
collaborations with other scientists having the requisite expertise, or 
make use of commercial products and services that standardize aspects 
of the technology.

Examples of situations in which a response to this RFA may be 
appropriate include, but are not limited to, the following:
 
o On-going NIAMS-funded projects in which comprehensive gene expression 
analysis was not originally included in the research design, but in 
which such analysis can be justified in pursuit of the original aims.

o On-going NIAMS-funded projects in which results to date justify 
expansion of the scope to include new but related aims requiring 
comprehensive gene expression analysis.

o On-going NIAMS-funded projects in which comprehensive gene expression 
analysis was included in the original design, but in which the 
originally budgeted funds have proven inadequate to support rigorous 
application of the technology.

o New projects in which existing comprehensive gene expression data, 
(e.g., from publicly accessible data resources) will be analyzed to 
achieve aims relevant to the NIAMS mission.

o New projects requiring comprehensive gene expression analysis, and 
making use of existing patient cohorts or specimen archives, whether the 
original development of the resource was NIAMS-supported or not.

o New projects that would have been impractical to undertake with older 
analytical methods, but which may be tractable with the application of 
comprehensive gene expression analysis techniques.

MECHANISM OF SUPPORT
 
This RFA will use NIH competing supplement and investigator-initiated 
research project grant (R01) 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 September 2003.

Competing supplement applications are subject to the requirements 
stated in the Form 398 instructions (see 
ftp://ftp.grants.nih.gov/forms/phs398.pdf.) Briefly, a competing 
supplement application may be submitted to request support for a 
significant expansion of a project's scope or research protocol. The 
principal investigator must be the same as the principal investigator 
of the parent application.  Supplemental applications must include both 
a Progress Report for the current grant and an Introduction, providing 
an overall description of the nature of the supplement and how it will 
influence the specific aims, research design, and methods of the 
current grant. Only R01, P01, R37, P30, P50, P60, and U01 awards are 
eligible for supplements under this initiative. In order to be 
considered for a supplement, the current grant must have at least two 
years of funding remaining at the time of the supplement award. A 
supplement request may not extend beyond the parent grant.  Applicants 
must identify supplemental applications by checking the "Supplement" 
box on the Checklist page and entering the number of the currently 
funded grant for which the supplement is being requested.

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.

FUNDS AVAILABLE
 
The NIAMS intends to commit approximately $2 million in FY 2003 to fund 
ten to fifteen supplements and/or new awards in response to this RFA.  
Supplement applications may request up to $100,000 per year in direct 
costs. A supplement may not extend beyond the parent project award 
period.  Research project (R01) grants may not exceed $250,000 per year 
in direct costs. The total project period for an R01 application 
submitted in response to this RFA may not exceed four years. 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 NIAMS 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. 

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   

Individuals with the skills, knowledge, and resources necessary to 
carry out the proposed research are 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 particularly encouraged to apply for support from 
NIAMS programs.

SPECIAL REQUIREMENTS

Data Sharing Plan

Because comprehensive gene expression analysis methods can record 
expression levels for thousands of genes, data may be useful for 
purposes beyond those prompting their original collection. Thus, 
applicants responding to this RFA must describe plans for making data 
available to other investigators.  For example, they may identify 
existing publicly accessible data repositories, such as the NCBI Gene 
Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) to which data 
will be submitted.  Data sharing plans must include a timetable 
specifying when data will be shared, relative to collection, analysis, 
and publication. Peer reviewers will be asked to comment on the 
adequacy of the plan.  The requirement for data sharing will be 
incorporated as a condition of any award made under this RFA.

Annual meetings

The technology of comprehensive gene expression analysis presents new 
challenges and is still changing rapidly. It is important for 
investigators applying this technology to exchange information 
regularly. The NIAMS plans to organize annual meetings of investigators 
supported under this initiative, to facilitate this exchange of 
information. In preparing budget requests, applicants should anticipate 
expenses for annual travel to Bethesda, Maryland for this purpose.
 
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:

William J. Sharrock, Ph.D.
Musculoskeletal Diseases Branch
National Institute of Arthritis and Musculoskeletal and Skin Diseases 
One Democracy Plaza
6701 Democracy Blvd., Suite 800
Bethesda, MD  20892-4872
Telephone:  (301) 594-5055
FAX:  (301) 480-4543
Email: [email protected]

o Direct your questions about peer review issues to:

Richard Bartlett, Ph.D.
Review Branch
National Institute of Arthritis and Musculoskeletal and Skin Diseases
One Democracy Plaza 
6701 Democracy Blvd, Suite 800
Bethesda, MD 20892-4872
Telephone: 301-594-4956 
Fax: 301-402-2406
Email: [email protected]

o Direct your questions about financial or grants management matters 
to:

Michael G. Morse
Deputy Chief, Grants Management Branch
National Institute of Arthritis and Musculoskeletal and Skin Diseases 
One Democracy Plaza
6701 Democracy Blvd. Suite 800
Bethesda, MD  20892-4872
Telephone:  (301) 594-3535
FAX:  (301) 480-5450
Email:  [email protected] 

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 IC 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:

William J. Sharrock, Ph.D.
Musculoskeletal Diseases Branch
National Institute of Arthritis and Musculoskeletal and Skin Diseases 
One Democracy Plaza
6701 Democracy Blvd., Suite 800
Bethesda, MD  20892-4872
Telephone:  (301) 594-5055
FAX:  (301) 480-4543
Email: [email protected]

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: [email protected].
 
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:
 
Richard Bartlett, Ph.D.
Review Branch
National Institute of Arthritis and Musculoskeletal and Skin Diseases
One Democracy Plaza 
6701 Democracy Blvd, Suite 800
Bethesda, MD 20892-4872
Telephone: 301-594-4956 
Fax: 301-402-2406
Email: [email protected]

APPLICATION PROCESSING: Applications must be received by the 
application receipt date listed in the heading of this RFA.  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 the NIAMS.  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 NIAMS 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 Arthritis and 
Musculoskeletal and Skin Diseases Advisory 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 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 DATA SHARING: The adequacy of the proposed plan to share data.

o BUDGET:  The reasonableness of the proposed budget and the requested 
period of support in relation to the proposed research.

RECEIPT AND REVIEW SCHEDULE

Letter of Intent Receipt Date: February 17, 2003
Application Receipt Date: March 17, 2003
Peer Review Date: June/July 2003
Council Review: September 2003
Earliest Anticipated Start Date: September 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.
 
REQUIRED FEDERAL CITATIONS 

MONITORING PLAN AND DATA SAFETY AND MONITORING BOARD: Research 
components involving Phase I and II clinical trials must include 
provisions for assessment of patient eligibility and status, rigorous 
data management, quality assurance, and auditing procedures.  In 
addition, it is NIH policy that all clinical trials require data and 
safety monitoring, with the method and degree of monitoring being 
commensurate with the risks (NIH Policy for Data Safety and Monitoring, 
NIH Guide for Grants and Contracts, June 12, 1998: 
http://grants.nih.gov/grants/guide/notice-files/not98-084.html).  

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 is 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. 93.846, 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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