art I Overview Information

Department of Health and Human Services

Participating Organizations
National Institutes of Health (NIH), (http://www.nih.gov)

Components of Participating Organizations
This Funding Opportunity Announcement (FOA) is developed as a Common Fund initiative (http://commonfund.nih.gov/) through the NIH Office of the NIH Director, Office of Strategic Coordination (http://dpcpsi.nih.gov/osc/). This FOA will be administered by the National Human Genome Research Institute (NHGRI) and the National Heart Lung and Blood Institute (NHLBI) on behalf of the NIH.

Title: Large Scale Production of Perturbagen-Induced Cellular Signatures (U54)

Announcement Type
New

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

• September 6, 2011 - See Notice NOT-RM-11-023. Notice of Request for Nomination of Human Cell Lines for Gene Expression Profiling in Response to Perturbing Agents in the Library of Integrated Network-Based Cellular Signatures (LINCS) Program.
• December 10, 2010 - See Notice NOT-RM-11-004 Notice of Instructions for Potential Applicants to Access LINCS Data.

Request For Applications (RFA) Number: RFA-RM-10-003

Catalog of Federal Domestic Assistance Number(s)
93.310

Key Dates
Release Date: February 26, 2010
Letters of Intent Receipt Date: April 1, 2010
Application Receipt Date: April 27, 2010
Peer Review Date(s): June/July, 2010
Council Review Date: August 2010
Earliest Anticipated Start Date: September 30, 2010
Additional Information To Be Available Date (Url Activation Date): For information on the pre-application technical assistance teleconference on March 31, 2010, see http://commonfund.nih.gov/LINCS/.
Expiration Date: April 28, 2010

Due Dates for E.O. 12372

Not Applicable

Additional Overview Content

Executive Summary

• Purpose. This FOA seeks to establish a pilot-scale data production effort to systematize approaches for identifying mechanism-based associations among the effects of disparate biological perturbations, a knowledge base that can be used to study functional relationships among the responding cellular components. The Library of Integrated Network-Based Cellular Signatures (LINCS) program will support the high-throughput collection and integrative computational analysis of informative molecular activity and cellular feature signatures generated in response to a variety of perturbing agents, including siRNAs and small bioactive molecules, which are applied to a set of carefully selected cell types. The resulting knowledge will form the basis of a long-lived resource that can be used broadly by the community. For example LINCS may inform association of disease states with detailed molecular or cellular phenotypes, and ultimately associate disease with specific gene networks, or inform the mechanism of action of known drugs. This FOA seeks to fund pilot-scale data production efforts that will produce a usable initial resource while addressing the following issues: optimization of methods, integration of data, and scalability. Pilot production efforts will interact with multiple future additional components (data analysis and informatics tools; and development and integration of new production-ready technologies) of the LINCS program.
• Mechanism of Support. This FOA will utilize the U54 specialized centers cooperative agreement award mechanism. It is intended to complement FOAs that will be issued in FY 2011 for development and integration of new production-ready technologies and for development of informatics and data analysis tools for LINCS.
• Funds Available and Anticipated Number of Awards. We expect to fund up to two awards in FY 2010. Three years of funding may be requested. Total funds available for the program are $2.7M in FY 2010, ramping to $5M in each of FY 2011 and FY 2012.
• Budget and Project Period. The maximum project period for an application submitted in response to this funding opportunity is three years. Direct costs are limited to a maximum of $900,000 in FY 2010 and $1.65M in each of FY 2011 and FY 2012.
• Application Research Strategy Length: The U54 Research Strategy section may not exceed 30 pages, including tables, graphs, figures, diagrams, and charts. See Table of Page Limits.
• Eligible Institutions/Organizations. Institutions/organizations listed in Section III, 1.A. are eligible to apply.
• Eligible Project Directors/Principal Investigators (PDs/PIs). Individuals with the skills, knowledge, and resources necessary to carry out the proposed research are invited to work with their institution/organization 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 support.
• Number of PDs/PIs. More than one PD/PI (i.e., multiple PDs/PIs), may be designated on the application.
• Number of Applications. Applicants may submit more than one application, provided they are scientifically distinct.
• Resubmissions. Resubmission applications are not permitted in response to this FOA.
• Renewals. Renewal applications are not permitted in response to this FOA.
• Special Date(s). This FOA uses non-standard due dates. See Receipt, Review and Anticipated Start Dates.
• Application Materials. See Section IV.1 for application materials.
  
• Hearing Impaired. Telecommunications for the hearing impaired are available at: TTY: (301) 451-5936

Table of Contents

Part I Overview Information

Part II Full Text of Announcement

Section I. Funding Opportunity Description
1. Research Objectives

Section II. Award Information
1. Mechanism(s) of Support
2. Funds Available

Section III. Eligibility Information
1. Eligible Applicants
A. Eligible Institutions
B. Eligible Individuals
2.Cost Sharing or Matching
3. Other - Special Eligibility Criteria

Section IV. Application and Submission Information
1. Address to Request Application Information
2. Content and Form of Application Submission
3. Submission Dates and Times
A. Receipt, Review and Anticipated Start Dates
1. Letter of Intent
B. Sending an Application to the NIH
C. Application Processing
D. Application Assignment
4. Intergovernmental Review
5. Funding Restrictions
6. Other Submission Requirements

Section V. Application Review Information
1. Criteria
2. Review and Selection Process
3. Anticipated Announcement and Award Dates

Section VI. Award Administration Information
1. Award Notices
2. Administrative and National Policy Requirements
A. Cooperative Agreement Terms and Conditions of Award
1. Principal Investigator Rights and Responsibilities
2. NIH Responsibilities
3. Collaborative Responsibilities
4. Dispute Resolution Process
3. Reporting

Section VII. Agency Contact(s)
1. Scientific/Research Contact(s)
2. Peer Review Contact(s)
3. Financial/ Grants Management Contact(s)

Section VIII. Other Information - Required Federal Citations

Part II - Full Text of Announcement

Section I. Funding Opportunity Description

1. Research Objectives

This initiative is funded through the NIH Common Fund, which supports cross-cutting programs that are expected to have exceptionally high impact. All Common Fund initiatives invite investigators to develop bold, innovative, and often risky approaches to address problems that may seem intractable or to seize new opportunities that offer the potential for rapid progress.

NIH seeks to establish a systematic approach for identifying mechanism-based associations among the effects of disparate biological perturbations, a knowledge base that can be used to study functional relationships among the responding cellular components and between perturbations. The LINCS program will support the high-throughput collection and integrative computational analysis of informative molecular activity and cellular feature signatures generated in response to a variety of perturbing agents, including siRNAs and small bioactive molecules, which are applied to a set of carefully selected cell types. The resulting knowledge will form the basis of a long-lived resource that can be used broadly by the community, for example to associate disease states with detailed molecular or cellular phenotypes, and ultimately with specific gene networks or small molecules with each other or disease states.

Background and Need. Much of modern molecular biomedical science rests on understanding gene function. Considerable progress has been made in understanding the functions of individual genes and a few limited networks of genes, as they pertain to human health and disease using a very wide range of approaches that investigate one or a few molecules at a time. However, a single gene or single network approach becomes a limiting factor considering the complex functional interactions that occur within biological systems, for example when seeking to identify optimal targets for therapeutic interventions or when attempting to decipher genotype-phenotype correlations, especially those underlying multigenic traits and diseases.

The LINCS program aims to stimulate a robust framework for understanding the effects on human cells of perturbations in a standardized, integrated, coordinated and generalizable manner. Studies using classical genetic screens demonstrate that disruptions at multiple steps within a biological pathway yield related phenotypes at both the cellular and molecular levels. Hence the generation of perturbation-induced molecular activity and cellular feature signatures can be used to infer mechanism-based relationships among perturbing conditions, as well as functional associations among responding cellular components, by revealing correlated effects of different perturbations.

A public resource of network-based molecular and cellular signatures will enable a wide range of researchers to relate their own data (for example, variants or mutations that result in a cellular or molecular phenotype) to the resource data, and thereby gain rapid understanding of other genes that may be involved in the same network, for example facilitating the derivation of mechanistic insights into disease etiology and the identification of novel drug targets. Even without making mechanistic inferences, it will be possible to use such a resource, for example, to make inferences about small molecules that may be relevant to a disease that affects a certain pathway and to better classify disease.

A number of approaches to developing such a resource have been undertaken already, using a variety of perturbagens (small molecules, siRNA s), different cell types, and different cellular readouts (RNA expression; protein modification; high-content cellular imaging; pathway-specific reporters). Each must be considered individually and in combination to most faithfully (with respect to human biology) and accurately reveal the relationship between perturbation and function, how best to inform on the entire space of possible cellular states, how to produce information that is most readily able to be integrated with existing data from the scientific community so as to make useful inferences, and which can scale up to produce a reasonably comprehensive community resource.

Although related efforts are going on independently, in order to become a truly comprehensive community resource with maximum utility there is a need to (1) further develop and compare current approaches to understand how they may scale to provide a reasonably comprehensive and coordinated resource, (2) assess how best to make the data available to the community, (3) develop new analysis tools, and (4) explore how other community data can be integrated into a unified resource.

Objectives This FOA is one component of a three-year pilot phase that will seek to inform the appropriateness and structure of a full-scale LINCS effort, while at the same time creating an initial useful LINCS community resource.

This FOA will fund up to two pilot data production centers. The principal task of the pilot center(s) will be to produce a necessarily limited but coherent initial LINCS data resource that can be used by the general research community. For example, a useful limited effort might fully investigate the effects of a specific class of perturbagens on a small number of representative cell lines using one or possibly two complementary response readouts.

Because this FOA seeks the production of an initial LINCS resource having immediate utility, it is expected that applicants will propose approaches that are already mature in terms of throughput, scalability, and biological informativeness.

At the same time, the pilot production effort is intended to address issues of optimization of methods, integration of data, and scalability (see below). Pilot production efforts will interact with multiple future additional components (data analysis and informatics tools; and development and integration of new production-ready technologies) of the LINCS pilot program.

Optimization of methods and approaches. For this particular FOA, applicants will need to establish that their approaches are at the stage where an initial production effort can be pursued. This FOA does not dictate what perturbagens, human cell lines or tissues and readouts are to be used. Rather, we seek efforts that have a reasonable likelihood of demonstrating in the pilot phase their ability to produce robust, high quality data that can be used as a LINCS resource, that is, that the data are faithful to human biology, useful for the community, and reasonably comprehensive in their ultimate ability to represent or capture most of the space of possible cellular responses. For example, for the conceivable future it may be impractical to test more than a limited number of cell types. Which limited sets will be adequate (these must be rationalized in terms of their ability to inform on human biology and disease)? Similarly, it may not be practical to assay the readout of every gene or protein. What practical alternatives should be used to best enable a full representation of cellular responses? Applicants must be able to evaluate more than one perturbagen/cell line/readout. Therefore, diverse approaches will be encouraged, for example, by funding diverse individual approaches, or encouraging applications in which more than a single approach is proposed.

Integration of data. The production groups should establish a database to store their own data as well as a public website that will provide query and access to this data. However, data integration is a critical aim of the LINCS program. In the pilot effort, we will evaluate the ability of the production groups to integrate each other s data (should more than one be funded), as well as data from other LINCS components and outside investigators. Integration has multiple aspects. Applicants should choose and justify their cell lines, perturbagens, and readouts with respect to how their data will in principle be able to be integrated with a wide variety of ongoing and future biological and biomedical studies. In addition, applicants should propose specific plans for how they will integrate outside data, including how external users will obtain and view data, and describe tools for users to analyze the integrated data. This element includes establishment of standard annotation terms and other standards that will allow data exchange, integration and interoperability. A related aim is to establish how useful a LINCS effort will be for the broader research community.

Scalability. The LINCS pilot phase is designed to inform whether a LINCS effort is scalable. Thus, this first component of the program will be evaluated with respect to both data production (cost and throughput), and for its quality and scientific utility and how those would be affected by an increase to a full-scale effort.

Other LINCS components and collaborations. With future pilot FOA s, NIH aims to establish several additional components with which LINCS pilot production groups will need to interact: 1. Informatics and data analysis tool development (especially with regard to standardized annotation, data integration and biological applications) as well as testing the ability to integrate data from outside studies; 2. Experimental technology development to explore new and innovative laboratory-based approaches to generating useful LINCS data, or assessment of technologies for adoption by LINCS that are promising but not yet mature enough for an initial production phase; issues related to data standardization and integration will be included as well. In addition to these collaborations, it is expected that LINCS pilot production groups will exchange data with each other and insure that related protocols, annotations and databases are interoperable and based on common standards. This goal may require, for example, the ability to exchange (or use common) perturbagens, cell lines or assays.

The objectives relating to data production, and to data handling (informatics, storage and integration of data) should be considered as separate core capabilities of a proposed effort, and should be discussed separately in the application research plan (See Section 6: Other Submission Requirements ). Applications should explicitly address scalability and overall management of the effort, including management towards the kinds of collaborations envisaged here.

Administration, operation and project management

This initiative seeks to engage outstanding expertise for each of the components, and standardization is a core component of the activities envisaged within the FOA. Therefore, all components will need to be carefully overseen and coordinated in order to achieve the specified goals within three years. This complex effort will require robust administrative structures and processes, objective and independent advice by appropriate experts, and strong professional project management by the grantee. In addition, the support of the project through a cooperative agreement mechanism will allow significant involvement of NIH staff in its conduct.

Outreach activities and informatics and database development are expected to begin in the first or second year and continue throughout the project. The NIH expects that the data and informatics framework will be maintained and supported beyond the termination of the award, by a means that will be determined during the pilot project. This may include a separate integrated database.

See Section VIII, Other Information - Required Federal Citations, for policies related to this announcement.

Section II. Award Information

1. Mechanism of Support

This funding opportunity will use the NIH specialized center cooperative agreement (U54) award mechanism(s).
The Project Director/Principal Investigator (PD/PI) will be solely responsible for planning, directing, and executing the proposed project.

This FOA uses Just-in-Time information concepts. It also uses non-modular budget formats described in the PHS 398 application instructions (see http://grants.nih.gov/grants/funding/phs398/phs398.html).

This funding opportunity will use a cooperative agreement award mechanism. In the cooperative agreement mechanism, the Project Director/Principal Investigator (PD/PI) retains the primary responsibility and dominant role for planning, directing, and executing the proposed project, with NIH staff being substantially involved as a partner with the Principal Investigator, as described under the Section VI. 2. Administrative Requirements, "Cooperative Agreement Terms and Conditions of Award".

This FOA represents a pilot phase. Should it be successful, NIH intends to encourage a full-scale effort based on the information obtained, contingent on the availability of funds.

2. Funds Available

• NIH expects to award $12.7M total funds for this FOA.
• NIH anticipates making no more than two awards.
• The expected direct cost amount for individual awards is a maximum of $900,000 in the initial year of the award; $1.65M in each of the two subsequent years.
• Three years of funding may be requested.

Future year amounts will depend on annual appropriations.

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 IC(s) provide support for this program, awards pursuant to this funding opportunity are contingent upon the availability of funds and the receipt of a sufficient number of meritorious applications.

Facilities and administrative costs requested by consortium participants are not included in the direct cost limitation, see NOT-OD-05-004.

NIH grants policies as described in the NIH Grants Policy Statement will apply to the applications submitted and awards made in response to this FOA.

Section III. Eligibility Information

1. Eligible Applicants

1.A. Eligible Institutions

The following organizations/institutions are eligible to apply:

• Public/State Controlled Institutions of Higher Education
• Private Institutions of Higher Education
• Hispanic-serving Institutions
• Historically Black Colleges and Universities (HBCUs)
• Tribally Controlled Colleges and Universities (TCCUs)
• Alaska Native and Native Hawaiian Serving Institutions
• Nonprofits with 501(c)(3) IRS Status (Other than Institutions of Higher Education)
• Nonprofits without 501(c)(3) IRS Status (Other than Institutions of Higher Education)
• Small Businesses
• For-Profit Organizations (Other than Small Businesses)
• State Governments
• Indian/Native American Tribal Governments (Federally Recognized)
• Indian/Native American Tribally Designated Organizations
• County Governments
• City or Township Governments
• Special District Governments
• Independent School Districts
• Public Housing Authorities/Indian Housing Authorities
• U.S. Territory or Possession
• Indian/Native American Tribal Governments (Other than Federally Recognized)
• Regional Organizations
• Non-domestic (non-U.S.) Entities (Foreign Organizations)
• Other(s):
  • Eligible Agencies of the Federal Government

1.B. Eligible Individuals

Any individual with the skills, knowledge, and resources necessary to carry out the proposed research as the PD/PI is invited to work with his/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 program support. In addition, investigators from the NIH Intramural Research Program are eligible to participate in this FOA. Applications from intramural investigators will be competitively reviewed.

More than one PD/PI, or multiple PDs/PIs, may be designated on the application for projects that require a team science approach and therefore clearly do not fit the single-PD/PI model. Additional information on the implementation plans, policies and procedures to formally allow more than one PD/PI on individual research projects is available at http://grants.nih.gov/grants/multi_pi. All PDs/PIs must be registered in the NIH eRA Commons prior to the submission of the application (see http://era.nih.gov/ElectronicReceipt/preparing.htm for instructions).

The decision of whether to apply for a grant with a single PD/PI or multiple PDs/PIs is the responsibility of the investigators and applicant organizations, and should be determined by the scientific goals of the project. Applications for grants with multiple PDs/PIs will require additional information, as outlined in the instructions below. When considering multiple PDs/PIs, please be aware that the structure and governance of the PD/PI leadership team as well as the knowledge, skills and experience of the individual PDs/PIs will be factored into the assessment of the overall scientific merit of the application. Multiple PDs/PIs on a project share the authority and responsibility for leading and directing the project, intellectually and logistically. Each PD/PI is responsible and accountable to the grantee organization, or, as appropriate, to a collaborating organization, for the proper conduct of the project or program, including the submission of required reports. For further information on multiple PDs/PIs, please see http://grants.nih.gov/grants/multi_pi.

Due to the complex nature of the anticipated effort, including managing data production, informatics/analysis, and collaborations, PI’s must invest a minimum of 15% of their time and effort to this award.

2. Cost Sharing or Matching

This program does not require cost sharing as defined in the current NIH Grants Policy Statement.

3. Other-Special Eligibility Criteria

Number of Applications. Applicants may submit more than one application, provided they are scientifically distinct.

Resubmissions. Resubmission applications are not permitted in response to this FOA.

Renewals. Renewal applications are not permitted in response to this FOA.

Section IV. Application and Submission Information

1. Address to Request Application Information

The current PHS 398 application instructions are available at http://grants.nih.gov/grants/funding/phs398/phs398.html in an interactive format. Applicants must use the currently approved version of the PHS 398. For further assistance contact GrantsInfo, Telephone (301) 710-0267, Email: [email protected].

Telecommunications for the hearing impaired: TTY 301-451-5936.

2. Content and Form of Application Submission
Prepare all applications using the PHS 398 application forms and in accordance with the PHS 398 Application Guide (http://grants.nih.gov/grants/funding/phs398/phs398.html).

Applications must have a D&B Data Universal Numbering System (DUNS) number as the universal identifier when applying for Federal grants or cooperative agreements. The D&B number can be obtained by calling (866) 705-5711 or through the web site at http://www.dnb.com/us/. The D&B number should be entered on line 11 of the face page of the PHS 398 form.

The title and number of this funding opportunity must be typed in item (box) 2 only of the face page of the application form and the YES box must be checked.

3. Technical Assistance

NIH encourages applicants to take advantage of a technical assistance conference call sponsored by LINCS program staff. The purpose of the conference call is to provide potential applicants with background information and respond to questions about the preparation of an application in response to this FOA. The conference call will take place on March 31, 2010 from 1:00 pm to 2:00 pm EDT. Information about this Pre-Application Conference Call will be available at URL: http://commonfund.nih.gov/LINCS/. Potential applicants are encouraged to contact LINCS staff with any questions (see Section VII, Agency Contacts, below).

See Section 6, Other Submission Requirements for additional information about the content of the application.

Foreign Organizations (Non-domestic (non-U.S.) Entity)

NIH policies concerning grants to foreign (non-U.S.) organizations can be found in the NIH Grants Policy Statement at: http://grants.nih.gov/grants/policy/nihgps_2003/NIHGPS_Part12.htm#_Toc54600260.

Applications from foreign organizations must:

• Request budgets in U.S. dollars.
• Contain detailed budgets. See NOT-OD-06-096.

In addition, for applications from foreign organizations:

• Charge back of customs and import fees is not allowed.
• Every effort should be made to comply with the format specifications, which are based upon a standard U.S. paper size of 8.5 x 11 within each PDF.
• Funds for up to 8% Facilities and Administrative (F&A) costs (excluding equipment) may be requested. See NOT-OD-01-028, March 29, 2001.
• Organizations must comply with Federal/NIH policies on human subjects, animals, and biohazards.
• Organizations must comply with Federal/NIH biosafety and biosecurity regulations. See Section VI.2., Administrative and National Policy Requirements

Proposed research should provide special opportunities for furthering research programs through the use of unusual talent, resources, populations, or environmental conditions in other countries that are not readily available in the United States or that augment existing U.S. resources.

Applications with Multiple PDs/PIs

When multiple PD/PIs are proposed, use the Face Page-Continued page to provide items 3a 3h for all PD/PIs. NIH requires one PD/PI be designated as the contact PD/PI for all communications between the PD/PIs and the agency. The contact PD/PI must meet all eligibility requirements for PD/PI status in the same way as other PD/PIs, but has no special roles or responsibilities within the project team beyond those mentioned above. The contact PD/PI may be changed during the project period. The contact PD/PI should be listed in block 3 of Form Page 1 (the Face Page), with all additional PD/PIs listed on Form Page 1-Continued. When inserting the name of the PD/PI in the header of each application page, use the name of the Contact PD/PI, et. al. The contact PD/PI must be from the applicant organization if PD/PIs are from more than one institution.

All individuals designated as PD/PI must be registered in the eRA Commons and must be assigned the PD/PI role in that system (other roles such as SO or IAR will not give the PD/PI the appropriate access to the application records). Each PD/PI must include their respective eRA Commons ID in the eRA Commons User Name field.

Multiple PD/PI Leadership Plan: For applications designating multiple PDs/PIs, the section of the Research Plan entitled Multiple PD/PI Leadership Plan must be included. A rationale for choosing a multiple PD/PI approach should be described. The governance and organizational structure of the leadership team and the research project should be described, and should include communication plans, process for making decisions on scientific direction, and procedures for resolving conflicts. The roles and administrative, technical, and scientific responsibilities for the project or program should be delineated for the PDs/PIs and other collaborators.

If budget allocation is planned, the distribution of resources to specific components of the project or the individual PDs/PIs should be delineated in the Leadership Plan. In the event of an award, the requested allocations may be reflected in a footnote on the Notice of Award.

Applications Involving the NIH Intramural Research Program

The requests by NIH intramural scientists will be limited to the incremental costs required for participation. As such, these requests will not include any salary and related fringe benefits for career, career conditional or other Federal employees (civilian or uniformed service) with permanent appointments under existing position ceilings or any costs related to administrative or facilities support (equivalent to Facilities and Administrative or F&A costs). These costs may include salary for staff to be specifically hired under a temporary appointment for the project, consultant costs, equipment, supplies, travel, and other items typically listed under Other Expenses. Applicants should indicate the number of person-months devoted to the project, even if no funds are requested for salary and fringe benefits.

If selected, NIH intramural scientists will participate in this program as PD/PIs in accord with the Cooperative Agreement Terms and Conditions provided in this RFA. Intellectual property will be managed in accord with established policy of the NIH in compliance with Executive Order 10096, as amended, 45 CFR Part 7; patent rights for inventions developed in NIH facilities are NIH property unless NIH waives its rights.

Should an extramural application include the collaboration with an intramural scientist, no funds for the support of the intramural scientist may be requested in the application. The intramural scientist may submit a separate request for intramural funding as described above.

3. Submission Dates and Times

Applications must be received on or before the receipt date described below (Section IV.3.A). Submission times N/A.

3.A. Receipt, Review and Anticipated Start Dates
Letter of Intent Receipt Date: April 1, 2010
Application Receipt Date: April 27, 2010
Peer Review Date(s): June/July, 2010
Council Review Date: August 2010
Earliest Anticipated Start Date: September 30, 2010

3.A.1. Letter of Intent

Prospective applicants are asked to submit a letter of intent that includes the following information:

• Descriptive title of proposed research
• Name, address, and telephone number of the Principal Investigator
• Names of other key personnel
• Participating institutions
• Number and title of this funding opportunity

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 in Section IV.3.A.

The letter of intent should be sent to:

Ajay
National Human Genome Research Institute
5635 Fishers Lane
Suite 4076
Bethesda, MD 20892
Telephone: (301) 594 7108
Email: [email protected]

3.B. Sending an Application to the NIH

Applications must be prepared using the forms found in the PHS 398 instructions for preparing a research grant application. 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 (U.S. Postal Service Express or regular mail)
Bethesda, MD 20817 (for express/courier service; non-USPS service)

Personal deliveries of applications are no longer permitted (see http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-040.html).

3.C. Application Processing

Applications must be received on or before the application receipt date described above (Section IV.3.A.). If an application is received after that date, the application may be delayed in the review process or not reviewed. Upon receipt, applications will be evaluated for completeness by the CSR and for responsiveness by the reviewing Institute. Incomplete and/or non-responsive applications will not be reviewed.

The NIH will not accept any application in response to this funding opportunity that is essentially the same as one currently pending initial review, unless the applicant withdraws the pending application. However, when a previously unfunded application, originally submitted as an investigator-initiated application, is to be submitted in response to a funding opportunity, it is to be prepared as a NEW application. That is, the application for the funding opportunity must not include an Introduction describing the changes and improvements made, and the text must not be marked to indicate the changes from the previous unfunded version of the application.

Information on the status of an application should be checked by the Principal Investigator in the eRA Commons at: https://commons.era.nih.gov/commons/.

4. Intergovernmental Review

This initiative is not subject to intergovernmental review.

5. Funding Restrictions

All NIH awards are subject to the terms and conditions, cost principles, and other considerations described in the NIH Grants Policy Statement. The Grants Policy Statement can be found at NIH Grants Policy Statement.

Pre-award costs are allowable. A grantee may, at its own risk and without NIH prior approval, incur obligations and expenditures to cover costs up to 90 days before the beginning date of the initial budget period of a new award if such costs: 1) are necessary to conduct the project, and 2) would be allowable under the grant, if awarded, without NIH prior approval. If specific expenditures would otherwise require prior approval, the grantee must obtain NIH approval before incurring the cost. NIH prior approval is required for any costs to be incurred more than 90 days before the beginning date of the initial budget period of a new award.

The incurrence of pre-award costs in anticipation of a competing or non-competing award imposes no obligation on NIH either to make the award or to increase the amount of the approved budget if an award is made for less than the amount anticipated and is inadequate to cover the pre-award costs incurred. NIH expects the grantee to be fully aware that pre-award costs result in borrowing against future support and that such borrowing must not impair the grantee's ability to accomplish the project objectives in the approved time frame or in any way adversely affect the conduct of the project (see NIH Grants Policy Statement http://grants.nih.gov/grants/policy/nihgps_2003/NIHGPS_Part6.htm.)

6. Other Submission Requirements

Cooperative Agreements: Awardees must agree to the "Cooperative Agreement Terms and Conditions of Award" in Section VI.2.A "Award Administration Information".

Organization of Application: Research plans should be organized to describe the two core functions outlined above: Data Production, and Informatics and Integration of Data. The Data Production section should describe and justify the choice of perturbations, cell lines, and readouts in terms of how they could provide a useful initial production community resource; how they will be optimized over the course of the pilot effort, etc. The Informatics and Integration section should discuss how internal project data will be handled and analyzed; how external data will be integrated, including annotation and other standards, and how data will be made available as a resource to the general research community.

In addition, applicants should describe how their combined proposed efforts will meet the other Research Objectives stated above, including providing information about the promise of scaling up the proposed approach, considering both analysis and data production. Finally, applicants should include a detailed management plan, including general plans for collaborations with future components of this program.

To address these elements, the application should be organized as stated below in PHS398 Research Plan Component Sections , with the following deviations:

Research Strategy should be a total of 30 pages or less and include separate sections for Data Production and Informatics and Integration . Each of these two sections should not exceed 12 pages. In addition, the Research Strategy section should contain a third separate section (not to exceed 6 pages) describing a management plan, including details of how the two different cores are to be coordinated, how standards for reporting experimental results will be developed, how community outreach will be carried out, and how collaborations with outside groups will be managed. Each of the Data Production and Informatics and Integration sections in the Research Strategy should include the standard Significance, Innovation, and Approach as separate sub-sections.

The detailed budget section (form page 4) should be provided for each of the two functional cores, Production and Informatics and Integration , and for any subcontractual or consortium agreements. A separate overall budget for the entire center should be prepared using form page 4. Costs for overall coordination and management, including management of collaborations, should be included in the overall center budget.

Outreach to engage and educate research community

As the LINCS Project will be developing significant new tools and new data, outreach to the research community will facilitate their use and adoption. Outreach will include both engagement of the community, for example, to solicit ideas for requirements of data models, analytic tools, and other aspects of the informatics platform, as well as education about how to use informatics tools, the relevance of connectivity data to other types of data, etc. This section should describe how this outreach will be conducted.

Site Visits and Meetings with NIH Staff. Because of the complexity and interactions of the LINCS program, the relevant NIH program officer and staff members will conduct site visits at mutually agreeable times. This will assist program in evaluations of progress on the grant. In addition to site visits, the principal investigator and key staff must agree to participate in meetings in the Bethesda, Maryland area to present progress to relevant NIH staff; these meetings are expected to be held at the end of the first and second year of the project. Funds should be requested in this application for this travel.

Awardees must agree to the Cooperative Agreement Terms and Conditions of Award in Section VI.2.A Award Administration Information.

Applicants must demonstrate in the application their ability to meet:

• Research objectives and scope defined in Section I of the FOA;
• Data, software, experimental protocol, and model sharing requirements as outlined in Section IV - Resource Sharing Plan; and Other Investigator responsibilities described in Section VI.2. A Cooperative Agreement Terms and Conditions of Award.

PHS398 Research Plan

All application instructions outlined in the PHS398 Application Instructions are to be followed, with the following additional requirements:

• Introduction (required for a resubmission or revision application) is limited to 1 page.
• Specific Aims is limited to 1 page.
• Research Strategy, including tables, graphs, figures, diagrams, and charts is limited to 30 pages. See Table of Page Limits.

Budget Component

This FOA uses non-modular budget formats described in the PHS 398 application instructions (see http://grants.nih.gov/grants/funding/phs398/phs398.html).

Appendix Materials

All paper PHS 398 applications submitted must provide appendix material on CDs only. Include five identical CDs in the same package with the application. See http://grants.nih.gov/grants/guide/notice-files/NOT-OD-08-031.html.

Do not use the Appendix to circumvent the page limitations. An application that does not observe the required page limitations may be delayed in the review process.

Resource Sharing Plan(s)

NIH considers the sharing of unique research resources developed through NIH-sponsored research an important means to enhance the value of, and advance research. When resources have been developed with NIH funds and the associated research findings published or provided to NIH, it is important that they be made readily available for research purposes to qualified individuals within the scientific community. If the final data/resources are not amenable to sharing, this must be explained in Resource Sharing section of the application. See http://grants.nih.gov/grants/policy/data_sharing/data_sharing_faqs.htm.

(a) Data Sharing Plan: Regardless of the amount requested, investigators are expected to include a brief 1-paragraph description of how final research data will be shared, or explain why data-sharing is not possible. Applicants are encouraged to discuss data-sharing plans with their NIH program contact. See Data-Sharing Policy or http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-032.html.

(b) Sharing Model Organisms: Regardless of the amount requested, all applications where the development of model organisms is anticipated are expected to include a description of a specific plan for sharing and distributing unique model organisms and related resources, or state appropriate reasons why such sharing is restricted or not possible. See Sharing Model Organisms Policy, and NIH Guide NOT-OD-04-042.

(c) Genome-Wide Association Studies (GWAS): Regardless of the amount requested, applicants seeking funding for a genome-wide association study are expected to provide a plan for submission of GWAS data to the NIH-designated GWAS data repository, or provide an appropriate explanation why submission to the repository is not possible. A genome-wide association study is defined as any study of genetic variation across the entire genome that is designed to identify genetic associations with observable traits (such as blood pressure or weight) or the presence or absence of a disease or condition. For further information see Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies, NIH Guide NOT-OD-07-088, and http://grants.nih.gov/grants/gwas/.

An important and core goal of the LINCS program is to produce a usable community resource. Detailed plans on how data will be made broadly available should be included as a portion of the plans for Informatics and Integration.

Plan for Sharing Research Data, Experimental Protocols, and Software:

The NIH is committed to the principle of rapid data, experimental protocol, model, and software release to the scientific community. LINCS awardees are expected to release to the research community data, experimental protocols, models, and software in a timely fashion through an informatics platform and other standard mechanisms. The development of policies, methods, and standards for such sharing are critically important for LINCS. The NIH expects that the LINCS awardees will develop such policies, methods, and standards in concert with the NIH and the LINCS Steering Committee and Project Team. These policies, methods, and standards will remain consistent with NIH-wide policies on data and resource sharing.

In their grant applications, all applicants should provide specific plans for data, experimental protocol, model, and software release. Key Elements that should be considered when developing such data sharing plan are detailed at: http://grants.nih.gov/grants/sharing_key_elements_data_sharing_plan.pdf.

The reasonableness of the applicant’s data and model sharing and software release plans will be assessed by the reviewers. Reviewers will factor the proposed data, experimental protocol, model sharing and software release plan into the determination of scientific merit or the impact/priority score.

After completion of the initial review, NIH LINCS program staff will be responsible for any additional administrative review of the data and model sharing and software release plans. The adequacy of these plans will be considered by program staff of the funding organization when making recommendations about funding applications. The accepted data, experimental protocol, and model sharing and software release plans will become a condition of the award of the cooperative agreement. The applicant s progress in implementing the data and model sharing and software release plan will be evaluated as part of the administrative review of each non-competing Grant Progress Report (PHS 2590). See Section VI.3. Reporting.

The applications are expected to include written statements from the officials responsible for intellectual property issues at all of the applicant institutions (including subcontractors) to the effect that the institution supports and agrees to abide by the software dissemination plans put forth in the application. Such letters would be clear expressions of commitment. A separate letter should be sent by each participating organization including each subcontractor. Please note that institutional sign-off on the grant application signifies that all relevant components of the institution, including the technology transfer office, have reviewed and approved the document. The filing of patent applications and/or the enforcement of resultant patents in a manner that might restrict use of the method(s) could substantially diminish the utilization of it to many disease areas and the potential public benefit they could provide. Approved Users and Investigators supported under this FOA, and their institutions, should acknowledge the program’s IP Policy, the goal of which is to ensure the greatest possible public benefit from the development of this LINCS application.

Specific Instructions for Foreign Applications

All foreign applicants must complete and submit budget requests using the PHS 398 detailed budget pages. See NOT-OD-06-096.

Section V. Application Review Information

1. Criteria

Only the review criteria described below will be considered in the review process.

2. Review and Selection Process

Review Process

Applications that are complete and responsive to the FOA will be evaluated for scientific and technical merit by an appropriate peer review group convened by the Center for Scientific Review and in accordance with NIH peer review procedures (http://grants1.nih.gov/grants/peer/), using the review criteria stated below.

As part of the scientific peer review, all applications will:

• Undergo a selection process in which only those applications deemed to have the highest scientific and technical merit, generally the top half of applications under review, will be discussed and assigned an impact/priority score.
• Receive a written critique.
• Receive a second level of review by the appropriate national advisory council or board.

The mission of the NIH is to support science in pursuit of knowledge about the biology and behavior of living systems and to apply that knowledge to extend healthy life and reduce the burdens of illness and disability. As part of this mission, applications submitted to the NIH for grants or cooperative agreements to support biomedical and behavioral research are evaluated for scientific and technical merit through the NIH peer review system.

Overall Impact

Reviewers will provide an overall impact/priority score to reflect their assessment of the likelihood for the project to exert a sustained, powerful influence on the research field(s) involved, in consideration of the following five scored review criteria, and additional review criteria (as applicable for the project proposed).

Scored Review Criteria

Reviewers will consider each of the five review criteria below in the determination of scientific and technical merit, and give a separate score for each. An application does not need to be strong in all categories to be judged likely to have major scientific impact. For example, a project that by its nature is not innovative may be essential to advance a field.

Significance. Does the project address an important problem or a critical barrier to progress in the field? If the aims of the project are achieved, how will scientific knowledge, technical capability, and/or clinical practice be improved? How will successful completion of the aims change the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field? Is the proposed project likely to result in a significant public resource? Are the proposed perturbagens/cell lines/readouts proposed biologically significant? Is the proposed project likely to facilitate progress on a wide range of biological or medical problems? How well does the application address the Research Objectives of the FOA?

Investigator(s). Are the PD/PIs, collaborators, and other researchers well suited to the project? If Early Stage Investigators or New Investigators, or in the early stages of independent careers, do they have appropriate experience and training? If established, have they demonstrated an ongoing record of accomplishments that have advanced their field(s)? If the project is collaborative or multi-PD/PI, do the investigators have complementary and integrated expertise; are their leadership approach, governance and organizational structure appropriate for the project?

Innovation. Does the application challenge and seek to shift current research or clinical practice paradigms by utilizing novel theoretical concepts, approaches or methodologies, instrumentation, or interventions? Are the concepts, approaches or methodologies, instrumentation, or interventions novel to one field of research or novel in a broad sense? Is a refinement, improvement, or new application of theoretical concepts, approaches or methodologies, instrumentation, or interventions proposed?

Approach. Are the overall strategy, methodology, and analyses well-reasoned and appropriate to accomplish the specific aims of the project? Are potential problems, alternative strategies, and benchmarks for success presented? If the project is in the early stages of development, will the strategy establish feasibility and will particularly risky aspects be managed?
If the project involves clinical research, are the plans for 1) protection of human subjects from research risks, and 2) inclusion of minorities and members of both sexes/genders, as well as the inclusion of children, justified in terms of the scientific goals and research strategy proposed? Does the proposed approach properly balance the need to produce a well-defined, useful data resource with the exploration of ways to optimize the components of the data production effort over time? Will the approach result in a resource that can eventually be integrated with other data from the community (e.g., genetic, expression, proteomic, etc. data; small molecules; pharmaceutical research)? Are the two major core functions (Data Production/Informatics and Data Integration) properly coordinated? Does the Data Production section describe and adequately justify appropriate goals, timelines, and milestones; are opportunities for obtaining increased efficiency over the period of the award described and justified? Does the database management plan that supports the data production core contain an adequate plan for an annual complete download and rebuild? Is the management plan appropriate to the complexity of the proposed effort? Is the data availability plan adequate? Is there a viable plan for coordinating data standardization? Will the overall plan provide useful information about scalability? How effectively will the chosen perturbagen/cell line/readout capture most of the space of possible cellular responses, and then scale to a complete representation in later efforts? Are the choices of the perturbagens, cell lines or tissues, proposed readouts and related experimental protocols adequately justified and likely to lead to the creation of a valuable public resource that can be used by the whole biomedical research community? Are the proposed plans for sharing the data, the experimental protocols, models and software release plans scientifically meritorious and beneficial to the overall goals of the LINCS program?

Environment. Will the scientific environment in which the work will be done contribute to the probability of success? Are the institutional support, equipment and other physical resources available to the investigators adequate for the project proposed? Will the project benefit from unique features of the scientific environment, subject populations, or collaborative arrangements?

Additional Review Criteria

As applicable for the project proposed, reviewers will consider the following additional items in the determination of scientific and technical merit, but will not give separate scores for these items.

Protections for Human Subjects. For research that involves human subjects but does not involve one of the six categories of research that are exempt under 45 CFR Part 46, the committee will evaluate the justification for involvement of human subjects and the proposed protections from research risk relating to their participation according to the following five review criteria: 1) risk to subjects, 2) adequacy of protection against risks, 3) potential benefits to the subjects and others, 4) importance of the knowledge to be gained, and 5) data and safety monitoring for clinical trials.

For research that involves human subjects and meets the criteria for one or more of the six categories of research that are exempt under 45 CFR Part 46, the committee will evaluate: 1) the justification for the exemption, 2) human subjects involvement and characteristics, and 3) sources of materials.

Inclusion of Women, Minorities, and Children. When the proposed project involves clinical research, the committee will evaluate the proposed plans for inclusion of minorities and members of both genders, as well as the inclusion of children.

Vertebrate Animals. The committee will evaluate the involvement of live vertebrate animals as part of the scientific assessment according to the following five points: 1) proposed use of the animals, and species, strains, ages, sex, and numbers to be used; 2) justifications for the use of animals and for the appropriateness of the species and numbers proposed; 3) adequacy of veterinary care; 4) procedures for limiting discomfort, distress, pain and injury to that which is unavoidable in the conduct of scientifically sound research including the use of analgesic, anesthetic, and tranquilizing drugs and/or comfortable restraining devices; and 5) methods of euthanasia and reason for selection if not consistent with the AVMA Guidelines on Euthanasia. For additional information, see http://grants.nih.gov/grants/olaw/VASchecklist.pdf.

Biohazards. Reviewers will assess whether materials or procedures proposed are potentially hazardous to research personnel and/or the environment, and if needed, determine whether adequate protection is proposed.

Resubmission Applications. Resubmission applications are not permitted in response to this FOA.

Renewal Applications. Renewals applications are not permitted in response to this FOA.

Revision Applications. When reviewing a Revision application (formerly called a competing supplement application), the committee will consider the appropriateness of the proposed expansion of the scope of the project. If the Revision application relates to a specific line of investigation presented in the original application that was not recommended for approval by the committee, then the committee will consider whether the responses to comments from the previous scientific review group are adequate and whether substantial changes are clearly evident.

Additional Review Considerations

As applicable for the project proposed, reviewers will address each of the following items, but will not give scores for these items and should not consider them in providing an overall impact/priority score.

Applications from Foreign Organizations. Reviewers will assess whether the project presents special opportunities for furthering research programs through the use of unusual talent, resources, populations, or environmental conditions that exist in other countries and either are not readily available in the United States or augment existing U.S. resources.

Select Agents Research. Reviewers will assess the information provided in this section of the application, including 1) the Select Agent(s) to be used in the proposed research, 2) the registration status of all entities where Select Agent(s) will be used, 3) the procedures that will be used to monitor possession use and transfer of Select Agent(s), and 4) plans for appropriate biosafety, biocontainment, and security of the Select Agent(s).

Resource Sharing Plans. Reviewers will comment on whether the following Resource Sharing Plans, or the rationale for not sharing the following types of resources, are reasonable: 1) Data Sharing Plan (http://grants.nih/gov/grants/policy/data_sharing/data_sharing_guidance.htm); 2) Sharing Model Organisms (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-04-042.html); and 3) Genome Wide Association Studies (GWAS) (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-07-088.html).

Budget and Period Support. Reviewers will consider whether the budget and the requested period of support are fully justified and reasonable in relation to the proposed research.

Selection Process

The following will be considered in making funding decisions:

• Scientific and technical merit of the proposed project as determined by peer review
• Availability of funds
• Relevance of the proposed project to program priorities
• Balance within the program, including the ability to assess more than a single approach (perturbation/cell line/readout) to generating a LINCS resource
• Compliance with NIH data and material sharing policies

NIH considers the following in evaluating Center grant applications:

• The scientific and technical merit of the proposed program; (use the 5 criteria above)
• The qualifications and experience of the center director and other key personnel;
• The statutory and program purposes to be accomplished;
• The extent to which the various components of the proposed program would be coordinated into one multi-disciplinary effort within the center;
• The extent to which the center's activities would be coordinated with similar efforts by other organizations;
• The administrative and managerial capability of the applicant; and
• Other factors which the awarding IC considers appropriate in light of its particular statutory mission.

3. Anticipated Announcement and Award Dates

Council Review Date: August 2010
Earliest Anticipated Start Date: September 30, 2010

Section VI. Award Administration Information

1. Award Notices

After the peer review of the application is completed, the PD/PI will be able to access his or her Summary Statement (written critique) via the eRA Commons.

If the application is under consideration for funding, NIH will request "just-in-time" information from the applicant. For details, applicants may refer to the NIH Grants Policy Statement Part II: Terms and Conditions of NIH Grant Awards, Subpart A: General.

A formal notification in the form of a Notice of Award (NoA) will be provided to the applicant organization. The NoA signed by the grants management officer is the authorizing document. Once all administrative and programmatic issues have been resolved, the NoA will be generated via email notification from the awarding component to the grantee business official.

Selection of an application for award is not an authorization to begin performance. Any costs incurred before receipt of the NoA are at the recipient's risk. These costs may be reimbursed only to the extent considered allowable pre-award costs. See Also Section IV.5. Funding Restrictions.

2. Administrative and National Policy Requirements

All NIH grant and cooperative agreement awards include the NIH Grants Policy Statement as part of the Notice of Award. For these terms of award, see the NIH Grants Policy Statement Part II: Terms and Conditions of NIH Grant Awards, Subpart A: General (http://grants.nih.gov/grants/policy/nihgps_2003/NIHGPS_Part4.htm) and Part II Terms and Conditions of NIH Grant Awards, Subpart B: Terms and Conditions for Specific Types of Grants, Grantees, and Activities (http://grants.nih.gov/grants/policy/nihgps_2003/NIHGPS_part9.htm).

The following Terms and Conditions will be incorporated into the award statement and will be provided to the Principal Investigator as well as to the appropriate institutional official, at the time of award.

2.A. Cooperative Agreement Terms and Conditions of Award

The following special terms of award are in addition to, and not in lieu of, otherwise applicable OMB administrative guidelines, HHS grant administration regulations at 45 CFR Parts 74 and 92 (Part 92 is applicable when State and local Governments are eligible to apply), and other HHS, PHS, and NIH grant administration policies.

The administrative and funding instrument used for this program will be the cooperative agreement an "assistance" mechanism (rather than an "acquisition" mechanism), in which substantial NIH programmatic involvement with the awardees is anticipated during the performance of the activities. Under the cooperative agreement, the NIH purpose is to support and stimulate the recipients' activities by involvement in and otherwise working jointly with the award recipients in a partnership role; it is not to assume direction, prime responsibility, or a dominant role in the activities. Consistent with this concept, the dominant role and prime responsibility resides with the awardees for the project as a whole, although specific tasks and activities may be shared among the awardees and the NIH as defined below.

2. A.1. Principal Investigator Rights and Responsibilities

The Principal Investigator will have the primary responsibility for: defining the details for the projects within the guidelines of this FOA, and for performing all scientific activities. The PI will agree to accept the close coordination, cooperation, and participation of the NIH staff (LINCS Program Officials, Project Scientists, the Project Team Leader, and the LINCS Project Team) in those aspects of scientific and technical management of the project as described below.

Specifically, the PI of this LINCS center will:

1. Determine experimental approaches, design protocols, set project milestones, conduct experiments, and analyze and interpret research data.

2. Provide goals for implementation, throughput, quality, and cost to the NIH Program Official and Project Scientist as requested (usually at the outset of the award and in six-month progress reports, but also at other times as requested by the Program Official and Project Scientist).

3. Serve on the LINCS Steering Committee, and participate, along with critical staff, in the LINCS Steering Committee meetings held once annually in the metropolitan Washington, DC area.

4. Adhere to LINCS policies regarding data release, data standardization, standardization of experimental protocols, and other policies that might be established, as agreed upon by the LINCS Steering Committee and the LINCS Project Team.

5. Ensure that all data, experimental protocols, and data on the perturbagens used will be deposited in an open access database according to the timeline agreed upon by the LINCS Steering Committee and the LINCS Project Team, and that resources developed as a part of this project (e.g., information about assays and chemical probes) are made publicly available according to LINCS policies. The LINCS Steering Committee and Project Team recommendation will be consistent with the ongoing genomic scale data sharing policies being developed by NIH.

6. Accept and implement all scientific, practical and policy decisions approved by the LINCS Steering Committee and the LINCS Project Team.

7. Submit data for quality assessment in any manner specified by the LINCS Steering Committee, LINCS Project Team, or External Scientific Panel (ESP; see below).

8. Share research resources, tools, and data of interest with other LINCS centers, components and collaborators as agreed upon by the LINCS Steering Committee and LINCS Project Team.

9. Agree not to disclose confidential information obtained from other members of the LINCS network.

10. Be prepared for annual administrative site visits by NIH staff.

11. Adhere to LINCS policies regarding intellectual property, data release and other policies that might be established during the course of this activity.

Awardees will retain custody of and have primary rights to the data and software developed under these awards, subject to Government rights of access consistent with current HHS, PHS, and NIH policies.

2. A.2. NIH Responsibilities

An NIH Project Scientist will have substantial programmatic involvement that is above and beyond the normal stewardship role in awards, as described below.

A LINCS Project Scientist will have substantial programmatic involvement that is above and beyond the normal stewardship role in awards, as described below.

Project Scientist Responsibilities. The LINCS Project Scientists are NIH extramural program scientists who will have substantial scientific involvement during the conduct of this activity, through technical assistance, advice, and coordination above and beyond normal program stewardship for grants. This includes facilitating the partnership relationship between NIH and the LINCS centers funded under this FOA, and with members of any future components of the LINCS project, helping to maintain the overall scientific balance in the program commensurate with new research and emerging research opportunities, and ensuring that the activities of the LINCS projects are consistent with the mission of the NIH LINCS project. However, the role of the Project Scientist will be to facilitate and not to direct. Each LINCS center will have one designated Project Scientist, and a given Project Scientist may be assigned to multiple centers.

The LINCS Project Scientists will have the following substantial involvement:

1. Provide ongoing coordination and tracking of the activities of individual LINCS grantees.

2. Provide relevant scientific expertise and overall knowledge.

3. Assist in the integration of the individual LINCS awardees into a research network, including coordinating regular conference calls for sharing of approaches and fostering collaborations.

4. Assist in efforts for data and experimental protocol standardization efforts.

5. Participate, as a voting member, with the other LINCS Steering Committee members in the group process of setting research priorities and milestones, deciding optimal research approaches and protocol designs, and contributing to the adjustment of research protocols or approaches as warranted. The Project Scientist will assist and facilitate the group process and not direct it.

6. Develop, with input from the LINCS Steering Committee and the LINCS Project Team, progress report formats (six-month and annually) for all grantees.

7. Provide relevant expertise and overall knowledge of NIH-sponsored research to facilitate the selection of scientists not affiliated with the awardee institutions to serve on the External Scientific Panel.

8. Participate in the External Scientific Panel (ESP) meetings.

9. Serve as scientific liaison between the awardees, other NIH program staff, and the LINCS Project Team.

10. Report periodically (e.g., monthly) on the progress of the LINCS program to the LINCS Project Team.

11. Assist in developing timelines for the wide distribution of data, experimental protocols and software tools to the scientific community in accordance with the decisions of the LINCS Steering Committee and the LINCS Project Team.

12. Assist in avoiding unwarranted duplication of effort across the LINCS program, and help coordinate collaborative research efforts that involve multiple grantees in the LINCS components.

13. Review and comment on critical stages of LINCS development for presentation to the LINCS Project Team and External Scientific Panel before subsequent stages are implemented.

14. Retain the option to recommend, with the advice of the External Scientific Panel, additional research endeavors within the constraints of the approved research and negotiated budget to the LINCS Project Team.

15. Retain the option to recommend, with the advice of the External Scientific Panel, re-allocation of NIH support among awardees, as scientific goals evolve.

16. To help carry out these duties, Project Scientists may consult with non-NIH experts in the field.

LINCS Project Team Responsibilities. The LINCS Project Team will serve as the trans-NIH body overseeing and coordinating the activities of all LINCS components. Project Team membership will include one or more representative(s) from each of the NIH Institutes and Centers (IC) participating in the LINCS program. Program Officials and Project Scientists can be members of the LINCS Project Team. Each participating NIH IC will have a single vote on the Project Team, no matter how many members from the NIH IC are involved. The Project Team will receive recommendations from the LINCS Steering Committee.

The LINCS Project Team will have the following involvement:

1. Review and implement guidelines and policies based on recommendations from the LINCS Steering Committee.

2. Communicate, through the chair of the Steering Committee, policy information to the LINCS Steering Committee, other LINCS components and the LINCS co-chairs.

3. Monitor the progress of all LINCS activities to determine the appropriateness of the use/continued use of LINCS resources (e.g., for implementing particularly difficult assays).

4. Evaluate progress of the LINCS program in consultation with the ESP.

5. Attend the ESP meetings and other LINCS meetings.

Additionally, an agency program official or IC program director will be responsible for the normal scientific and programmatic stewardship of the award and will be named in the award notice.

2.A.3. Collaborative Responsibilities

LINCS Steering Committee Functions. The LINCS Steering Committee is the operational group responsible for coordination of the activities of all components of the LINCS. The LINCS Steering Committee will identify scientific and policy issues that need to be addressed by all components of the LINCS program, develop recommendations to the Project Team for addressing such issues, coordinate the primary recommendations for choice of experimental protocol, and coordinate the dissemination of data, assay protocols, and other materials with the wider scientific community.

The LINCS Steering Committee membership will include the PI of each of the components of the LINCS program, and the Project Scientists.

The PI of each center (or designee) will have one vote on the LINCS Steering Committee. The Project Scientists may vote, but the total votes will count as a maximum of one-third of the total LINCS Steering Committee votes. Membership on the Steering Committee becomes effective upon issuance of the Notice of Award. The Steering Committee may add additional members if technology development, data generation, coordination, standardization or integration activities will benefit from such an expansion. Other NIH staff may attend the Steering Committee meetings, if their expertise is required for specific discussions. The LINCS Steering Committee may establish additional subcommittees or workgroups for specific tasks. No NIH staff member may chair any committee or subcommittee of the Steering Committee.

The LINCS Steering Committee will:

1. Convene at least once per year. The purpose of these meetings is to assess scientific progress, identify new research opportunities, establish priorities, consider policy recommendations, and discuss strategies. One of the meetings will be in conjunction with the annual meeting of the ESP.

2. Make decisions by a majority vote of a quorum, with an attempt for a consensus. A quorum will be the presence of a majority of the center PIs or their designees, and at least one Project Scientist. Outside consultants/experts may be asked to participate in these discussions as nonvoting advisors.

3. Establish a chair, or workgroups for specific tasks; the Project Scientists may not chair any committee or workgroup.

4. Hold conference calls of the full committee and any workgroups as needed; monthly calls are anticipated.

5. Develop recommendations for guidelines and policies for choosing cell types, perturbations, quality control and quality assurance of assay, data reliability and quality, and quality assurance and other standards that are needed for the perturbations used implement and monitor quality control/quality assurance procedures to assure consistency across all LINCS components.

6. Develop recommendations for choice of reagents, data, standardized terms used to describe the experimental results and software interoperability standards.

7. Develop policies to facilitate the timely deposition of data and protocols in accordance with the LINCS data release policy.

8. Serve as a venue for coordination on improving the state-of-the-art for all LINCS activities by reporting progress, disseminating best practices, and collectively evaluating new procedures, resources, and technologies.

9. Identify opportunities to increase the interoperability of all relevant components within the LINCS program; grantees will be expected to have a high degree of flexibility and be willing to adopt uniform policies and procedures recommended by the Steering Committee and approved for implementation by the LINCS Project Team.

10. Develop recommendations for guidelines for publication of results, and global data analyses, etc. resulting from the LINCS effort.

11. Address recommendations made by the External Scientific Panel and approved for implementation by the LINCS Project Team.

External Scientific Panel (ESP): The ESP will be responsible for reviewing and evaluating the progress of the LINCS program in meeting their individual and collective milestones and goals, and making recommendations about the progress and directions of the LINCS program and individual components to the LINCS Project Team. The ESP will be composed of 4-6 senior non-federal scientists who are not directly involved in the activities of the LINCS program. The LINCS Project Team will appoint members to the ESP. The LINCS Project Team will select one member as chair. The LINCS Project Scientists and LINCS Project Team members may attend the External Scientific Panel meetings as non-voting participants.

The ESP will have the following involvement:

1. The chair will schedule, develop agendas, and oversee the annual meetings and conference calls. The membership of the Panel may be enlarged permanently, or on an ad hoc basis by action of the original members.

2. The ESP will review progress of the LINCS program and individual components, and make recommendations regarding any changes that may be needed in the direction of the LINCS program to the LINCS Project Team.

3. The ESP will be consulted by the Project Scientists and Project Team when changes in a center’s funding level are being considered because of either outstanding or poor technical performance, or for other reasons.

4. Any LINCS component PI who considers a LINCS Steering Committee decision unacceptable may appeal to the ESP.

5. ESP members will be invited to attend as observers at the annual meetings of the LINCS Steering Committee.

Each full member will have one vote. Awardee members of the Steering Committee will be required to accept and implement policies approved by the Steering Committee.

2.A.4. Dispute Resolution Process

Any disagreements that may arise in scientific or programmatic matters (within the scope of the award) between award recipients and the NIH may be brought to Dispute Resolution. A Dispute Resolution Panel composed of three members will be convened. It will have three members: a designee of the Steering Committee chosen without NIH staff voting, one NIH designee, and a third designee with expertise in the relevant area who is chosen by the other two; in the case of individual disagreement, the first member may be chosen by the individual awardee. This special dispute resolution procedure does not alter the awardee's right to appeal an adverse action that is otherwise appealable in accordance with PHS regulations 42 CFR Part 50, Subpart D and HHS regulations 45 CFR Part 16.

3. Reporting

Awardees will be required to submit the Non-Competing Continuation Grant Progress Report (PHS 2590) annually and financial statements as required in the NIH Grants Policy Statement.

A final progress report, invention statement, and Financial Status Report are required when an award is relinquished when a recipient changes institutions or when an award is terminated.

Section VII. Agency Contacts

We encourage your inquiries concerning this funding opportunity 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:

1. Scientific/Research Contacts:

Jennie Larkin
National Heart, Lung, and Blood Institute
6701 Rockledge Dr.
Rockledge 2, room 8200
Bethesda, MD 20892-7940
Telephone: 301-435-0513
Email: [email protected]

Adam Felsenfeld
National Human Genome Research Institute
5635 Fishers Lane
Bethesda, MD 20892
Telephone: (301) 984-5930
Email: [email protected]

Ajay
National Human Genome Research Institute
5635 Fishers Lane
Bethesda, MD 20892
Telephone: (301) 594-7108
Email: [email protected]

Weiniu Gan
Genetics, Genomics, and Advanced Technologies
Division of Lung Diseases
National Heart, Lung and Blood Institute
Two Rockledge Center, Suite 10164
6701 Rockledge Dr. MSC 7952
Bethesda, Maryland 20892-7952
Telephone: (301) 435-0202
Email: [email protected]

2. Peer Review Contacts:

Noni Byrnes, Ph.D.
Division of Basic and Integrative Biological Sciences
Center for Scientific Review
Room 5130
6701 Rockledge Dr
Bethesda, MD 20892
Telephone: (301) 435-1023
Email: [email protected]

3. Financial or Grants Management Contacts:

Cheryl Chick
Chief Grants Management Officer
Grants Administration Branch, DER
National Human Genome Research Institute, NIH
5635 Fishers Lane, Ste 3058
Bethesda, MD 20892-9307
Courier services should use:
Rockville, Maryland 20852
TEL: 301-435-7858
FAX: 301-451-5434
Email: [email protected]

Section VIII. Other Information

Required Federal Citations

Use of Animals in Research:
Recipients of PHS support for activities involving live, vertebrate animals must comply with PHS Policy on Humane Care and Use of Laboratory Animals (http://grants.nih.gov/grants/olaw/references/PHSPolicyLabAnimals.pdf) as mandated by the Health Research Extension Act of 1985 (http://grants.nih.gov/grants/olaw/references/hrea1985.htm), and the USDA Animal Welfare Regulations (http://www.nal.usda.gov/awic/legislat/usdaleg1.htm) as applicable.

Human Subjects Protection:
Federal regulations (45CFR46) require that applications and proposals involving human subjects must be evaluated with reference to the risks to the subjects, the adequacy of protection against these risks, the potential benefits of the research to the subjects and others, and the importance of the knowledge gained or to be gained (http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.htm).

Data and Safety Monitoring Plan:
Data and safety monitoring is required for all types of clinical trials, including physiologic toxicity and dose-finding studies (phase I); efficacy studies (Phase II); efficacy, effectiveness and comparative trials (Phase III). Monitoring should be commensurate with risk. The establishment of data and safety monitoring boards (DSMBs) is required for multi-site clinical trials involving interventions that entail potential risks to the participants (NIH Policy for Data and Safety Monitoring, NIH Guide for Grants and Contracts, http://grants.nih.gov/grants/guide/notice-files/not98-084.html).

Sharing Research Data:
Investigators submitting an NIH application seeking $500,000 or more in direct costs in any single year are expected to include a plan for data sharing or state why this is not possible (http://grants.nih.gov/grants/policy/data_sharing).

Investigators should seek guidance from their institutions, on issues related to institutional policies and local IRB rules, as well as local, State and Federal laws and regulations, including the Privacy Rule.

Policy for Genome-Wide Association Studies (GWAS):
NIH is interested in advancing genome-wide association studies (GWAS) to identify common genetic factors that influence health and disease through a centralized GWAS data repository. For the purposes of this policy, a genome-wide association study is defined as any study of genetic variation across the entire human genome that is designed to identify genetic associations with observable traits (such as blood pressure or weight), or the presence or absence of a disease or condition. All applications, regardless of the amount requested, proposing a genome-wide association study are expected to provide a plan for submission of GWAS data to the NIH-designated GWAS data repository, or provide an appropriate explanation why submission to the repository is not possible. Data repository management (submission and access) is governed by the Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies, NIH Guide NOT-OD-07-088. For additional information, see http://grants.nih.gov/grants/gwas/

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 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 funding opportunity 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.

Sharing of Model Organisms:
NIH is committed to support efforts that encourage sharing of important research resources including the sharing of model organisms for biomedical research (see http://grants.nih.gov/grants/policy/model_organism/index.htm). At the same time the NIH recognizes the rights of grantees and contractors to elect and retain title to subject inventions developed with Federal funding pursuant to the Bayh Dole Act (see the NIH Grants Policy Statement http://grants.nih.gov/grants/policy/nihgps_2003/index.htm). All investigators submitting an NIH application or contract proposal, beginning with the October 1, 2004 receipt date, are expected to include in the application/proposal a description of a specific plan for sharing and distributing unique model organism research resources generated using NIH funding or state why such sharing is restricted or not possible. This will permit other researchers to benefit from the resources developed with public funding. The inclusion of a model organism sharing plan is not subject to a cost threshold in any year and is expected to be included in all applications where the development of model organisms is anticipated.

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 "NIH Guidelines for Inclusion of Women and Minorities as Subjects in Clinical Research (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 Clinical Research:
The NIH maintains a policy that children (i.e., individuals under the age of 21) must be included in all clinical research, conducted or supported by the NIH, unless there are scientific and ethical reasons not to include them.

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 (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 applications for research involving human subjects and individuals designated as key personnel. The policy is available 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://stemcells.nih.gov/index.asp and at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-09-116.html. Only research using hESC lines that are registered in the NIH Human Embryonic Stem Cell Registry will be eligible for Federal funding (http://escr.nih.gov). It is the responsibility of the applicant to provide in the project description and elsewhere in the application as appropriate, the official NIH identifier(s) for the hESC line(s) to be used in the proposed research.

NIH Public Access Policy Requirement:
In accordance with the NIH Public Access Policy (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-08-033.html) investigators must submit or have submitted for them their final, peer-reviewed manuscripts that arise from NIH funds and are accepted for publication as of April 7, 2008 to PubMed Central (http://www.pubmedcentral.nih.gov/), to be made publicly available no later than 12 months after publication. As of May 27, 2008, investigators must include the PubMed Central reference number when citing an article in NIH applications, proposals, and progress reports that fall under the policy, and was authored or co-authored by the investigator or arose from the investigator’s NIH award. For more information, see the Public Access webpage at http://publicaccess.nih.gov/.

Standards for Privacy of Individually Identifiable Health Information:
The Department of Health and Human Services (DHHS) issued final modification to the "Standards for Privacy of Individually Identifiable Health Information", the "Privacy Rule", on August 14, 2002. The Privacy Rule is a federal regulation under the Health Insurance Portability and Accountability Act (HIPAA) of 1996 that governs the protection of individually identifiable health information, and is administered and enforced by the DHHS Office for Civil Rights (OCR).

Decisions about applicability and implementation of the Privacy Rule reside with the researcher and his/her institution. The OCR website (http://www.hhs.gov/ocr/) provides information on the Privacy Rule, including a complete Regulation Text and a set of decision tools on "Am I a covered entity?" Information on the impact of the HIPAA Privacy Rule on NIH processes involving the review, funding, and progress monitoring of grants, cooperative agreements, and research contracts can be found at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-025.html.

URLs in NIH Grant Applications or Appendices:
All applications and proposals for NIH funding must be self-contained within specified page limitations. For publications listed in the appendix and/or Progress report, internet addresses (URLs) must be used for publicly accessible on-line journal articles. Unless otherwise specified in this solicitation, Internet addresses (URLs) should not be used to provide any other information necessary for 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 FOA 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 at http://www.cfda.gov/ and is not subject to the intergovernmental review requirements of Executive Order 12372. 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.

Loan Repayment Programs:
NIH encourages applications for educational loan repayment from qualified health professionals who have made a commitment to pursue a research career involving clinical, pediatric, contraception, infertility, and health disparities related areas. The LRP is an important component of NIH's efforts to recruit and retain the next generation of researchers by providing the means for developing a research career unfettered by the burden of student loan debt. Note that an NIH grant is not required for eligibility and concurrent career award and LRP applications are encouraged. The periods of career award and LRP award may overlap providing the LRP recipient with the required commitment of time and effort, as LRP awardees must commit at least 50% of their time (at least 20 hours per week based on a 40 hour week) for two years to the research. For further information, please see: http://www.lrp.nih.gov.