Part I Overview Information   


Department of Health and Human Services

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

Components of Participating Organizations
National Human Genome Research Institute (NHGRI),  (http://www.nhgri.nih.gov)

Title: 1000 Genomes Project Data Processing (U01)

Announcement Type
New

Request For Applications (RFA) Number:  RFA-HG-09-001

Catalog of Federal Domestic Assistance Number(s)
93.172

Key Dates  
Release Date: November 4, 2008  
Letters of Intent Receipt Date: December 12, 2008
Application Receipt Date: January 12, 2009
Peer Review Dates:  February-March, 2009
Council Review Date: May 2009
Earliest Anticipated Start Date: July 2009
Additional Information To Be Available Date (Url Activation Date): Not applicable
Expiration Date: January 13, 2009

Due Dates for E.O. 12372

Not Applicable

Additional Overview Content

Executive Summary

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 and Information

Section V. Application Review Information
1. Criteria
2. Review and Selection Process
    A. Additional Review Criteria
    B. Additional Review Considerations
    C. Resource Sharing Plan(s)
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. Arbitration 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

Background

In the last two years, genome-wide association (GWA) studies have been successful in finding hundreds of variants that are associated with diseases or other traits.  These discoveries became possible because of the availability of a large catalog of single nucleotide polymorphisms (SNPs) across the human genome and the development of dense genotyping microarrays.  These arrays are based on data from the International HapMap Project that show the pattern of variation across the genome.  The arrays allow genotyping to be done in case and control samples at sufficient resolution to find regions of the genome that are associated with particular diseases or other traits. 

This approach can provide only a general genomic location for the actual disease-causing or risk-elevating variants.  The arrays type only a fraction of the variants found in the genome, because the HapMap data consist mostly of variants with a frequency of at least 5%.  However, many other variants, both SNP and structural, also occur in any genomic region, and variants with lower frequencies also contribute to disease risk.  Thus the initial follow-up to a GWA study finding that a region is associated with a disease or other trait is to try to discover all the other, untyped, variants in the region.   Even then, it is usually not clear which genes and variants in the region causally contribute to the disease risk, because generally many variants in a region are statistically associated with each other.  Thus, finding the full set of variants in the region is necessary, but determining which variants and genes cause the disease risk requires additional, functional studies to analyze their potential roles.   

The international 1000 Genomes Project (www.1000genomes.org) is designed to support GWA studies by providing a public resource of almost all genetic variants across the human genome with a frequency of 1% or higher, and of genetic variants with even lower frequencies in gene regions.  When the 1000 Genomes resource is available, investigators will not have to take the time and expense to follow up a GWA study by sequencing the regions of interest; they will be able to look in a public database and find an almost complete catalog of the variants in those regions, including almost all of the ones that functionally cause the increased disease risk. 

The 1000 Genomes Project has developed rapidly since its adoption at an international meeting in September of 2007.  It will be the first large-scale project to use the next-generation sequencing platforms for extensive human resequencing.  The sequence data for the Project will be generated at the NHGRI-funded centers at the Baylor College of Medicine, the Broad Institute of MIT and Harvard, and Washington University in St. Louis, as well as centers at the Wellcome Trust Sanger Institute, the Beijing Genomics Institute Shenzhen, the Max Planck Institute for Molecular Genetics, Applied Biosystems, Illumina, and Roche.  

The strategy initially proposed for the 1000 Genomes Project is to sequence the genomes of 1200-1500 individuals to a depth of coverage of at least 4X (haploid equivalents) across the genome and 12X in gene regions.  To test the value of this approach and to address several other issues related to the design of the full-scale effort, the Project has begun with three pilot projects.  Sequence data production for the pilot projects started in January 2008 and should be finished early in 2009.  The data from these pilots will be analyzed, and the design for the full-scale project will be developed by early 2009.  Sequencing for the full-scale project should start in the fall of 2008 and continue for about two years, through about the end of 2010.  The entire sequence dataset is anticipated to be at least 20 Terabases, a massive amount of data. 

The 1000 Genomes Project dataset has been identified as a community resource, as described in the proceedings of the Meeting on Sharing Data from Large-Scale Biological Research Projects (http://www.wellcome.ac.uk/doc_wtd003208.html).  The Project plans to release the raw sequence data and many processed data types publicly, quickly, and on a regular basis.  The sequencing centers already send the raw sequence reads regularly to the Project’s Data Coordination Center (DCC), provided jointly by the European Bioinformatics Institute (EBI) and the National Center for Biotechnology Information (NCBI) of NIH, which quickly deposits them in the public Short-Read Archive database. 

Because the next-generation sequencing platforms are in an early stage for production use, a number of analytical methods are still being developed to use the raw sequence reads to produce the derived data types that most users will need.  Some of these methods, such as generating data quality scores, will apply to many types of sequencing projects.  Others, such as combining data across samples, will be more specific to the 1000 Genomes Project.  Data-processing pipelines are currently being developed that will allow the DCC to use the sequence reads to provide several derived data types, such as read alignments, SNPs and structural variants, and genotypes of individual samples, along with their quality measures.  When the Project has produced the full 1000 Genomes dataset, many other types of analyses will be needed to characterize it and make it more useful for the research community.  The Project plans to release publicly the software that will be used to produce the various data types and analyze the dataset.    

All of the data processing activities for the 1000 Genomes Project are being coordinated through the Project’s Production, Analysis, and Data Processing Groups, working with the DCC.  Some of the participating research groups have funding from NIH or elsewhere to work on specific analyses.  Other critical analysis work, however, is as yet unfunded.

Objectives of This Research Program

This FOA and its companion FOA (RFA-HG-09-002)aim to address the analysis needs of the 1000 Genomes Project on two timescales: 

1.  This FOA (RFA-HG-09-001 “1000 Genomes Project Data Processing”) solicits proposals to perform the analyses needed to produce the 1000 Genomes dataset.  It calls for proposals to carry out the analysis work needed to process the primary sequence data to produce the full derived Project dataset.

This FOA solicits proposals to continue to develop, evaluate, and implement the methods needed to produce the derived data types from the sequence data, monitor the quality of the data, integrate the data types, develop the tools needed to work with the data, and develop new processes as needed to produce the full derived Project dataset. 

Because of the timing of this FOA, the initial software pipelines for the DCC to process the data will already have been set up when the awards are made.  The two-year award period (July 2009 to June 2011) should allow for the development and implementation of the processes needed to produce the several derived data types on a regular basis.  The sequencing is anticipated to be finished before these awards end, so that the full derived dataset can be produced using the entire set of Project sequence data. 

2.  The companion FOA (RFA-HG-09-0021000 Genomes Project Dataset Analysis”), in contrast, solicits proposals to analyze the full Project dataset, after it has been produced by work funded through (this) RFA-HG-09-001.  The companion RFA-HG-09-002 calls for proposals to carry out the analysis work needed to maximize the value of the full 1000 Genomes Project dataset to the general research community.

The companion FOA solicits proposals to characterize the dataset, provide additional derived data types, perform global analyses on the data, and develop better tools for using the dataset to study biomedical and biological research problems.

Because of the timing of the companion FOA, awardees will start to work with the dataset in about April 2010, before it is complete.  This will allow them time to become familiar with the data, develop the methods using subsets of the data, and then be ready to analyze the full dataset when it becomes available, which is anticipated to be roughly in early 2011.  Awardees will then have about a year to perform the analyses on the data.  These awards are being made for only two years because it will be important to provide these characterizations, analyses, and tools rapidly so that the research community will be able to make full use of the 1000 Genomes resource as soon as possible.     

Research Scope

Applicants for this FOA should propose to (a) improve the methods used by the data-processing pipelines that have already been implemented, either at the DCC or by a group participating in the 1000 Genomes Project, or (b) develop new methods for processing the data.  They should also propose to develop the software to implement these methods, including documentation.  Software developed by awardees should be modular, so that it can work as a stand-alone package.  When possible, the software should use standard formats for data input and output, to facilitate its use and incorporation into central pipelines.  These standard formats should be ones that the Project has already decided on, or, if new standard formats are needed, ones that the awardees develop in close collaboration with others in the Project Analysis Group and the DCC.  The DCC is responsible for incorporating any software into its pipelines.  Awardees will also be responsible for monitoring the Project data produced using their methods, and making adjustments to the methods as needed to correct problems or make improvements.

As part of developing the data processing methods, awardees may generate resource datasets, such as simulated datasets, test datasets, or annotated validation datasets, that would be useful to others in the Project or more broadly. These datasets should be released publicly at the time that they are used to develop or analyze the main Project dataset.

Examples of research topics for this FOA include, but are not limited to, those listed below:    

1. Monitor data quality.  Each sequencing center will monitor the quality of its own data.  However, methods will need to be developed to monitor the quality of the sequence data in a standard way on an ongoing basis during the 1000 Genomes Project to ensure that the quality is consistent across the different platforms and the centers that will be producing data, and to facilitate the combination of the data from different sources.  Long reads and paired-end data from some platforms will make up for some of the limitations of the short-read data, and the coverage of the various types of sequence data will need to be continually monitored across the genome, particularly for structurally complex regions.  This monitoring will ensure that the data quality remains high and adequate for the goals of the Project. 

2.  Validate variants.  The sequencing centers will validate samples of variants of different frequencies and types by genotyping or additional sequencing to provide experimental estimates of false positive and negative rates.  These validation experiments will need to be designed (e.g., the number of variants to be tested of each type will need to be determined), and the validation experiments will need to be interpreted. 

3.  Combine data across samples.  The central analytical method of the Project will be to combine data from low sequence coverage of many samples to find almost all of the variants that are present, including those with low frequencies.  This combining of data across samples and use of the entire dataset means that, although individual samples will not be genotyped with high confidence, the variants will be found with high confidence.  Methods for combining data across samples will need to be fully developed, applied to the large amounts of data that will be produced, and evaluated for effectiveness across the genome and in gene regions.  Achievement of the depth of coverage that provides sufficiently accurate variant discovery will need to be monitored to determine when the Project has reached its goals. 

4.  Produce genotypes, haplotypes, and other derived data types for release to the community.  The methods for calling bases and structural variants will need to be fully implemented and improved as more data become available, as will methods used to produce genotypes, haplotypes, and LD patterns. 

5.  Integrate data types.  Methods will need to be developed to integrate data on SNPs and structural variants into one map, and place them on the same set of haplotypes.  Other data types may also need to be integrated.

6.  Develop tools to work with the data to produce the final dataset.  The massive amounts of data to be produced will require new tools to visualize, simulate, and summarize the data. 

As much as possible, the methods developed should apply to the entire genome or the entire set of gene regions, using all the samples.  This FOA will not support the use of 1000 Genomes data for the analysis of the genetics of specific human diseases or other phenotypes. 

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

Section II. Award Information


1. Mechanism of Support

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 U01 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".  

Plans beyond the current funding opportunity are indefinite.

2. Funds Available

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.

3. Other-Special Eligibility Criteria

Applicants are not permitted to submit a resubmission application in response to this FOA.

Renewal applications are not permitted in response to this FOA. 

Applicants may submit more than one application, provided each application is scientifically distinct.

Section IV. Application and Submission Information


1. Address to Request Application Information

The 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) 435-0714, Email: GrantsInfo@nih.gov.

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

2. Content and Form of Application Submission

Applications must be prepared using the most current PHS 398 research grant application instructions and forms. 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.

Additional information is available in the PHS 398 grant application instructions.

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
Letters of Intent Receipt Date: December 12, 2008
Application Receipt Date: January 12, 2009
Peer Review Dates: February-March 2009
Council Review Date: May 2009
Earliest Anticipated Start Date: July 2009

3.A.1. Letter of Intent

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

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:

Lisa D. Brooks, Ph.D.
NHGRI
5635 Fishers Lane, Suite 4076  
Bethesda, MD 20892-9305
(301) 435-5544
lisa.brooks@nih.gov

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 three signed photocopies in one package to:

Center for Scientific Review
National Institutes of Health
6701 Rockledge Drive, Room 1040, MSC 7710
Bethesda, MD 20892-7710 (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).

At the time of submission, two additional copies of the application and all copies of the appendix material must be sent to:

Rudy Pozzatti, Ph.D.
NHGRI Review Branch
5635 Fishers Lane
Suite 4076, MSC 9306
Bethesda, MD  20892-9306
(For courier service use Rockville, MD 20852)
301-496-7531
rp7s@nih.gov

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/archive/grants/policy/nihgps_2003/index.htm.)

6. Other Submission Requirements and Information

Applicants should describe their familiarity with the 1000 Genomes data and their expertise with analyses of 1000 Genomes data or similar data.  They should describe any analyses or methods they have developed that are being used by the Project.  They should describe how the proposed analyses would coordinate with analyses already being done by the Project.  See www.1000genomes.org for a list of analyses currently being done by the Project.

Applicants should describe how they will develop the methods and the software to run the methods.  They should describe the input and output data types and formats.  They should explain how they will transfer the software to the DCC and work with the DCC to implement the methods.  Alternatively, if applicants propose that the DCC should not run a particular data processing step centrally, they should justify why they or some other group should run that step, and explain how they would transfer the processed dataset to the DCC.

Applicants should describe any resource datasets (e.g., simulated data) that they would develop, and explain how they would disseminate them.  

Applicants should describe the computing resources that are needed for the development work and what resources they have available. 

The Project has regular conference calls and meetings.  Applicants should request funds over the two years to attend Project meetings once in the U.K., in May 2010 and May 2011 at the Cold Spring Harbor Laboratory, and prior to the 2009 and 2010 meetings of the American Society of Human Genetics.

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

Research Plan Page Limitations

The page limit is the standard 25 pages.

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 of the Research Plan component. 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.

NHGRI has identified the 1000 Genomes Project as a community resource project.  A primary objective of the 1000 Genomes Project is to maximize the public benefit of the data produced.  NIH strongly endorses rapid release of genomic data and software as a general practice.  The 1000 Genomes Project aims to release all Project data rapidly before publication.  The Project data produced by the sequencing centers and the data-processing pipelines of the DCC are not supported by this FOA.  This RFA supports the development of the methods that will be used to produce the various processed data types from the sequence reads. 

i.  Methods and datasets:  As awardees develop methods to process 1000 Genomes data, they may also generate resource datasets that would be of use to other researchers.  Examples of such resource datasets include simulated data, test datasets, and annotated validation data.  These datasets and descriptions of all the methods developed would be useful to the research community when the methods are implemented in the 1000 Genomes production pipelines (generally by the DCC but possibly by other groups).  Applicants should describe the schedule for methods and resource dataset sharing, the formats of the datasets, the documentation to be provided, and the mode of data sharing (e.g., mailing a disk, posting on a web site, or providing the data and methods descriptions to the DCC or other database).    

ii.  Software:  Applications that propose to develop software must include a dissemination plan, with appropriate timelines.  There is no particular prescribed license for software produced through awards supported through this FOA, although open-source software sharing is strongly encouraged.  NHGRI has goals for software dissemination, and reviewers will be instructed to evaluate the dissemination plan relative to these goals:

1. The software, including the source code, should be freely available to the broad research community.

2. The terms of software availability should permit the commercialization of enhanced or customized versions of the software, and incorporation of the software or pieces of it into other software packages.

3. To preserve utility to the community, the software should be transferable so that another group could continue development if the original investigators were unwilling or unable to do so.

4. The terms of software availability should allow researchers to modify the source code and to share modifications with other colleagues.  An awardee should be responsible for creating the original and subsequent “official” versions of a piece of software, and should provide a plan to manage the dissemination, adoption of improvements, or customizations of that software by others.  This plan should include a method to distribute other user's contributions such as extensions, compatible modules, or plug-ins.

 (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/.

Section V. Application Review Information


1. Criteria (Update: Enhanced review criteria have been issued for the evaluation of research applications received for potential FY2010 funding and thereafter - see NOT-OD-09-025).

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

2. Review and Selection 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 NHGRI 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:

The following will be considered in making funding decisions:

The goals of NIH supported research are to advance our understanding of biological systems, to improve the control of disease, and to enhance health. In their written critiques, reviewers will be asked to comment on each of the following criteria in order to judge the likelihood that the proposed research will have a substantial impact on the pursuit of these goals. Each of these criteria will be addressed and considered in assigning the overall score, weighting them as appropriate for each application. Note that an application does not need to be strong in all categories to be judged likely to have major scientific impact and thus deserve a meritorious priority score. For example, an investigator may propose to carry out important work that by its nature is not innovative but is essential to move a field forward.

Significance: Does this study address an important problem? If the aims of the application are achieved, how will scientific knowledge or clinical practice be advanced? What will be the effect of these studies on the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field?  Will the proposed analyses be useful for a large part of the community of users of the dataset?

Approach: Are the conceptual or clinical framework, design, methods, and analyses adequately developed, well integrated, well reasoned, and appropriate to the aims of the project? Does the applicant acknowledge potential problem areas and consider alternative tactics?  Are the approaches integrated with other analyses for the Project?  Are the plans for sharing the methods, software, and any datasets adequate and appropriate for the Project?

Innovation: Is the project original and innovative? For example: Does the project challenge existing paradigms or clinical practice; address an innovative hypothesis or critical barrier to progress in the field? Does the project develop or employ novel concepts, approaches, methodologies, tools, or technologies for this area?  Is the level of innovation appropriate for the role of the proposed analyses in the Project?

Investigators: Are the investigators appropriately trained and well suited to carry out this work? Is the work proposed appropriate to the experience level of the principal investigator and other researchers? Does the investigative team bring complementary and integrated expertise to the project (if applicable)?  Do the investigators have experience in working cooperatively with others and sharing data and methods in a timely manner?

Environment: Does the scientific environment in which the work will be done contribute to the probability of success? Do the proposed studies benefit from unique features of the scientific environment, or subject populations, or employ useful collaborative arrangements? Is there evidence of institutional support?  

2.A. Additional Review Criteria:

In addition to the above criteria, the following items will continue to be considered in the determination of scientific merit and the rating:

Protection of Human Subjects from Research Risk: The involvement of human subjects and protections from research risk relating to their participation in the proposed research will be assessed (see the Research Plan section on Human Subjects in the PHS 398 instructions).

Inclusion of Women, Minorities and Children in Research: The adequacy of plans to include subjects from both genders, all racial and ethnic groups (and subgroups), and children as appropriate for the scientific goals of the research will be assessed. Plans for the recruitment and retention of subjects will also be evaluated (see the Research Plan section on Human Subjects in the PHS 398 instructions). 

Care and Use of Vertebrate Animals in Research: If vertebrate animals are to be used in the project, the five points described in the Vertebrate Animals section of the Research Plan will be assessed.

Biohazards: If materials or procedures are proposed that are potentially hazardous to research personnel and/or the environment, determine if the proposed protection is adequate.

2.B. Additional Review Considerations

Budget: The reasonableness of the proposed budget and the requested period of support in relation to the proposed research. The priority score should not be affected by the evaluation of the budget.

2.C. Resource Sharing Plan(s)   

When relevant, reviewers will be instructed to comment on the reasonableness of the following Resource Sharing Plans, or the rationale for not sharing the following types of resources. However, reviewers will not factor the proposed resource sharing plan(s) into the determination of scientific merit or priority score, unless noted otherwise in the FOA. Program staff within the IC will be responsible for monitoring the resource sharing.

All applications must include a plan for sharing research data.  All investigators responding to this funding opportunity should include a description of how methods, datasets, and software will be shared, or explain why data sharing is not possible.  However, rapid release of the methods, datasets, and software would benefit the scientific user community because of the scope of this community resource project.

Data Sharing Plans:  For this FOA, the reasonableness of the plans for sharing methods, datasets, and software or the rationale for not sharing them will be assessed by the reviewers.  Reviewers will factor the proposed data sharing plan into the determination of scientific merit and the priority score.  The adequacy of the sharing plans will be considered by Program staff of the funding organization when making recommendations about funding applications.  Program staff may negotiate modifications of the sharing plans with the awardee before recommending funding of an application.  The final version of the sharing plans will become a condition of the award of the grant.  The funding organization will be responsible for monitoring the data sharing policy.

3. Anticipated Announcement and Award Dates

It is anticipated that applications will be reviewed early in 2009 and that awards will be made in the summer of 2009.

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 (designated in item 12 on the Application Face Page). If a grantee is not email enabled, a hard copy of the NoA will be mailed to the 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

Samples:  The samples to be used by the 1000 Genomes Project will have been decided on by the Project.  They include many samples from both sexes, most racial groups, and several ethnic groups, as well as some children (although subject age is not scientifically relevant for this study).  Awardees will analyze publicly available data from anonymized subjects, so the research is not considered to be on human subjects. 

Intellectual property:  A primary objective of the 1000 Genomes Project is to maximize the public benefit of the data produced.  Accordingly, awardees should manage intellectual property (IP) and data in a way that achieves this goal.  For the 1000 Genomes Project, awardees are expected to contribute to the generation of a large collection of data that will serve as a foundation for the scientific community to develop future diagnostics, therapeutics, and other medical applications. To achieve the objective of producing and broadly sharing the resources generated by the 1000 Genomes Project, applicants should develop a comprehensive IP and data management strategy that is consistent with the NIH Research Tools Policy (http://ott.od.nih.gov/policy/research_tool.html).  Examples that applicants may wish to consider include the recommendations cited in NIH’s Best Practices for the Licensing of Genomic Inventions (http://www.ott.nih.gov/policy/genomic_invention.html).  Program staff may negotiate modifications of the IP management plan with the awardee before recommending funding of an application.  The final version of the IP management plan will become part of the Terms and Conditions of the award.

All NIH grant and cooperative agreement awards include the NIH Grants Policy Statement as part of the NoA. 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/archive/grants/policy/nihgps_2003/index.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/archive/grants/policy/nihgps_2003/index.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 project within the guidelines of RFA HG-09-001 and for performing the scientific activities.  The P.I. will agree to accept close coordination, cooperation, and participation of NIH staff in those aspects of scientific and technical management of the project as described under "NIH Program Staff Responsibilities".

The P.I. of a 1000 Genomes data processing research group will:

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

The NIH Program Director is a scientist of the NHGRI extramural staff who will provide normal stewardship of the award and, in addition, will have substantial scientific and programmatic involvement during the conduct of this activity through technical assistance, advice, and coordination.  However, the role of NIH staff will be to facilitate and not to direct the activities.  It is anticipated that decisions in all activities will be reached by consensus of the 1000 Genomes Steering Committee and Analysis Group and that NIH staff will be given the opportunity to offer input to this process.  The NIH Program Director will participate as a member of the Steering Committee and Analysis Group and will have one vote.  The NIH Program Director will have the following substantial involvement:

2.A.3. Collaborative Responsibilities 

The 1000 Genomes Steering Committee will continue to serve as the main governing board of the 1000 Genomes Consortium.  It includes the co-chairs of the Project as well as the co-chairs of all the working groups, a representative from each sequencing center, and some additional members, including the NHGRI Program Director.  Almost all calls of the Steering Committee are open to all Project participants.  The 1000 Genomes Analysis Group includes all the participants in the Project working on data processing and analyses, as well as the NIH Program Director.  The P.I. from each awarded cooperative agreement as well as his/her relevant staff would be added to the Analysis Group.  The Steering Committee and Analysis Group may add additional members.  Other government staff may attend the Steering Committee and Analysis Group calls and meetings if their expertise is required for specific discussions. 

To address particular issues, the Steering Committee and Analysis Group may establish groups as needed, which would include representatives from the grantees and the funding agencies, and possibly other experts.   Each awardee P.I. will have one vote on the Analysis Group.  Awardees will be required to accept and implement the common guidelines, procedures, and policies approved by the Steering Committee and the Analysis Group.

2.A.4. Arbitration 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 arbitration. An Arbitration 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 arbitration procedure in no way affects 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 report progress on a regular basis to the Analysis Group, in a way that the Analysis Group decides on.

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:

Lisa D. Brooks, Ph.D.
NHGRI
5635 Fishers Lane, Suite 4076  
Bethesda, MD 20892-9305
(301) 435-5544
lisa.brooks@nih.gov

2. Peer Review Contacts:

Rudy Pozzatti, Ph.D.
NHGRI Review Branch
5635 Fishers Lane
Suite 4076, MSC 9306
Bethesda, MD  20892-9306
(For courier service use Rockville, MD 20852)
301-496-7531
rp7s@nih.gov

3. Financial or Grants Management Contacts:

Ms. Cheryl Chick
NHGRI
5635 Fishers Lane, Suite 4076
Bethesda, MD 20892-9306
(301) 435-7858
chickc@mail.nih.gov

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. Reviewers will consider the data sharing plan but will not factor the plan into the determination of the scientific merit or the priority score.

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/archive/archive/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-02-005.html. Only research using hESC lines that are registered in the NIH Human Embryonic Stem Cell Registry will be eligible for Federal funding (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. Applications that do not provide this information will be returned without review.

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.


Weekly TOC for this Announcement
NIH Funding Opportunities and Notices


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