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 Cancer Institute (NCI), (http://www.nci.nih.gov)

Title: Cancer Genome Characterization Centers (U24)

Announcement Type
New

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

Request For Applications (RFA) Number: RFA-CA-07-014

Catalog of Federal Domestic Assistance Number(s)
93.393, 93.394, 93.395, 93.396

Key Dates
Release Date: March 10, 2006
Letters of Intent Receipt Date(s): April 12, 2006
Application Receipt Dates(s): May 12, 2006
Peer Review Date(s): July 2006
Council Review Date(s): September 2006
Earliest Anticipated Start Date: September 26, 2006
Additional Information To Be Available Date (URL Activation Date): Not Applicable.
Expiration Date: May 13, 2006

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 and Review and Anticipated Start Dates
      1.  Letter of Intent
    B.  Sending an Application to the NIH
    C.  Application Processing
  4.  Intergovernmental Review
  5.  Funding Restrictions
  6.  Other Submission Requirements

Section V.  Application Review Information
  1.  Criteria
  2.  Review and Selection Process
    A.  Additional Review Criteria
    B.  Additional Review Considerations
    C.  Sharing Research Data
    D.  Sharing Research Resources
  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. External Science Committee
      5.  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

Purpose.  This funding opportunity is part of The Cancer Genome Atlas (TCGA) Pilot Project recently announced by the NCI and NHGRI, with the overall purpose of accelerating our understanding of the genomic alterations associated with the onset and progression of human cancers.  Specifically, this funding opportunity is intended to solicit applications for Cancer Genome Characterization Centers (CGCCs), which will be an important component of the TCGA Pilot Project.  The pilot project is intended to explore the feasibility and benefits of a systematic effort to rigorously, comprehensively, and reproducibly identify, quantify, and characterize these molecular alterations for specific tumor types and sub-types.  The outcomes are expected to provide valuable insights into the understanding and control of cancer.  In addition to serving the TCGA Pilot Project, the CGCCs will provide a unique reference resource on cancer-specific genomic aberrations for the cancer research community at large.

To serve the overarching goals of the TCGA Pilot Project, this RFA is designed to establish a collaborative group of multidisciplinary Cancer Genome Characterization Centers (CGCCs) that will use various genomic and/or epigenomic analysis technologies to pioneer the systematic, high-resolution, comprehensive characterization of cancer-related genomic alterations.  Several CGCCs will be established to compare, optimize, and standardize high-throughput technologies to survey cancer biospecimens through the analysis of appropriate biomolecules (e.g., DNA and/or RNA) to be provided by the Biospecimen Core Resource of the TCGA Pilot Project.  To achieve its primary research objectives, the CGCC program sets a high priority on the optimized and cost efficient implementation of existing technologies, rigorous and standardized quality control assessments, and construction of a unique bioinformatics infrastructure to catalog, evaluate, analyze, and disseminate the data generated.  Moreover, it is the goal of the TCGA to make the resulting data publicly available as soon as their quality is verified, usually within a few weeks of generation.  In conjunction with extensive clinical annotation for all samples analyzed, data on the cancer-associated molecular alterations identified by the CGCCs will be deposited into public databases and shared with other components of the TCGA Pilot Project Research Network and with the research community at large.  The genes and other genomic regions of interest identified by the CGCCs will be analyzed via sequencing by the high-throughput Genome Sequencing Centers participating in the TCGA Pilot Project that are funded separately.

Background.  Cancer is a complex and heterogeneous disease in which mutations and other genomic and epigenomic abnormalities play a role in both its initiation and progression.  Accumulated research data implicate numerous somatic mutations and a more limited number of inherited mutations in carcinogenesis.  These cancer-specific mutations provide important clues to the understanding of many of the molecular processes underlying the development and progression of certain tumors.  Among such aberrations are the amplification of the gene encoding the human epidermal growth factor receptor 2 (HER2) found in about 20% of breast cancers, the activation of an abnormal chimeric kinase gene resulting from the BCR-ABL translocation that is characteristic of chronic myelogenous leukemia, mutations in the gene for the B-type Raf (BRAF) kinase in melanomas, and mutations in the gene for phosphatidylinositol 3-kinase catalytic subunit (PIK3CA) in colon carcinomas.  Moreover, in-depth studies of the respective aberrant genes, their products and the pathways they participate in have already resulted in the development of novel and promising anti-cancer strategies.  Examples of drugs designed to directly target protein products of cancer-specific aberrant and/or deregulated genes include: trastuzumab, an antibody against HER2; imatinib mesylate, an inhibitor of the abnormal BCR-ABL kinase; as well as gefitinib and erlotinib, which target the mutant form of the epidermal growth factor receptor (EGFR) tyrosine kinase.  Encouraging clinical results with these drugs have provided the proof-of-principle that cancer-specific somatic genomic alterations are indeed viable targets for therapy.  A more comprehensive identification of alterations involved in carcinogenesis, in particular somatic mutations, can therefore be expected to lead to additional novel therapeutic and prevention strategies, as well as to facilitate tumor diagnosis, prognosis, and monitoring.

Given cancer’s complexity, it is generally believed that only a fraction of alterations that may be useful as characteristic markers of specific tumor types and/or potential molecular targets have been identified to date.  Therefore, to be successful, a comprehensive genomic analysis of cancer must overcome a broad range of challenges stemming from the biological complexity of human tumors and the heterogeneity of the many tumor types and subtypes.  An important role in tumor heterogeneity is played by the inherent genomic instability, which increases during the progression of cancer.  The dynamic changes in tumor genomes are influenced by the cellular and biological context, genetic characteristics of individual persons, and environmental factors.  Thus, while certain similarities exist across tumor types, any effort to characterize the genomes of tumors in a comprehensive, systematic manner must address the heterogeneity across distinct cancer types and subtypes.

Many independent research groups are working to identify and catalog a variety of cancer-relevant genomic changes (e.g., alterations in expression profiles, chromosome deletions, amplifications, and/or translocations).  Cancer-relevant changes have been identified at several diverse levels of genomic organization; they include point mutations, chromosomal deletions, amplifications, translocations, and/or changes in the number of individual chromosomes, all of which can, in principle, contribute to transcriptional aberrations.  While individual uncoordinated efforts can reveal important abnormalities in cancer, such information remains fragmentary.  The unique aspect of the TCGA Pilot Project is the intent to conduct a coordinated and comprehensive, genome-wide analysis of cancer-relevant alterations by simultaneously applying several technologies to interrogate the transcriptome, genome, or epigenome in large collections of quality controlled cancer biospecimens derived from specific cancer types.  To accomplish this goal, the TCGA Pilot Project will include multidisciplinary teams of investigators and associated institutions that will collectively provide biological data, as well as inform and develop a rational approach for the selection of appropriately qualified candidate cancer genes and genomic regions of interest for sequencing.  As a consequence of the essential completion of the sequencing of a reference human genome, technologies to sequence and interrogate the genome in other ways have evolved rapidly.  Taken together, the progress in understanding some cancer-associated molecular alterations and the accompanying advances in technology suggest that it is now possible to obtain comprehensive genomic information from multiple tumor types to catalog most, if not all, of the genomic changes associated with cancer.  Ultimately, in collaboration with and in support of the NCI’s extensive program of individual projects in cancer research, such efforts are expected to accelerate the identification of markers for prevention and diagnosis and novel targets for the development of therapeutic drugs, as well as provide the basis for a refined clinical understanding of patient stratification in therapy.

The Cancer Genome Atlas (TCGA).  In 2005, the NCI initiated a collaboration with the National Human Genome Research Institute (NHGRI) to pursue a 3-year pilot project to determine the feasibility of cataloging the genomic alterations associated with a set of human cancers.  The 3-year pilot project is designed to focus on a small number of tumor types (at least two) to assess the technical feasibility and clinical relevance of conducting a relatively comprehensive analysis of the associated genomic alterations.  The pilot project will verify whether cancer-associated genes and/or genomic regions can be identified by combining diverse information from genome analyses (as defined in the previous paragraph), with tumor biology and clinical data, and whether the sequencing of selected regions can be efficiently and cost-effectively achieved.  Successful completion of the pilot project is a prerequisite for an expanded phase that would rapidly and efficiently generate analogous genomic data for all major cancer types.  Collectively, genomic and clinical data generated by all the components of the pilot project will provide the initial contributions to a comprehensive Web-based resource describing the genomic “fingerprints” of specific cancer types.  This resource will be known as The Cancer Genome Atlas.

The TCGA Pilot Project Research Network comprises the following major organizational and functional components:

Organization of CGCCs within the TCGA Pilot Project StructureWhile each CGCC team will work independently, their activities will be integrated into a cohesive TCGA Pilot Project Research Network.  A Steering Committee will be established as a governing body for the entire TCGA Pilot Project Research Network (TCGA Pilot Project Research Network Steering Committee), with a mandate to govern also the CGCCs and oversee the integration of the individual components into a cohesive research network (for details, see Section VI.2.A Cooperative Agreement Terms and Conditions of Award).  Importantly, guidelines and recommendations will be developed by the Steering Committee that will pertain to all participants of the Research Network, including the CGCCs.  An agreement to abide by such Network policies will be required to obtain funding under this RFA.

Overview of the Required Expertise and Unique Resources.  Interdisciplinary cooperation among cancer molecular biologists, clinical researchers, genomic technology specialists, bioinformaticians, and biostatisticians will be essential for the success of both the CGCC Program and the TCGA Pilot Project as a whole.  Therefore, each applicant group responding to this RFA must have documented current expertise in all these areas.  Each group should have in place the appropriate laboratory infrastructure to support technologically-advanced genome analysis instrumentation, computational data analysis, and genomics-specific bioinformatics and be capable of high throughput analyses of biomolecules from clinically diagnosed cancer patients.  Details regarding the required multidisciplinary expertise and capabilities of the applicant team are provided in Section IV.6. Other Submission Requirements.

Collective Goals of the CGCCs.  To achieve a comprehensive genomic characterization of the cancer types chosen for analysis, this RFA is intended to fund up to four CGCCs that will be dedicated to high-throughput genomic and/or epigenomic technologies.  The funded centers as a group will include diverse platforms capable of genome-wide, comprehensive high-resolution screening for genomic, and/or epigenomic, and/or transcriptome alterations.  Here, the term “technology” is used to describe an analytical methodology or approach (e.g., expression microarray analysis, comparative genome hybridization microarray analysis, serial analysis of gene expression, etc.).  The term “technology platform” refers to the specific application of a given technology using defined experimental parameters, protocols, and reagents, including data analysis and processing, such as those unique to a particular supplier or vendor.  Ideally, the collective group of CGCCs will use at least two platforms for each genomic alteration feature, allowing for evaluation of the experimental protocols, methodologies, and data processing standards in the analysis of clinical biospecimens.  To ensure the generation of complementary data and corroboration of findings while avoiding excessive duplication of efforts, this RFA will support no more than two CGCCs to conduct comprehensive expression profiling, each using complementary (non-identical) technology platforms, and no more than two CGCCs to perform high-throughput, genome-wide chromosomal aberration detection, again using complementary (non-identical) technology platforms.  Any high-throughput technology platforms interrogating complete genome-scale cancer-associated genomic or epigenomic features are eligible, provided that they conform to the additional guidelines specified below.

Research Objectives.  Each participating CGCC will be required to rigorously, comprehensively, and reproducibly detect and analyze genomic and/or epigenomic alterations in the biomolecules from cancer samples and appropriate matched controls provided by the Biospecimen Core Resource.  As a tangible measure of the desired productivity of the CGCC initiative, it is expected that each CGCC will have achieved the operational capacity to conduct analyses at a minimum rate of 1000 samples per year by the end of the first 6 months.  It is anticipated that throughout the project each group will implement protocols that further enhance sample throughput capabilities  Thus, by the end of the 3-year award period, the collective CGCC initiative should produce a comprehensive genomic and/or epigenomic characterization of at least 3000 total biospecimens (the total includes both biomolecules from cancer and control biospecimens).  To cross-validate technology platforms across the CGCC network, each team will analyze biomolecules (e.g., RNA or DNA, depending on the analysis) derived from the same set of clinical specimens.

It is expected that this integrated effort will significantly improve the overall performance of tools and technologies for genome-wide analyses by identifying sources of experimental error and bias and by improving experimental reproducibility and specificity.  In addition, improvements are sought in sensitivity and resolution in the detection of cancer-associated genomic and/or epigenomic and/or transcriptome alterations, with specific emphasis on enhancing throughput and decreasing the unit cost per sample for the chosen technology platform(s).  Another planned outcome of this initiative is the creation of a public resource containing rigorously validated data for clinical biospecimens whose content will be continuously updated as the information is generated.  CGCCs are required to submit a Data Sharing Plan documenting how and when data will be released and shared.  The Data Sharing Plan should be consistent with the goals of the TCGA described in this RFA and with NIH data sharing guidelines.

Each CGCC will address the following specific objectives:

Objective 1: Use high-throughput, cost-effective technologies to map and characterize comprehensively genomic and/or epigenomic and/or transcriptome alterations of any type known to be generally relevant to human cancer, and make the data publicly available.  Characterization and analysis may include, but are not limited to: the detection of changes in DNA segment copy numbers; aberrant gene expression profiles; translocations; breakpoints; and/or methylation patterns.

Objective 2: Improve performance of large-scale genomic characterization technology platform(s) proposed for use in Objective 1 including, but not limited to: optimization of detection sensitivity and/or resolution; throughput; genome coverage; and/or unit cost per analysis.

Objective 3: Design and/or adapt cohesive analysis and data mining tools that will allow for integration and cross-validation of the comprehensive genomic data obtained across the CGCC network, and will facilitate a consistent identification of genomic regions of interest for sequencing by the high-throughput sequencing component of the TCGA.

Note:  The procurement of cancer-related clinical samples and high-throughput sequencing projects are ineligible for this RFA as those initiatives are covered by other components of the TCGA Pilot Project. 

Each application responsive to this RFA must address all three specific objectives.  For each of these Objectives, applicants must adhere to the guidelines under Scope and Requirements Pertinent to Specific Objectives that are summarized below.

  1. Use high-throughput, cost-effective technologies to map and characterize comprehensively genomic and/or epigenomic and/or transcriptome alterations of any type known to be generally relevant to human cancer, and make the data publicly available.  Characterization and analysis may include, but are not limited to: the detection of changes in DNA segment copy numbers; aberrant gene expression profiles; translocations; breakpoints; and/or methylation patterns.  The goal of Objective 1 is to utilize currently available, robust high-throughput technology platforms to analyze biomolecules obtained from cancer biospecimens and matched normal tissue (where appropriate) that will be provided by the Biospecimen Core Resource.  All CGCCs will analyze a common set of biological samples from the same source of highly-annotated, quality-controlled human cancer biospecimens.  Use of the same materials will allow the CGCCs to evaluate protocols and procedures, determine technology and platform variability, and perform intra- and inter-laboratory comparative studies.

    1a) Clinical biospecimens for analysis.  The Human Cancer Biospecimen Core Resource will provide the respective biomolecules needed for analysis to each CGCC from a given set (or sets) of cancer biospecimens.  Additional samples may include appropriate matched control biospecimens (e.g., buccal cells, lymphocytes, or other tissues).  Analyses will be conducted using biomolecules obtained from a minimum of 500 biospecimens each for no less than two types of human cancer (i.e. no less than 1000 samples), and an equal number of matched control tissues (as appropriate).  As the project matures, samples from different cancers will likely be profiled, although the analytic details will be evaluated and improved based on the results of analyses conducted in years 1-2.  Applicants should describe their vision of the design of analytical studies; however, they must also acknowledge in their applications that it will be the ultimate responsibility of the TCGA Pilot Project Research Network Steering Committee to identify sample sets to be analyzed and provide overall guidelines for improvements in study design and data analysis.  By the end of the three year program, it is anticipated that each CGCC team will have analyzed a minimum of 3000 total biospecimens.  In addition, the Biospecimen Core Resource will provide reference samples for technology improvement experiments.

    (1b) Eligible technologies for genome-wide screening.  Applicants responding to this RFA must propose to perform analysis using a minimum of one, and a maximum of two, technology platform(s) of their choice (as defined in Specific Research Objectives of the CGCC).  To be eligible, a platform must have a high throughput and interrogate as completely as possible either the transcriptome or the genome in the complete set of samples provided.  The genomic and/or epigenomic features to be assayed must represent types of aberrations that are, in general, known be relevant to human cancers.  Also, respective technology platforms should be pre-validated for the analysis of biomolecules obtained from clinical biospecimens.  For the purposes of this RFA, a technology platform is considered pre-validated if it satisfies at least one of the following: (1) the chosen platform has been established as a standard for the detection of a specific genomic feature as evidenced by a significant scientific literature (i.e., more than 20 peer-reviewed publications), (2) the results of genomic feature detection using the chosen platform have been corroborated (at a statistically significant rate) by at least one alternative technology as evidenced by previously published comparative analyses; (3) for the chosen technology platform, a validated method has been previously established (and can be readily implemented) for accepting or rejecting a data set based on concomitant analyses of appropriate, known positive and/or negative control samples.  Alternatively, if such evidence is not available for the chosen technology platform, applicants should describe in detail the pre-validation data generated by their group or other researchers.  Gene expression profiling and comparative genomic hybridization analysis using microarrays are examples of two technologies that currently meet these requirements.  However, applicants are encouraged to propose any high-throughput comprehensive technology platform to survey cancer biospecimens for cancer-relevant genomic or epigenomic features (e.g., transcriptome, translocations, loss of heterozygosity, copy number alternation, DNA methylation, etc.), provided that the platform conforms to the guidelines listed in this RFA.

    The TCGA Pilot Project aims to conduct a genome-wide determination of cancer-associated alterations; though the specific requirements for complete coverage could change during the course of the Pilot Pilot.  For example, the estimated number of genes within the human genome is decreasing based on data currently being generated; therefore, the term genome coverage can only be defined within the framework of the knowledge available at the time of submission.  Applicants should specify the advantages of the technology platform(s) proposed with respect to the genome coverage, the achievable resolution and other measures of performance, as appropriate.  For example, in describing the detection of copy number alterations, applicants should state at what base pair resolution the regions of deletion or amplification would be mapped.  Will alternative splice variants be detected when the transcriptome is analyzed; if yes for how many genes?  Applicants must have expertise in the chosen genome analysis technology(ies).

    (1c) Sample throughput.  For applications to be considered responsive to this RFA, the proposed technology platforms and analysis protocols must support sample throughput rates which meet the strategic goals of the TCGA Pilot Project.  The NCI recognizes that significant effort may be required at the start of the project to establish the necessary infrastructure to meet the demands of the large-scale analyses solicited in this RFA.  However, by the end of the first 6 months, each CGCC team will be expected to have achieved the operational capacity to conduct analyses at a minimum rate of 1000 samples per year.  Within the first 2 years, it is anticipated that each group will have implemented methods and protocols that further enhance sample throughput capabilities (see Objective 2 and its subheadings); thus, throughput rates are expected to exceed 1000 samples per year in years 2 and 3 of the TCGA Pilot Project.  It is important to note that certain technology platforms, which are designed to detect specific genomic features, may already be poised to exceed the throughput requirements listed here.  Applicants proposing to utilize such platforms will be expected to exceed the minimum requirements listed here to achieve throughput rates that are consistent with the capabilities of comparable technology platforms.

    (1d) Cost of genomic analysis.  An important factor in the successful conduct of a high-throughput research project is cost analysis.  Internal, monitoring of costs is an important aspect of project management at each center.  Moreover, to facilitate strategic planning for the entire TCGA, NCI intends to collect cost and throughput data from the funded centers at regular intervals (at least once a year and perhaps more frequently).  To the extent possible, applicants should propose one or more parameters (e.g. cost per sample at a defined genome coverage) by which the cost of the proposed data generation can be measured.  Using this metric, the research plan should include cost analysis for the proposed studies and the applicants’ plans for cost monitoring during the execution of the project.  Applicants should discuss the basis for determining the costs of applying the proposed technology(ies) at the scale that must be achieved to meet the proposed quantitative throughput goals.  The analysis should be developed for 3 time periods: first, the initial cost of using the proposed technology platform(s); second, the expected cost by the end of the first year of operation of the CGCC;, and third, any further reductions in the cost of applying the platform(s) over the course of the three-year award (see Objective 2 below). 

    (1e) Data processing, deposition, and reporting standards.  Applications must contain a thoroughly developed plan to address data processing, standards for deposition and reporting, as well as statistical and bioinformatics aspects of the proposed experimental design.  These plans should also discuss the procedures and time frames for results validation and for the immediate deposition of data after validation of data quality.  Examples of other areas that may require particular attention include sources of experimental variability, measures of confidence limits, quality control and quality assurance procedures and measures.  Other technical considerations may be specific to the chosen technology platform(s) and may include reporting on parameters such as genome coverage, resolution metrics of the results (e.g., are the sizes of the amplicons known within a few nucleotides or only in the range of 100s of kb) and sensitivity.  A description of the proposed reporting format should be included in the application, with the understanding that an integrated data reporting standard will ultimately be implemented across the CGCC network.  A reporting system should allow for performance evaluation and optimization and should facilitate data mining as part of an integrated bioinformatics infrastructure (see Objective 3 and its subheadings).  Proposed reporting solutions must be compliant with the cancer Biomedical Informatics Grid (caBIG, see more details below under “General Requirements”) as a unified platform for sharing and disseminating information.  In addition, data will be deposited into other public databases as appropriate.

  2. Improve performance of large-scale genomic characterization technology platform(s) proposed for use in Objective 1 including, but not limited to: optimization of detection sensitivity and/or resolution; throughput; genome coverage; and/or unit cost per analysis.  The capabilities described for meeting the goals of Objective 1 will provide a baseline quality standard for the large-scale analysis of clinical biospecimens upon which the CGCCs will be expected to improve.  The aim is to obtain improved throughput, data content and quality as well as cost efficiency (using the cost analysis strategy described above).  Applicants should describe in detail their plans for enhancements of the performance of the genomic analysis technologies and data processing methods proposed.  This discussion should include the approaches for identifying the experimental factors that contribute to measurement variability among platforms and laboratories.  While the development of new genomic analysis technologies is beyond the scope of this RFA, the overall plan should include a strategy for adopting improvements and technologies that could emerge during the course of the 3-year pilot program that would offer advantages over the currently available technologies used in the CGCCs.  Collectively, the CGCC network will compare analytical data across technologies and platforms and use the results to deliver optimized procedures and approaches for a comprehensive genomic analysis of cancer.

  3. Design and/or adapt cohesive analysis and data mining tools that will allow for integration and cross-validation of the comprehensive genomic data obtained across the CGCC network, and will facilitate a consistent identification of genomic regions of interest for sequencing by the high-throughput sequencing component of the TCGA.  Standardized formats for data reporting and analysis will be implemented for all genomic analyses conducted across the CGCC network from the start of the project.  This standardized system of data reporting will be required in order to interface with the existing bioinformatics infrastructure at the NCI and the National Library of Medicine, as well as to provide a common basis for data evaluation and data mining across the CGCC and the TCGA networks.

    (3a) Cross-comparison of technology platforms across the CGCC network.  In addressing data reporting standards, applicants’ plans should include strategies to maximize the benefits of interaction with other CGCCs analyzing the same set of samples using alternative technology platforms.  Specifically, significant progress in the protocols for cross-evaluation of datasets between the CGCCs is expected within the first year of the 3-year program.  Although it is not possible to predict the specific technology platforms that will be used by the other CGCCs, applicants should discuss how the data obtained with their chosen technology platform(s) would complement, and/or reinforce, the data obtained using alternative technology platform(s), which assay the same genomic and/or epigenomic and/or transcriptome features (for at least one of the other commonly used technology platforms if they exist).  In addition, applicants are encouraged to present their vision regarding how the results obtained from technology assessment studies would inform and shape the network-wide standard operating procedures in data reporting and data mining for all CGCCs.

    (3b) Algorithms and data mining tools.  Applicants should present detailed plans for the use of existing, and the development of modified, data mining bioinformatics tools which analyze the generated data to select specific genomic regions and/or genes for sequencing (to be carried out by other components of the TCGA Pilot Project Research Network).  Applicants should propose algorithms and bioinformatics tools that are suitable for large sets of genomic data and utilize well characterized annotation and ontology schemes.  The methods should include the generation of statistical values that will allow the determination of experimental support for each choice.  Algorithms and other tools to correlate the detected aberrations with clinical parameters, such as treatment outcome, should also be included.  In addition, applicants should propose a strategy to implement data mining tools which incorporate all data generated by the CGCCs no later than 9 months following the start date of the program.  All proposed solutions must be compliant with the caBIG (see more details below under “General Requirements”) as a unified platform for data sharing and dissemination.  The proposed approaches and bioinformatics tools will be shared among the CGCCs and the entire TCGA Pilot Project Research Network.  Upon validation, these tools will be made publicly available as an additional resource to the scientific community under an open source license consistent with caBIG principals.

General Requirements and Obligations Pertinent to All Objectives:

To maximize the overall performance of the CGCCs and harmonize their activities with the TCGA Pilot Project goals, each Center will be required to operate within a framework of general guidelines and requirements (listed below).  It is expected that these requirements will be collaboratively refined during the course of the Pilot Project through an ongoing assessment of generated data, experimental methodologies, data analysis procedures, and administrative protocols.  This will be coordinated by the TCGA Pilot Project Research Network Steering Committee (for details, see Section VI.2.A.3, Collaborative Responsibilities).  The Steering Committee will provide guidance in this process and provide recommendations to the individual CGCCs regarding operational improvements.  In addition, the Committee will foster communication among the participating centers in the form of regular meetings (see VI.2.A.3), Web-based information sharing, and other appropriate methods of disseminating information to assist in achieving program objectives (for details see Section VI. 2.A. Cooperative Agreement Terms and Conditions of Award).

Data release and sharing of standardized protocols.  NCI has designated its large-scale genomic characterization program to be a “community resource project” as discussed in the report “Sharing Data from Large-Scale Biological Research Projects – 2003: A System of Tripartite Responsibility” available at http://www.wellcome.ac.uk/doc_wtd003208.html.  In making this designation, NCI strongly endorses the rapid release of generated data resources since the utility of the data is largely dependent on how quickly they can be deposited into public databases and accessed by the scientific community.  As part of a comprehensive data sharing and intellectual property management strategy, CGCCs will be required to share data and protocols with other CGCCs.  In addition, the NCI stipulates that data and other resources developed through the TCGA Pilot Project be made publicly available.  The optimized platform implementations, including standard protocols, algorithms and tools for data analysis, will be shared among the TCGA components and ultimately made publicly available to the scientific community at large.  Unreasonable delays or waiting until publication to release data would be viewed as hindering the progress of TCGA.  Algorithms, data mining tools, etc., will be made available to the research community under an open source license consistent with caBIG principals.  Therefore, the applicant must include a data release and sharing plan in the application, as well as a statement that s/he will abide by the TCGA Data Release Policy that will be developed by the TCGA Pilot Project Research Network Steering Committee and be consistent with NIH data sharing guidelines.  The approved plan will be become a component of the Terms and Conditions of the award.

Patient confidentiality.
 As some of the information that will be produced as part of the TCGA Pilot Project could raise issues about patient confidentiality, it may be appropriate for the information generated within the CGCCs to be released with certain safeguards that protect confidentiality; the applicant’s proposed data release policy should address that issue, including the possibility that each type of data may require separate consideration.  The TCGA Pilot Project Research Network Steering Committee’s data release guidelines will need to address the protection of patient confidentiality.

caBIG compatibility.
The applicants must plan for analytical algorithms and bioinformatics software tools, ontologies, and data formats to be integrated into caBIG (https://cabig.nci.nih.gov).  caBIG is an open source/open access information network for the sharing of cancer research data and related software tools.  caBIG has developed four levels of compliance and interoperability (i.e., Legacy, Bronze, Silver, and Gold) that address such aspects as: data format and programming/ messaging interfaces, common data elements, information models, vocabularies, and ontologies.  The required degree of caBIG compliance for CGCC applicants is Silver.  More information on caBIG compatibility is available at https://cabig.nci.nih.gov/guidelines_documentation/caBIGCompatGuideRev2_final.pdf.

Intellectual property.
  A primary objective of The Cancer Genome Atlas Project (TCGA) is for TCGA awardees to manage intellectual property (IP) and data in a way that will maximize the public benefit of the data produced.  High throughput identification and characterization of genomic and epigenomic aberrations is expected to generate a large collection of data that will serve as a foundation for the research community to develop future cancer therapeutics and diagnostics.  To achieve the objective of producing and broadly sharing TCGA data, applicants should develop a comprehensive IP and data management strategy that is consistent with the recommendations cited in NIH’s Best Practices for the Licensing of Genomic Inventions (http://www.ott.nih.gov/policy/genomic_invention.html) and the NIH Research Tools Policy (http://ott.od.nih.gov/policy/research_tool.html).  
It is intended that the tools of scientific discovery necessary to rapidly and effectively develop new therapeutics and diagnostics be widely available for research use.  Accordingly, awardees will be expected to manage IP in a way that is consistent with the goals of the initiative and in accordance with NIH guidelines and best practices.  Applicants should submit an IP Management Plan that assures that data is rapidly released according to approved criteria (see above), that licensing and sharing practices ensure the availability of data and research resources for future use by the scientific community, and that research collaboration or sponsorship agreements are consistent with the requirements of TCGA.  IP Management Plans, once approved, will also become one of Terms and Conditions of award.
Restrictive licensing and sharing practices for TCGA technologies and data could substantially diminish the value and public benefit provided by this community resource project.  Management practices that would prevent or block access to, or use of TCGA data and resources for research use will be considered to be hindering the goals of TCGA.  Applicants are encouraged to clearly demonstrate in their IP Management plan how their strategies achieve the desired public benefit through effective sharing of TCGA data and tools.

For general policies related to this announcement, see Section VIII, Other Information - Required Federal Citations.

Section II.  Award Information


1.  Mechanism(s) of Support

This funding opportunity will use the NIH U24 award mechanism.  The NIH U24 is a cooperative agreement award mechanism.  In the cooperative agreement mechanism, the Principal Investigator (PI) retains the primary responsibility and dominant role for planning, directing, and executing the proposed project, with NCI staff being substantially involved as a partner with the PI, as described under the Section VI.  2.  Administrative Requirements, "Cooperative Agreement Terms and Conditions of Award."

This RFA is a one-time solicitation.

This funding opportunity uses just-in-time budget concepts.  It also uses the non-modular budget format described in the PHS 398 application instructions (see http://grants.nih.gov/grants/funding/phs398/phs398.html).  A detailed categorical budget for the "Initial Budget Period" and the "Entire Proposed Period of Support" is to be submitted with the application.
 
2.  Funds Available

The NCI intends to commit approximately $35 M in FY 2006-2009 (approximately $11.7 M in FY 2006) to fund up to four 3-year awards.  Because the nature and scope of the proposed research will vary from application to application, it is anticipated that the size of each award will vary.  Although the budget plans of the NCI anticipate support for this the CGCC program, awards pursuant to the CGCC RFA are contingent upon availability of funds and receipt of a sufficient number of meritorious applications.

Section III.  Eligibility Information


1.  Eligible Applicants

1.A.  Eligible Institutions

You may submit (an) application(s) if your organization has any of the following characteristics:

Foreign institutions and organizations are not eligible to apply, but may participate as collaborators or subcontractors within a CGCC.

1.B.  Eligible Individuals

Any individual with the skills, knowledge, and resources necessary to carry out the proposed research is invited to work with his/her institution to develop an application for support.  Individuals from under-represented racial and ethnic groups as well as individuals with disabilities are always encouraged to apply for NIH programs.

2.  Cost Sharing or Matching

Cost sharing is not required for eligibility.

The most current Grants Policy Statement can be found at http://grants.nih.gov/grants/policy/nihgps_2003/nihgps_Part2.htm#matching_or_cost_sharing.

3.  Other-Special Eligibility Criteria

An institution may submit only one application in response to this funding opportunity announcement.

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 Grants Info, 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 DUNS number can be obtained by calling (866) 705-5711 or through the web site at http://www.dnb.com/us/.  The DUNS 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 on line 2 of the face page of the application form and the YES box must be checked.

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(s): April 12, 2006
Application Receipt Dates(s): May 12, 2006
Peer Review Date(s): July 2006
Council Review Date(s): September 2006
Earliest Anticipated Start Date: September 26, 2006

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 NIH staff to estimate the potential review workload and plan the review.

The letter of intent is to be sent by the date listed at the beginning of this document.

The letter of intent should be sent to:

Daniela S Gerhard, Ph.D.
Director
Office of Cancer Genomics
Office of the Director
National Cancer Institute
Building 31, Room 10A07, MSC 2580
31 Center Drive
Bethesda, MD 20892-2580
Telephone:  (301) 451-8027
FAX:  (301) 480-4368
Email: gerhardd@mail.nih.gov

3.B.  Sending an Application to the NIH

Applications must be prepared using the most current PHS 398 research grant application instructions and forms.  For this RFA, originals of figures that appear in the body of the application plus up to seven additional documents, that in aggregate are no more than 100 pages, are acceptable as appendices.  Appendix material should not be sent with the application, but applicants should await specific instructions in a later contact from the Scientific Review Administrator.  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 (for U.S. Postal Service express or regular mail)
Bethesda, MD 20817 (for express/courier delivery; 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 the pdf version of the appendix materials and any colored figures must be sent to:

Referral Officer
National Cancer Institute
Division of Extramural Activities
6116 Executive Boulevard, Room 8041, MSC 8329
Bethesda, MD 20892-8329 (for U.S. Postal Service express or regular mail)
Rockville, MD 20852 (for express/courier delivery)
Telephone: (301) 496-3428

FAX: (301) 402-0275
Email:
ncirefof@dea.nci.nih.gov

Using the RFA Label: The RFA label available in the PHS 398 application instructions must be affixed to the bottom of the face page of the application.  Type the RFA number on the label.  Failure to use this label could result in delayed processing of the application such that it may not reach the review committee in time for review.  In addition, the RFA title and number must be typed on line 2 of the face page of the application form and the YES box must be marked.  The RFA label is also available at http://grants.nih.gov/grants/funding/phs398/labels.pdf.

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, it will be returned to the applicant without review.  Upon receipt, applications will be evaluated for completeness by the CSR and for responsiveness by the NCI.  Incomplete and non-responsive applications will not be reviewed.  If the application is not responsive to the RFA, NIH staff may contact the applicant to determine whether to return the application to the applicant or submit it for review in competition with unsolicited applications at the next appropriate NIH review cycle.

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 this funding opportunity, it is to be prepared as a NEW application.  That is, the application for this 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.

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

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 http://grants.nih.gov/grants/policy/policy.htm.

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 or competing continuation award if such costs: are necessary to conduct the project, and 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 or competing continuation 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 the NIH Grants Policy Statement at http://grants.nih.gov/grants/policy/nihgps_2003/NIHGPS_Part6.htm.

6.  Other Submission Requirements

Applications must be prepared as outlined below.  After submission of the application, the Scientific Review Administrator (SRA) will provide instructions for sending acceptable appendix material (see Section IV.3.B, Sending an Application to the NIH).  No additional supplementary material of any kind will be allowed, unless directed as a specific request from the SRA.

Submission Requirements

Budget and Budget Justification sections of the PHS 398 must reflect the following:

Research Plan. For this RFA, the organization of the “Research Plan” (sections A-D) in the PHS 398 grant application format is modified as follows:

The page limit has been increased from 25 to 50 pages.

Sections A-D of Research Plan in the standard PHS 398 format are substituted by the following new sections:  Section 1. Applicant Group; Section 2. Scope of Research; Section 3. Analytic Capacity of the Instrumental Resources; Section 4. Plan for Sharing Research Data, Resources, and Intellectual Property; and Section 5. Collaboration with Other Organizations. These sections must cover the following elements:

Section 1: Applicant Group.  Applicants should describe in detail the roles of the key personnel and their expertise as it relates to the scientific and technical scope of the RFA and specific objectives of their applications, including any pertinent ongoing, grant-supported research.  Applicants should emphasize, where applicable, the expertise and track record of their group in collaborative programs and activities.  In addition, this section should describe the unique resources, supportive infrastructure and instrumentation available to the project.  The PI of a large-scale project funded under this RFA is expected to devote at least 20% effort to the project.  Management and governance plans for the group and the PI’s relevant experience in this regard should be discussed.  The following expertise components and organizational elements must be addressed:

Section 2: Scope of Research. The applicants must describe in detail experimental and developmental activities addressing the three Specific Research Objectives as outlined in Section I.1 of this RFA. Reviewers will evaluate how well the applicants have fulfilled all the general and objective-specific requirements and obligations.  In addition, applicants must acknowledge that the samples to be analyzed will be provided by the Biospecimen Core Resource as stated under Specific Research Objectives outlined in Section I.1 of this RFA.  Applicants may not propose to conduct analyses using more than two technology platforms.  If two platforms are included in a meritorious proposal, a programmatic decision may be made to fund only one technology platform in order to achieve the TCGA goals. 

Section 2 of the application may contain preliminary data relevant to the proposed methods and/or specific technologies.  The applicants should demonstrate an understanding and capability to meet throughput requirements.  Furthermore, there should be evidence for the quality of the data that may be anticipated from the proposed technology platforms when utilized by the applicant.  Where appropriate, timeliness of the proposed activities and milestones should be discussed.

Section 3. Analytic Capacity of the Instrumental Resources.  This section of the application must provide evidence of the analytic capacity that is needed to meet the objectives of the TCGA Pilot Project.  Applicants should demonstrate the capability to meet throughput requirements, including detailed plans to improve upon the minimal throughput requirements presented in Section I.1.  Applicants should define milestones, specific to the technology platform(s) chosen for sample analysis, which describe the acceleration of sample throughput rates throughout the course of the project.  Here, applicants should present an explicit, estimated timeline for achieving the operational capacity to conduct analyses at a minimum rate of 1000 samples per year (during the course of the first 6 months of the project).  Information should be provided on the availability of skilled personnel needed to conduct the experimental analyses, as well as data processing and bioinformatics analysis, for the proposed number of samples.  If personnel, equipment and other resources related to operation of a technology platform have a shared commitment to other projects (e.g. core resources, other awards, etc.), the applicant must address how sufficient access will be guaranteed for the purposes of the CGCC.  If the applicants have appropriate experience, instrumentation, and infrastructure, but need additional equipment to reach the required minimal throughput for a specific technology, a request for such additional capital equipment will be considered on a case by case basis as indicated above.  Except for such requested additional equipment, all other capital equipment instruments must be operational and available no later than three months following the anticipated start of the project. 

Section 4: Plan for Sharing Research Data, Resources and Intellectual Property.  Applicants must expressly acknowledge and agree that all data, datasets, algorithms, and protocols generated through the CGCCs will rapidly become available through the TCGA for public use in accordance with the data release and sharing plan that will be adopted by the TCGA Pilot Project Research Network.  Sharing/dissemination of intellectual property should also be described in this section.  Please see the guidelines for sharing plans below.

Section 5: Collaboration with Other Organizations.  Applicants should briefly describe existing as well as planned partnerships with other organizations or state “Not Applicable” if there are no such collaborations.  In addition to academic and non-profit domestic organizations, such collaborations may involve sub-contracts with foreign institutions.  The role of such partners should be clearly delineated, reiterating the adherence to the policies of data sharing and immediate data release.  Letters of collaboration from all collaborators and consultants should succinctly indicate institutional commitment to the program and their respective roles.  These letters should be included at the end of Section 5 in the application and be paginated with appropriate sequential numbering.  These letters do not count towards the stated 50-page limit.

Plan for Sharing Research Data

All applicants must include a plan for sharing research data in their application.  The NIH data sharing policy is available at http://grants.nih.gov/grants/policy/data_sharing.  All investigators responding to this funding opportunity must include a description of how final research data will be shared, or explain why data sharing is not possible.

The reasonableness of the data sharing plan or the rationale for not sharing research data will be assessed by the reviewers.  The data sharing plan will not be a factor in the determination of scientific merit.  However, since data sharing is essential for this project, an acceptable data sharing plan must be in place before an award can be made.

All data acquired by the awarded CGCCs must be made publicly available through the NCI.  The precise content of the data sharing plan will vary, depending on the data being collected.  Applicants should include a description of the criteria for data evaluation, submission, and storage.  Applicants should describe briefly the expected schedule for data sharing, the format of the datasets, the documentation to be provided, and any analytic tools provided.  The NCI requires that throughout each CGCC’s funding period, all data, datasets, and algorithms be immediately released to the caBIG and other public databases (as appropriate) as they are generated and validated.  Algorithms and software tools will be released as open source consistent with caBIG principals.  In addition, each applicant must outline plans to store and maintain the anticipated large amounts of genomic data in-house on a temporary basis and propose appropriate arrangements with the caBIG for storage and maintenance.  A plan to release the data upon completion of the funding period is not acceptable.  Data submission release plans should aim for immediate automatic submissions once the data are verified.  If this is not possible, applicants must provide an adequate rationale as to why this data release activity cannot be achieved.

Sharing Research Resources

NIH policy requires that grant awardee recipients make unique research resources readily available for research purposes to qualified individuals within the scientific community after publication (see the NIH Grants Policy Statement at http://grants.nih.gov/grants/policy/nihgps_2003/index.htm and at http://grants.nih.gov/grants/policy/nihgps_2003/NIHGPS_Part7.htm#_Toc54600131).  Investigators responding to this funding opportunity must include a plan for sharing research resources addressing how unique research resources will be shared or explain why sharing is not possible.  This includes the development of all algorithms developed through or acquired by the awarded CGCCs; such algorithms must be open-source programming code, where applicable, to be effectively shared through caBIG.

The adequacy of the resources sharing plan and any related data sharing plans will be considered by Program staff of the funding organization when making recommendations about funding applications.  The effectiveness of the resource sharing will be evaluated as part of the administrative review of each non-competing Grant Progress Report (PHS 2590, http://grants.nih.gov/grants/funding/2590/2590.htm).  See Section VI.3.  Reporting.

Guidelines for Preparation of Research Tools Sharing Plan and Intellectual Property Plan.  The NIH wishes to ensure that the data and research resources developed as a result of awards made through this RFA become readily available to the broader research community in a timely manner for further research, development, and application, with the expectation that this arrangement will lead to products and knowledge of benefit to the public health.

The policy of the NIH is to make available to the public the results and accomplishments of the activities that it funds.  This RFA explicitly stipulates that applicants are required to submit a plan: (1) for sharing the research resources/tools generated; and (2) addressing how they will exercise intellectual property rights, should any be generated, while making such research resources available to the broader scientific community consistent with this initiative.  Research tools sharing plans and intellectual property management plans are needed to ensure that unique research resources will be readily available for research purposes to qualified individuals within the scientific community in accordance with the NIH Grants Policy Statement (http://grants.nih.gov/grants/policy/ and the Principles and Guidelines for Recipients of NIH Research Grants and Contracts on Obtaining and Disseminating Biomedical Research Resources: Final Notice, December 1999 http://ott.od.nih.gov/NewPages/64FR72090.pdf) (“NIH Research Tools Guidelines Policy”) and the Best Practices for the Licensing of Genomic Inventions (http://ott.od.nih.gov/policy/lic_gen.html).  These documents also: (1) define terms, parties, and responsibilities; (2) prescribe the order of disposition of rights and a chronology of reporting requirements; and (3) delineate the basis for and extent of government actions to retain rights.  Patent rights clauses may be found at 37 CFR Part 401.14 and are accessible from the Interagency Edison web page (http://www.iedison.gov); see also, 35 USC § 210(c); Executive Order 12591, 52 FR 13414 (Apr. 10, 1987); and Memorandum on Government Patent Policy (Feb. 18, 1983).  If applicants plan to collaborate with third parties, the research tools sharing plan would need to address how such collaborations would not restrict their ability to share research materials produced with NIH funding.  The applicant's institution should avoid exclusively licensing those inventions that are research tools, unless either: (1) the field of use of the exclusive license is restricted to commercial use; or (2) the exclusive licensee will make the research tool broadly available on reasonable terms.  In the development of any research resource sharing and intellectual property management plans, applicants should confer with their institutions' office(s) responsible for handling technology transfer related matters and/or sponsored research.  If applicants or their representatives require additional guidance in preparing such plans, they are encouraged to make further inquiries to the appropriate contacts listed above for such matters.  Further, applicants may wish to independently research and review examples of approaches considered by other institutions such as those described on the NCI Technology Transfer Branch web site (http://ttc.nci.nih.gov/intellectualproperty/).  The foregoing guidance is provided by way of example to assist applicants in preparing the expected research resources sharing and intellectual property management plans.  While these approaches will likely suit most situations, these approaches are not exclusive and applicants should feel free to submit alternative versions for consideration.

Transfers of materials between the Biospecimen Core Resource (BCR) and the CGCCs and transfers to not-for-profit entities should be implemented under terms no more restrictive than the Uniform Biological Materials Transfer Agreement (UBMTA) (http://ott.od.nih.gov/NewPages/UBMTA.pdf).  In particular, CGCCs are expected to use the Simple Letter Agreement (SLA) provided at http://ott.od.nih.gov/NewPages/SimplLtrAgr.pdf, or another document with no more restrictive terms, to readily transfer unpatented tools developed with NIH funds to other recipients for use in NIH-funded projects.  If the materials are patented or licensed to an exclusive provider, other arrangements may be used, but commercialization option rights, royalty reach-through rights, or product reach-through rights back to the provider are inappropriate.  Similarly, when for-profit entities are seeking access to NCI-funded tools for internal use purposes, recipients should ensure that the tools are transferred with the fewest encumbrances possible.  The SLA may be expanded for use in transferring tools to for-profit entities, or simple internal use license agreements with execution or annual use fees may be appropriate.  The BCR will provide the CGCCs with materials under a Material Transfer Agreement, approved by the NCI, that has terms no more restrictive than those found in the SLA or UBMTA and that is consistent with NIH policies and guidelines on sharing of research resources.

Section V.  Application Review Information


1.  Criteria

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

The following will be considered in making funding decisions:

2.  Review and Selection Process

Applications that are complete and responsive to the RFA will be evaluated for scientific and technical merit by an appropriate peer review group convened by the NCI in accordance with the review criteria stated below.

As part of the initial merit review, all applications will:

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 high priority score.  For example, an investigator may propose to carry out important work that by its nature is not innovative but is essential to move a field forward.

U24 Review Criteria as applicable to this RFA are presented below.

1.  Significance:

2.  Approach:

3.   Innovation: 

4.   Investigators:

5.  Environment:  

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 priority score:

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 E on Human Subjects in the PHS Form 398).

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 E on Human Subjects in the PHS Form 398).

Care and Use of Vertebrate Animals in Research: If vertebrate animals are to be used in the project, the five items described under Section F of the PHS Form 398 research grant application instructions 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.  Sharing Research Data

Data Sharing Plan: The reasonableness of the data sharing plan or the rationale for not sharing some research data will be assessed by the reviewers.  Reviewers will not factor the proposed data sharing plan into the determination of scientific merit or the priority score.  The presence of a data sharing plan will be part of the terms and conditions of the award.  The funding organization will be responsible for monitoring the data sharing policy.

2.D.  Sharing Research Resources

NIH policy requires that grant award recipients make unique research resources readily available for research purposes to qualified individuals within the scientific community after publication (see the NIH Grants Policy Statement at http://grants.nih.gov/grants/policy/nihgps_2003/NIHGPS_Part7.htm#_Toc54600131) and at http://www.ott.nih.gov/policy/rt_guide_final.html).  Investigators responding to this funding opportunity must include a sharing research resources plan addressing how unique research resources will be shared or explain why sharing of some resources is not possible.  Program staff will be responsible for the administrative review of the plan for sharing research resources.

The adequacy of the resources sharing plan will be considered by Program staff of the funding organization when making recommendations about funding applications.  Program staff may negotiate modifications of the data and resource sharing plans with the awardee before recommending funding of an application.  The final version of the data and resource sharing plans negotiated by both will become a condition of the award of the grant.  The effectiveness of the resource sharing will be evaluated as part of the administrative review of each non-competing Grant Progress Report (PHS 2590).  See Section VI.3.  Reporting.

3.  Anticipated Announcement and Award Dates
Not applicable.

Section VI.  Award Administration Information


1.  Award Notices

After the peer review of the application is completed, the Principle Investigator 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 (http://grants.nih.gov/grants/policy/nihgps_2003/NIHGPS_part4.htm).

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

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/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 PI 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 is a cooperative agreement (U24), an "assistance" mechanism (rather than an "acquisition" mechanism), in which the TCGA Pilot Project Research Network Steering Committee is anticipated to have substantial scientific and/or programmatic involvement with the grantee during performance of the activity.  Under the cooperative agreement, the TCGA Pilot Project Research Network Steering Committee supports and/or stimulates the recipient's activity by being involved in and otherwise working jointly with the award recipient in a partner role, but it is not to assume direction, prime responsibility, or a dominant role in the activity.  Consistent with this concept, the dominant role and prime responsibility for the activity resides with the awardees for each project, although specific tasks and activities in carrying out the studies will be shared among the awardees and the TCGA Pilot Project Research Network Steering Committee.  These are summarized below.

2.A.1.  Principal Investigator (PI) Rights and Responsibilities.  The PI will coordinate project activities scientifically and administratively at the awardee and collaborating institutions, including research design and protocol development, data collection, quality control, interim data and safety monitoring, final data analysis and interpretation, and preparation of publications.  The PI will have primary responsibility for defining the details of the projects within the guidelines of this RFA and for performing all scientific activities.  The PI will agree to accept the close coordination, cooperation, and participation of the NCI and NHGRI Project Scientists and the TCGA Pilot Project Research Network Steering Committee in those aspects of scientific and technical management of the project as described below.

Specifically, the PI of the CGCC will:

Awardees will retain custody and have primary rights to the data and software developed under these awards, subject to Government rights of access consistent with current HHHs, PHS, and NIH policies and requirements in this RFA CA-07-014.

2.A.2.  NIH Responsibilities with respect to the TCGA Pilot Project. An NCI and an NHGRI Project Scientist will have substantial scientific/programmatic involvement  above and beyond normal stewardship during the conduct of this activity through technical assistance, advice and coordination as described below. 

It is anticipated that decisions for all appropriate activities will be reached by a consensus of the TCGA Pilot Project Research Network Steering Committee and that NCI and NHGRI program staff will be given the opportunity to offer input throughout this process.  One NCI Project Scientist and one NHGRI Project Scientist shall participate as members of the TCGA Pilot Project Research Network Steering Committee, and each shall have one vote.

The Project Scientist will:

Additionally, an NCI program official (i.e., Program Director) will be responsible for the normal scientific and programmatic stewardship of the award and will be named in the award notice.  The assigned Program Director may also serve as the NIH Project Scientist.

2.A.3.  Collaborative Responsibilities

The TCGA Pilot Project Research Network Steering Committee will serve as the main governing board of the TCGA Pilot Project Research Network, including the CGCCs and Genome Sequencing Centers (GSCs) funded under the partner NHGRI initiative.  Full membership on the TCGA Pilot Project Research Network Steering Committee will include the NCI and NHGRI Project Scientists (one from each Institute), the PIs of each of the awarded cooperative agreement CGCCs, and the PIs of each of the NHGRI-funded Genome Sequencing Centers participating in the TCGA Pilot Project.  The TCGA Pilot Project Research Network Steering Committee Chair will not be an NIH staff member.  Additional members may be added by action of the TCGA Pilot Project Research Network Steering Committee and may include, for example, a representative from the NCI Center for Bioinformatics and/or from the Human Cancer Biospecimen Core Resource.  Other NIH staff may attend the TCGA Pilot Project Research Network Steering Committee meetings if their expertise is required for specific discussions.  Each full member will have one vote including each NCI and NHGRI Project Scientist.  Awardee members of the TCGA Pilot Project Research Network Steering Committee will be required to accept and implement policies approved by the entire TCGA Pilot Project Research Network Steering Committee. It is anticipated that decisions for all appropriate activities will be reached by a consensus of TCGA Research Network Steering Committee and that NCI and NHGRI program staff will be given the opportunity to offer input throughput this process.

The TCGA Pilot Project Research Network Steering Committee will:

2.A.4.  TCGA External Scientific Committee

The TCGA External Scientific Committee will be responsible for reviewing and evaluating the progress of the members of the TCGA Pilot Project Research Network toward meeting their individual and collective goals.  The External Scientific Committee will provide recommendations to the Director of the NCI and the Director of the NHGRI about continued support of the components of the TCGA Pilot Project Research Network.  The External Scientific Committee is composed of senior scientists and clinicians with relevant expertise in cancer, genomics, and ethics; the members of the External Scientific Committee are not PIs of a cooperative agreement involved in The Cancer Genome Atlas Pilot Project.  The membership of the External Scientific Committee may be enlarged permanently, or on an ad hoc basis, as needed.

The External Scientific Committee will meet at least once per year.  During part of this meeting, there will be a joint meeting with the TCGA Pilot Project Research Network Steering Committee to allow the External Scientific Committee members to interact directly with the awardees.  Annually, the External Scientific Committee will make recommendations regarding progress of the TCGA Pilot Project Research Network and present advice about changes, if any, which may be necessary in the Cancer Genome Characterization Center program to the Director of the NCI and the Director of the NHGRI.

2.A.5.  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, including: 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 submit the PHS Non-Competing Grant Progress Report, Form 2590, annually (http://grants.nih.gov/grants/funding/2590/2590.htm) and financial statements as required in the NIH Grants Policy Statement.

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:

Daniela S Gerhard, Ph.D.
Director
Office of Cancer Genomics
Office of the Director
National Cancer Institute
Building 31, Room 10A07, MSC 2580
31 Center Drive
Bethesda, MD 20892-2580
Telephone:  (301) 451-8027
FAX:  (301) 480-4368
Email: gerhardd@mail.nih.gov

2.  Peer Review Contacts:

Referral Officer
National Cancer Institute
Division of Extramural Activities
6116 Executive Boulevard, Room 8041, MSC 8329
Bethesda, MD 20892-8329 (for U.S. Postal Service express or regular mail)
Rockville, MD 20852 (for express/courier delivery)
Telephone: (301) 496-3428
FAX: (301) 402-0275
Email: ncirefof@dea.nci.nih.gov

3.  Financial or Grants Management Contacts:

Ms.  Kathryn Dunn
Grants Management Specialist
National Cancer Institute
6120 Executive Boulevard, Room 243, MSC 7150
Bethesda, MD 20892-7150 (for U.S. Postal Service express or regular mail)
Rockville, MD 20852 (for express/courier delivery)
Telephone: (301) 846-6829
FAX: (301) 402-3409
E-mail:  dunnkath@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); and 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 (see the NIH Policy for Data and Safety Monitoring in the NIH Guide for Grants and Contracts at 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.

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-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:
NIH-funded investigators are requested to submit to the NIH manuscript submission (NIHMS) system (http://www.nihms.nih.gov) at PubMed Central (PMC) an electronic version of the author's final manuscript upon acceptance for publication, resulting from research supported in whole or in part with direct costs from NIH.  The author's final manuscript is defined as the final version accepted for journal publication, and includes all modifications from the publishing peer review process.

NIH is requesting that authors submit manuscripts resulting from: 1) currently funded NIH research projects or 2) previously supported NIH research projects if they are accepted for publication on or after May 2, 2005.  The NIH Public Access Policy applies to all research grant and career development award mechanisms, cooperative agreements, contracts, Institutional and Individual Ruth L.  Kirschstein National Research Service Awards, as well as NIH intramural research studies.  The Policy applies to peer-reviewed, original research publications that have been supported in whole or in part with direct costs from NIH, but it does not apply to book chapters, editorials, reviews, or conference proceedings.  Publications resulting from non-NIH-supported research projects should not be submitted.

For more information about the Policy or the submission process, please visit the NIH Public Access Policy Web site at http://publicaccess.nih.gov/ and view the Policy or other Resources and Tools including the Authors' Manual (http://publicaccess.nih.gov/publicaccess_Manual.htm).

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.  Unless otherwise specified in an NIH solicitation, Internet addresses (URLs) should not be used to provide information necessary to the review because reviewers are under no obligation to view the Internet sites.  Furthermore, we caution reviewers that their anonymity may be compromised when they directly access an Internet site.

Healthy People 2010:
The Public Health Service (PHS) is committed to achieving the health promotion and disease prevention objectives of "Healthy People 2010," a PHS-led national activity for setting priority areas.  This PA is related to one or more of the priority areas.  Potential applicants may obtain a copy of "Healthy People 2010" at http://www.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 or Health Systems Agency review.  Awards are made under the authorization of Sections 301 and 405 of the Public Health Service Act as amended (42 USC 241 and 284) and under Federal Regulations 42 CFR 52 and 45 CFR Parts 74 and 92.  All awards are subject to the terms and conditions, cost principles, and other considerations described in the NIH Grants Policy Statement.  The NIH Grants Policy Statement can be found at http://grants.nih.gov/grants/policy/policy.htm.

The PHS strongly encourages all grant recipients to provide a smoke-free workplace and discourage the use of all tobacco products.  In addition, Public Law 103-227, the Pro-Children Act of 1994, prohibits smoking in certain facilities (or in some cases, any portion of a facility) in which regular or routine education, library, day care, health care, or early childhood development services are provided to children.  This is consistent with the PHS mission to protect and advance the physical and mental health of the American people.

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 2 years to the research.  For further information, please see: http://www.lrp.nih.gov.


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