Department of Health and Human Services
Part 1. Overview Information
Participating Organization(s)

National Institutes of Health (NIH)

Components of Participating Organizations

National Cancer Institute (NCI)

Funding Opportunity Title

Proteogenomic Data Analysis Centers for Clinical Proteomic Tumor Analysis Consortium (U24)

Activity Code

U24 Resource-Related Research Projects – Cooperative Agreements

Announcement Type

New

Related Notices
  • NOT-OD-16-004 - NIH & AHRQ Announce Upcoming Changes to Policies, Instructions and Forms for 2016 Grant Applications (November 18, 2015)
  • NOT-OD-16-006 - Simplification of the Vertebrate Animals Section of NIH Grant Applications and Contract Proposals (November 18, 2015)
  • November 16, 2015 - Notice of Pre-application Webinar for Clinical Proteomic Tumor Analysis Consortium. See Notice NOT-CA-15-044.
Funding Opportunity Announcement (FOA) Number

RFA-CA-15-023

Companion Funding Opportunity

RFA-CA-15-021, U24 Resource-Related Research Project - Cooperative Agreements

RFA-CA-15-022, U01 Research Project - Cooperative Agreements

Catalog of Federal Domestic Assistance (CFDA) Number(s)

93.393, 93.394, 93.396

Funding Opportunity Purpose

This Funding Opportunity Announcement (FOA) is a part of the NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC). This reissuance of the CPTAC program leverages recent advancements in cancer proteomics and genomics and accelerates research in these areas by disseminating research resources for the scientific community. The program will support broad efforts focused on several cancer types to explore further the complexities of cancer proteomes and their connections to abnormalities in cancer genomes. The potential of proteomic and proteo-genomic approaches will also be explored in translational research focused on clinically-relevant problems, such as the ability to predict which treatments are likely to be effective against a specific patient's tumor.

This FOA solicits applications for multidisciplinary Proteogenomic Data Analysis Centers (PGDACs), which will provide data analysis and biological and clinical interpretation of CPTAC data. PGDAC awardees will be expected to develop computational tools for data analysis, data integration, and visualization and apply these tools to CPTAC data.

PGDACs will interact with additional CPTAC sub-programs that include:

  • Proteome Characterization Centers (PCCs, to be supported by RFA-CA-15-021) that will use various standardized proteomic analysis technologies for the systematic and comprehensive proteome-wide characterization of defined sets of genomically-characterized samples. These samples (human biospecimens, cultured cells, and animal cancer models) will be provided by the NCI; and
  • Proteogenomic Translational Research Centers (PTRCs, to be supported under RFA-CA-15-022) that will apply state-of-the-art proteomic and proteo-genomic approaches to elucidate responses to cancer therapeutic agents, e.g., in order to predict which therapeutic agents are likely to be effective against a specific patient's tumor.
Key Dates
Posted Date

November 2, 2015

Open Date (Earliest Submission Date)

December 27, 2015

Letter of Intent Due Date(s)

30 days prior to application due date

Application Due Date(s)

January 27, 2016, by 5:00 PM local time of applicant organization. All types of non-AIDS applications allowed for this funding opportunity announcement are due on this date.

No late applications will be accepted for this Funding Opportunity Announcement.

Applicants are encouraged to apply early to allow adequate time to make any corrections to errors found in the application during the submission process by the due date.

AIDS Application Due Date(s)

Not Applicable

Scientific Merit Review

April - May 2016

Advisory Council Review

August 2016

Earliest Start Date

September 2016

Expiration Date

January 28, 2016

Due Dates for E.O. 12372

Not Applicable

Required Application Instructions

It is critical that applicants follow the instructions in the SF424 (R&R) Application Guide, except where instructed to do otherwise (in this FOA or in a Notice from the NIH Guide for Grants and Contracts). Conformance to all requirements (both in the Application Guide and the FOA) is required and strictly enforced. Applicants must read and follow all application instructions in the Application Guide as well as any program-specific instructions noted in Section IV. When the program-specific instructions deviate from those in the Application Guide, follow the program-specific instructions. Applications that do not comply with these instructions may be delayed or not accepted for review.


Table of Contents

Part 1. Overview Information
Part 2. Full Text of the Announcement

Section I. Funding Opportunity Description
Section II. Award Information
Section III. Eligibility Information
Section IV. Application and Submission Information
Section V. Application Review Information
Section VI. Award Administration Information
Section VII. Agency Contacts
Section VIII. Other Information


Part 2. Full Text of Announcement
Section I. Funding Opportunity Description
Purpose

This Funding Opportunity Announcement (FOA) is a part of the NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC). This reissuance of the CPTAC program leverages recent advancements in cancer proteomics and genomics and accelerates research in these areas by disseminating research resources for the scientific community. The program will support broad efforts focused on several cancer types to explore further the complexities of cancer proteomes and their connections to abnormalities in cancer genomes. The potential of proteomic and proteo-genomic approaches will also be explored in translational research focused on clinically-relevant problems.

This FOA solicits applications for multidisciplinary Proteogenomic Data Analysis Centers (PGDACs), which will provide data analysis and biological and clinical interpretation of CPTAC data. PGDAC awardees will be expected to develop computational tools for data analysis, data integration, and visualization and apply these tools to CPTAC data. The tools and approaches to be proposed for PGDACs should be suitable for analyses and meaningful interpretations of data derived from diverse types of samples (such as clinical specimens, cultured cells, animal models of human cancers, etc.).

PGDACs will interact with additional CPTAC sub-programs that include:

  • Proteome Characterization Centers (PCCs, to be supported under RFA-CA-15-021) that will use various standardized proteomic analysis technologies for the systematic and comprehensive proteome-wide characterization of defined sets of genomically-characterized samples. These samples (human biospecimens, cultured cells, and animal cancer models) will be provided by the NCI; and
  • Proteogenomic Translational Research Centers (PTRCs, to be supported under RFA-CA-15-022) that will apply state-of-the-art proteomic and proteo-genomic approaches to elucidate responses to cancer therapeutic agents, e.g., in order to predict which therapeutic agents are likely to be effective against a specific patient's tumor.

This FOA is open to all qualified applicants regardless of whether or not they participated in the previous issuance of the program.

This unique combination of coordinating research approaches, sharing of research data, and combining proteomic with genomic analysis, should allow the CPTAC program to produce a more unified understanding of cancer biology with translational potential. In addition, data and resources (assays) are to be made publicly available to the research community through CPTAC's Data Coordinating Center (DCC), Assay Portal, and other portals to maximize utility and public benefit. These open community resources and knowledge are expected to lead to novel translational approaches and, ultimately, to accelerate the development of new cancer diagnostic, prevention, and treatment strategies.

Key Definitions:

The following key terms are used in the FOA as defined below.

  • "Cancer proteomics" refers to the comprehensive characterizations and analyses of proteins and their derivatives translated from a cancer genome using a human biospecimen or a preclinical model (cultured cell or animal model). The term "discovery proteomics" refers to the "untargeted and unbiased" identification and quantification of a maximal number of proteins in a biological or clinical sample. The term targeted proteomics” refers to the quantitative measurements focused on a defined subset of total proteins in a biological or clinical sample.
  • "Cancer proteogenomics" denotes the intersection of cancer proteomics and genomics and, specifically, understanding how various distinct changes at the proteome level are related to abnormalities in cancer genomes and/or changes at the functional level (i.e., in gene expression), while protein information helps improve and refine cancer genome annotation. In the context of this FOA, particularly important is the potential of proteogenomic approaches to better explain cancer complexities than genomics or proteomics alone.
  • For the CPTAC program, the term "comprehensive proteomic characterizations" means the generation of proteome-wide experimental data using human specimens/model samples, whereas "proteomic/proteogenomic data analysis" refers to the use of bioinformatic approaches and computation tools to analyze the primary data in various ways and in conjunction with other available complementary data, aiming to achieve higher levels of data/pathways/concepts integration.  Three levels of data analysis are envisioned below:
  • Level 1:
  • Discovery Proteomics Research - Analysis of raw experimental data to generate results on peptide/protein identification and quantitation, post-translational modifications (PTMs) identification, site localization and quantitation using a reference genome;
  • Targeted Proteomics Research - Analysis of raw experimental data to generate quantitative results on peptide/protein concentrations of the selected targets from Discovery Proteomics Research.
  • Level 2: Integration of genome-proteome data at the linear sequence level (DNA, RNA, peptides/proteins with relative quantitation obtained from Discovery Proteomics Research using personalized genomic data).
  • Level 3: Integration, visualization and analysis of omics data mapped onto networks and pathways obtained from Discovery Proteomics Research.
Background

Despite significant progress in understanding cancer at the molecular level, the complexity that comprises this disease remains a daunting barrier to developing interventions that are needed to diagnose, treat and prevent cancer in the era of precision medicine.  Vital to the progress in these areas are the discovery and understanding of cancer-specific aberrations at various molecular and cellular levels. Although proteins reflecting the genomic changes in cancer have the potential to become clinically meaningful molecular markers, their discovery and confirmation for clinical use have proven to be extremely challenging. In the past decade, cancer researchers have made significant progress in identifying a new molecular taxonomy of cancer through the use of genomics.  This FOA aims to leverage the investments in cancer genomics by building on the achievements in cancer proteomics in order to accelerate molecularly-oriented cancer research toward basic discovery and clinical impact.

The CPTAC program (RFA-CA-07-012) began in 2006 as a part of the Clinical Proteomic Technologies for Cancer initiative at the NCI, the purpose of which was to understand and address the experimental and analytical sources of error in existing proteomics technologies, in order to complement genomic and transcriptomic analyses used to improve diagnostics, therapeutics, and prevention for cancer. Program highlights include the standardization of mass spectrometry (MS) methodologies for untargeted protein analyses (discovery proteomics), standardization of multiple reaction monitoring (MRM) mass spectrometry in targeted protein analyses (targeted proteomics), adoption of a MRM assay for thyroglobulin by clinical reference laboratories, development of an open-source computational tool (Skyline) for designing MRM assays that is supported by major instrument vendors, development of mock 510(k) device clearance documents using targeted proteomic platforms in coordination with the Food and Drug Administration (FDA) and the American Association for Clinical Chemistry (AACC), and development of open data sharing policies in proteomics that are supported by peer-reviewed journals.

To begin to apply these outputs, the second phase of CPTAC was initiated in 2011 (RFA-CA-10-016) as a pilot collaborative network to utilize the CPTAC’s state-of-the-art standardized proteomic workflows to study genomically-characterized tumors (such as those from The Cancer Genome Atlas (TCGA) and others) to add an additional layer of biology to cancer. The goal was to apply deep proteomic analysis to tumors that have undergone comprehensive genomic characterization, to gain additional biological insights that  would have been difficult or impossible to obtain solely through genomics. All data and analytical tools were made broadly available to the research community through public databases (CPTAC's Research Resources: Data Portal, https://cptac-data-portal.georgetown.edu/cptacPublic; Assay Portal, https://assays.cancer.gov; Antibody Portal, http://antibodies.cancer.gov), in order to democratize proteomics science. The current CPTAC program is composed of Proteome Characterization Centers (PCCs) with expertise in proteomics, genomics, cancer biology, oncology and clinical chemistry that perform coordinated research projects to comprehensively characterize and analyze cancer specimens selected for study. PCCs have interrogated three cancer types (colorectal, ovarian and breast tumors), while successfully demonstrating the scientific benefits of integrating proteomic research with genomics to produce a more unified understanding of cancer biology, while creating open community resources that are widely used by the cancer community. Such an integrated proteogenomics approach is now bringing key insights into genomic abnormalities manifested at the protein network and pathway level.

Overall CPTAC Structure and Functions

The CPTAC program will consist of the following sub-programs:

  • Proteome Characterization Centers (PCCs). To improve the molecular understanding of cancer biology, PCC awards (RFA-15-021) will comprehensively characterize the proteomic composition of human biospecimens and preclinical models (to be provided by the NCI). PCC teams will provide experimental raw data and metadata to the Data Coordinating Center (see below), and coordinate data analysis activities with PGDACs.
  • Proteogenomic Translational Research Centers (PTRCs). To complement the comprehensive approaches of the PCCs, PTRC awards (RFA-15-022) will address clinical questions of drug response/toxicity prediction and resistance. PTRCs will include well-conceived translational and/or clinical questions, access to appropriate clinical trial biospecimens (tumors), state-of-the-art proteomic capability, and a proteogenomic-based research approach. Research would support cancer research model studies (comprehensive proteogenomic discovery research), clinical trial sample acquisition, followed by targeted assay development and application on clinical trial samples. PTRCs will provide experimental raw data, metadata and preliminary analysis results to the Data Coordinating Center (see below), and coordinate data analysis activities with PGDACs.
  • Proteogenomic Data Analysis Centers (PGDACs, covered by this FOA). In collaboration with PCCs and PTRCs, PGDAC awards will support innovative bioinformatics development and application to integrate data analyses across the entire proteome and genome. PGDACs are to assist researchers (PCCs, and PTRCs accordingly) to integrate, visualize and analyze the data at linear sequence, network and pathway level, including PTMs of proteins and protein-protein interactions.

Additional resources (supported by the NCI beyond the scope of this FOA) available to CPTAC awardees:

To facilitate the activities of individual PGDACs and other research components of the CPTAC program, the NCI has created and directly supports additional resources beyond the scope of this FOA.  These resources include:

  • NCI-supported Biospecimen Resources:
  • Tissue Source Sites (TSS), which collect human biospecimens and clinical data.
  • Biospecimen Core Resource (BCR) that serves as a centralized laboratory(s) that receives, processes, qualifies, and distributes treatment-naïve tumor and matched normal control human biospecimens to the PCCs. The BCR serves as the interface between the CPTAC program and the TSSs collecting, ensuring and verifying that CPTAC human subjects protections and guidelines are adhered to and that all regulations are followed at each TSS, including use of language consistent with the CPTAC informed consent documents. Note: only PCC awardees will receive NCI-collected specimens.
  • Genomic Characterization Center (GCC) that will genomically characterize NCI-provided CPTAC biospecimens to be characterized and analyzed by the PCCs.
  • Clinical Data Resource (CDR) that will receive, qualify, store, and distribute clinical data.
  • Quality Management System (QMS). The QMS works with all CPTAC awardees to define quality processes and metrics, and to track nonconforming events.
  • Data Coordinating Center (DCC): All CPTAC awardees will have to use DCC as the repository for their data, protocols, tools, etc. DCC serves as the hub and central repository of all data, and facilitates the transfer of data between the Centers and quality control of data. The DCC will also implement the CPTAC common data analysis pipeline, consisting of quality control metrics applied to genomic and proteomic data and peptide/protein identification and quantification for proteomic data.
  • CPTAC Research Resources. The CPTAC program currently has three dedicated public resources for disseminating its research findings. Applicants are encouraged to consider using the items in these portals, as appropriate. These resources include:
  • Data Portal (https://cptac-data-portal.georgetown.edu/cptacPublic), which serves as a centralized repository for the dissemination of proteomic data collected by the CPTAC program.
  • Assay Portal (https://assays.cancer.gov), which serves as a public repository of well-characterized, targeted proteomic assays. The Assay Portal contains analytically validated assays and standard operating procedures (SOPs) that can be used to compare results across the board. Assays in the portal adhere to “Fit-for-Purpose” validation guidelines distinguished by their performance and extent of analytical characterization (Tiers 1-3). (http://proteomics.cancer.gov/newsevents/newsannouncements/archive/2013/standardstargeted).
  • Antibody Portal (http://antibodies.cancer.gov), which serves as a community resource of unbiased renewable antibodies (monoclonal) with all associated SOPs and characterization data made publicly available to the research community.
  • Proteomic informatics tools (http://proteomics.cancer.gov/resources/softwaretools). Various informatics tools (developed or refined by CPTAC investigators) are available (e.g., for analytical metric quality control, along with data visualization, analysis and integration of cancer-relevant networks and pathways, etc.).
  • Other NCI research resources: Applicants for one or more of the CPTAC sub-programs are encouraged to consider establishing partnerships with other groups, and divisions and programs within NCI that may benefit the overall program goals. For example, the awardees could take advantage of the TCGA (http://cancergenome.nih.gov), Cancer Target Discovery and Development Network (CTD2; http://ocg.cancer.gov/programs/ctd2), Early Detection Research Network (EDRN, http://edrn.nci.nih.gov), the Cancer Diagnosis Program (CDP, http://www.cancerdiagnosis.nci.nih.gov), and Cancer Therapy Evaluation Program (CTEP, http://ctep.cancer.gov) including the National Clinical Trials Network (NCTN) and Experimental Therapeutics Clinical Trials Network (ET-CTN), and databases of clinical studies of human participants such as publicly supported clinical trials around the world (https://clinicaltrials.gov).
 
Research Objectives and Main Requirements for this FOA

PGDACs will participate in one or more of the following activities: computational tool development, data analysis, data integration, and data visualization. These activities may use as input any and all levels of CPTAC data, from instrument files to protein/gene identifications to clinical data.  PGDAC research aims may span a range of topics, including, but not limited to: cancer biology, clinical diagnostics/therapeutics, quality control, and/or novel computation.  The goal is that the aggregate analysis from all PGDACs will provide a comprehensive analysis of CPTAC data.

Each PGDAC will be expected to apply its style of analysis to the data generated by the PCCs (collected for 5-6 human tumor types using NCI-provided biospecimens) as well as data  generated by: NCI's Human Cancer Model Initiative, Patient-Derived Xenograft (PDX) Repository, and the PTRCs.

Note. Human biospecimens (primary emphasis of this FOA) and preclinical models (cell lines and patient-derived xenografts) will be provided by the NCI to the PCCs.  PGDACs are expected to analyze PCC data on this biospecimen cohort.

Human biospecimens (treatment-naïve tumor, accompanied by adjacent normal tissue when available), will be prospectively collected using standardized protocols optimized for proteomics-based measurement technologies.  Biospecimens are to include well-annotated clinical data and undergo genomic characterization (anticipated analyses are whole exome sequencing; RNA sequencing; genotyping and DNA copy number). Biospecimens will be from a selection of cancer types, potentially including glioblastoma multiforme (GBM), lung adenocarcinoma, lung squamous cell carcinoma, pancreatic ductal adenocarcinoma, clear cell kidney carcinoma, cutaneous melanoma, head and neck squamous cell carcinoma, sarcomas, uterine corpus endometrial carcinoma, and acute myeloid leukemia (AML). Anticipated are 200 cases (tumor with adjacent normal) for each cancer type, with 100 cases to be used in the Discovery Research Arm and 100 cases in the Confirmatory Research Arm. The number of specimens will be sufficient to ensure appropriate statistical power. Additional information pertaining to the type of biospecimens to be provided by the NCI will be forthcoming.

PGDACs are expected to also collaborate with two NCI programs - NCI’s Human Cancer Model Initiative (cell lines) and Patient-Derived Xenograft (PDX) Repository program. Each PGDAC is expected to apply its data analysis tools to data generated by the PCCs from these preclinical samples (anticipated 1000 samples from each program for a total of 2000 samples).

To foster the development of collaboration among PCC, PTRC, and PGDAC applicants, a Teaming Website has been developed. Please visit and register at http://proteomics.cancer.gov.

Specific Research Objective 1: Develop one or more computational tools to elucidate some aspects of the molecular complexity of cancer.

Tools may fall into one of the following categories: (1) new bioinformatics and computational tools to capture key biological parameters such as pathway analysis, data integration with visualization, and integrated cancer biology, (2) pipeline and network-wide quality control methods for the system, (3) processing or integration of analytical data from other sub-programs of CPTAC to generate disease level findings and interpretations.  These goals will necessitate continuous communication and interactions among the members of the CPTAC network.  Each member of the PGDAC group will have distinct functions and capabilities and will be responsible for individual analytical pieces of the pipeline.

The overall pipeline and individual tools should be automated and include user interface(s) appropriate for scientists who are not necessarily experts in bioinformatics and computer science.  The pipeline will need to be flexible and efficient so that data analysis can occur in "real time."  Tool development, integration of results and report generation could occur simultaneously or in succession depending on the requirements of the data set under analysis and current status of the computational capacity of the applicants.  PGDAC tools should complement the analyses done by the DCC's Common Data Analysis Pipeline (CDAP).  The CDAP will use the reference genome to identify and quantify peptides/proteins and the genes from which they derived.

Specific Research Objective 2: Apply computational tools to CPTAC data.

PGDACs are expected to deploy computational tools on CPTAC-wide test data within six months of the award kick-off.

Data to analyze will include the comprehensive inventory of proteomic, genomic, epigenomic and transcriptomic aberrations, including: differential expression of proteins, somatic variation of protein sequence, alterations in DNA segment copy numbers, translocations, loss of heterozygosity, altered epigenetic patterns, changes in gene expression, mutations, or other CPTAC generated data. Each PGDAC is to utilize integrative tools/methods with which to: (1) analyze Genome Characterization Center (GCC), PCC, PTRC and/or PGDAC generated data, (2) integrate CPTAC data (to include data and metadata derived from CPTAC biospecimens), and (3) identify potentially cancer-related molecular alterations. These tools/methods should be applied to normalized data obtained from the molecular characterizations by GCCs, PCCs, or PTRCs, or to data generated by the PGDACs.

If appropriate and desirable, PGDAC applicants are encouraged to develop custom tools for some types of analyses mentioned.

Specific Research Objective 3: Identify candidates for targeted protein assays

CPTAC characterizations of specimens entail a Discovery Research Arm and a Confirmatory Research Arm. The Discovery Research Arm will include unbiased characterization of all detectable protein forms in a sample using analytically validated proteomic discovery technologies. The Confirmatory Research Arm will include targeted multiplex proteomic assays against corresponding protein targets. 

The prioritization of corresponding proteins/peptides of interest will be done in coordination with the PCCs and PTRCs, with final selection made by the Protein Candidate Selection Subcommittee and the Steering Committee (see below). The CPTAC Research Resource will facilitate the development and application of reference materials and key reagents for network studies if needed. All characterization data will be made available to the PGDAC network, other units of the CPTAC program, and to the public through the CPTAC DCC.

Effort Coordination with PCCs. PCCs are expected to use various standardized proteomic analysis platforms and technologies to systematically and comprehensively characterize cancer proteomes that derive from genomic alterations and abnormalities in samples (predominantly tumors), as well as confirming discovered protein/peptide findings in a set of independent biospecimens. Thus, the PCCs will coordinate and provide experimental raw, metadata and Level 1 (see Section IV.2 below) analysis results to the DCC. The DCC will, in turn, perform proteomic analysis via a Common Data Analysis to ensure the quality of data prior to distributing the data to the PGDACs and others for integrative analyses and public data release.

Effort Coordination with PTRCs. PTRCs are expected to address clinical questions of drug response/toxicity prediction and resistance. PTRCs will provide experimental raw data, metadata and preliminary analysis results to the Data Coordinating Center, and coordinate data analysis activities with PGDACs. Bioinformatics teams in the PTRCs are required to conduct proteogenomic data analyses and contribute to the overall interpretation of the results. However, all data produced by the PTRCs for transfer to the PGDACs are expected to enable more extensive and comprehensive integrative analyses to enhance deeper data visualization, analysis, and interpretation. PTRCs will provide all data and analysis results to the CPTAC DCC where quality control and assurance of the data will be performed prior to distributing the data to the PGDACs and others for integrative analyses and releasing the data to the public (see Section IV).

Governance of the NCI Clinical Proteomic Tumor Analysis Consortium

The CPTAC program will be governed by CPTAC Steering Committee (SC). The SC will oversee and coordinate the activities of all PCCs, PTRCs, and PGDACs. Details on the composition and functions of SC are provided in Section VI. Award Administration Information, Terms and Conditions of Cooperative Agreement, “Areas of Joint Responsibility.”

Evaluation of the Program

PGDACs will be required to participate in an external evaluation process of the CPTAC program coordinated by NCI Program Staff.  The purpose of the evaluation process is to monitor and assess the performance of the PGDACs in achieving the goals of this FOA.  Criteria for the evaluation part will be developed by NCI Program Staff in partnership with the CPTAC External Scientific Panel (ESP) (as described in Section VI).

Section II. Award Information
Funding Instrument

Cooperative Agreement: A support mechanism used when there will be substantial Federal scientific or programmatic involvement. Substantial involvement means that, after award, NIH scientific or program staff will assist, guide, coordinate, or participate in project activities.

Application Types Allowed

New

The OER Glossary and the SF424 (R&R) Application Guide provide details on these application types.

Funds Available and Anticipated Number of Awards

The NCI intends to commit $4.5 million in FY2016 to fund up to 4 awards.

Future year amounts are anticipated to be at the same levels, but will ultimately depend on annual appropriations.

Award Budget

Application budgets for each Center may not exceed $675,000 in direct costs per year and need to reflect the actual needs of the proposed project. 

Award Project Period

Applicants may request up to 5 years of support.  

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

Section III. Eligibility Information
1. Eligible Applicants
Eligible Organizations

Higher Education Institutions

  • Public/State Controlled Institutions of Higher Education
  • Private Institutions of Higher Education

The following types of Higher Education Institutions are always encouraged to apply for NIH support as Public or Private Institutions of Higher Education:

  • Hispanic-serving Institutions
  • Historically Black Colleges and Universities (HBCUs)
  • Tribally Controlled Colleges and Universities (TCCUs)
  • Alaska Native and Native Hawaiian Serving Institutions
  • Asian American Native American Pacific Islander Serving Institutions (AANAPISIs)

Nonprofits Other Than Institutions of Higher Education

  • Nonprofits with 501(c)(3) IRS Status (Other than Institutions of Higher Education)
  • Nonprofits without 501(c)(3) IRS Status (Other than Institutions of Higher Education)

For-Profit Organizations

  • Small Businesses
  • For-Profit Organizations (Other than Small Businesses)

Governments

  • State Governments
  • County Governments
  • Eligible Agencies of the Federal Government
  • U.S. Territory or Possession
Foreign Institutions

Non-domestic (non-U.S.) Entities (Foreign Institutions) are not eligible to apply.
Non-domestic (non-U.S.) components of U.S. Organizations are not eligible to apply.
Foreign components, as defined in the NIH Grants Policy Statement, are allowed.

Required Registrations

Applicant Organizations

Applicant organizations must complete and maintain the following registrations as described in the SF 424 (R&R) Application Guide to be eligible to apply for or receive an award. All registrations must be completed prior to the application being submitted. Registration can take 6 weeks or more, so applicants should begin the registration process as soon as possible. The NIH Policy on Late Submission of Grant Applications states that failure to complete registrations in advance of a due date is not a valid reason for a late submission.

  • Dun and Bradstreet Universal Numbering System (DUNS) - All registrations require that applicants be issued a DUNS number. After obtaining a DUNS number, applicants can begin both SAM and eRA Commons registrations. The same DUNS number must be used for all registrations, as well as on the grant application.
  • System for Award Management (SAM) (formerly CCR) – Applicants must complete and maintain an active registration, which requires renewal at least annually. The renewal process may require as much time as the initial registration. SAM registration includes the assignment of a Commercial and Government Entity (CAGE) Code for domestic organizations which have not already been assigned a CAGE Code.
  • NATO Commercial and Government Entity (NCAGE) Code – Foreign organizations must obtain an NCAGE code (in lieu of a CAGE code) in order to register in SAM. 
  • eRA Commons - Applicants must have an active DUNS number and SAM registration in order to complete the eRA Commons registration. Organizations can register with the eRA Commons as they are working through their SAM or Grants.gov registration. eRA Commons requires organizations to identify at least one Signing Official (SO) and at least one Program Director/Principal Investigator (PD/PI) account in order to submit an application.
  • Grants.gov – Applicants must have an active DUNS number and SAM registration in order to complete the Grants.gov registration.

Program Directors/Principal Investigators (PD(s)/PI(s))

All PD(s)/PI(s) must have an eRA Commons account.  PD(s)/PI(s) should work with their organizational officials to either create a new account or to affiliate their existing account with the applicant organization in eRA Commons. If the PD/PI is also the organizational Signing Official, they must have two distinct eRA Commons accounts, one for each role. Obtaining an eRA Commons account can take up to 2 weeks.

Eligible Individuals (Program Director/Principal Investigator)

Any individual(s) with the skills, knowledge, and resources necessary to carry out the proposed research as the Program Director(s)/Principal Investigator(s) (PD(s)/PI(s)) is invited to work with his/her organization to develop an application for support. Individuals from underrepresented racial and ethnic groups as well as individuals with disabilities are always encouraged to apply for NIH support.

For institutions/organizations proposing multiple PDs/PIs, visit the Multiple Program Director/Principal Investigator Policy and submission details in the Senior/Key Person Profile (Expanded) Component of the SF424 (R&R) Application Guide.

An investigator designated as a PD/PI on a PCC application in response to RFA-15-021 cannot be designated as a PD/PI under this FOA. However, these individuals can serve as key personnel within a PGDAC application.

2. Cost Sharing

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

3. Additional Information on Eligibility
Number of Applications

Applicant organizations may submit more than one application, provided that each application is scientifically distinct.

The NIH will not accept duplicate or highly overlapping applications under review at the same time.  This means that the NIH will not accept:

  • A new (A0) application that is submitted before issuance of the summary statement from the review of an overlapping new (A0) or resubmission (A1) application.
  • A resubmission (A1) application that is submitted before issuance of the summary statement from the review of the previous new (A0) application.
  • An application that has substantial overlap with another application pending appeal of initial peer review (see NOT-OD-11-101).
Section IV. Application and Submission Information
1. Requesting an Application Package

Applicants must download the SF424 (R&R) application package associated with this funding opportunity using the “Apply for Grant Electronically” button in this FOA or following the directions provided at Grants.gov.

2. Content and Form of Application Submission

It is critical that applicants follow the instructions in the SF424 (R&R) Application Guide, including Supplemental Grant Application Instructions except where instructed in this funding opportunity announcement to do otherwise. Conformance to the requirements in the Application Guide is required and strictly enforced. Applications that are out of compliance with these instructions may be delayed or not accepted for review.

For information on Application Submission and Receipt, visit Frequently Asked Questions – Application Guide, Electronic Submission of Grant Applications.

Letter of Intent

Although a letter of intent is not required, is not binding, and does not enter into the review of a subsequent application, the information that it contains allows IC staff to estimate the potential review workload and plan the review.

By the date listed in Part 1. Overview Information, prospective applicants are asked to submit a letter of intent that includes the following information:

  • Descriptive title of proposed activity
  • Name(s), address(es), and telephone number(s) of the PD(s)/PI(s)
  • Names of other key personnel
  • Participating institution(s)
  • Number and title of this funding opportunity

The letter of intent should be sent to:

Henry Rodriguez, MS, PhD, MBA
Office of Cancer Clinical Proteomics Research
Center for Strategic Scientific Initiatives
Office of the Director
National Cancer Institute
31 Center Drive, Room 10A52, MSC 2580
Bethesda, MD 20892
Telephone: 301-451-8883
Fax: 301-496-7807
Email: rodriguezh@mail.nih.gov

Page Limitations

All page limitations described in the SF424 Application Guide and the Table of Page Limits must be followed.

Instructions for Application Submission

The following section supplements the instructions found in the SF424 (R&R) Application Guide and should be used for preparing an application to this FOA.

SF424(R&R) Cover

All instructions in the SF424 (R&R) Application Guide must be followed.  

SF424(R&R) Project/Performance Site Locations

All instructions in the SF424 (R&R) Application Guide must be followed.  

SF424(R&R) Other Project Information

All instructions in the SF424 (R&R) Application Guide must be followed.

Facilities and Other Resources: In addition to standard information, list/document unique and critical resources and/or infrastructure (e.g., any unique proteomic platforms/technologies/tools, capabilities of institutional information technology systems in terms of handling massive flows of data that are to be expected, etc.). For each main resource, provide key characteristics, such as processing capacity and/or ability to apply rigorous quality control/quality assurance procedures. If resources listed are shared (i.e., not exclusive to the proposed PGDAC, such as institutional information technology systems, shared resources cores, etc.), specify and document arrangements through which sufficient access will be granted for the purposes of the project. The list in this attachment may include the capacity for data submission and storage, as well as the ability to develop specific criteria for evaluating data quality. List briefly the formats of the datasets, and accompanying documentation and their volumes that are expected for the required and proposed PGDAC activities. Document the ability of the available resources to handle these needs as well as the ability to implement changes in the systems available if needed to integrate bioinformatics infrastructure across the PGDACs (which may require such elements as: a uniform data reporting standard; optimization, integrated data mining, and others).

Other Attachments: Upload software documentation for research software expected to be used by the PGDAC. Upload the items indicated as a single attachment using file name "SOPs" (this file name will become a bookmark in the application). If SOPs to be used have been previously developed within CPTAC, list those SOPs but do not attach their full text.

SF424(R&R) Senior/Key Person Profile

All instructions in the SF424 (R&R) Application Guide must be followed. 

R&R Budget

All instructions in the SF424 (R&R) Application Guide must be followed.

Capital equipment requests (i.e., for equipment with unit cost over $5,000) are not allowed under this FOA.

Site visits. Because of the complexity of the PGDACs, NIH/NCI Program Staff members will conduct annual administrative site visits. PGDAC applicants should be prepared for annual visits and should budget appropriately (including travel for collaborators and other necessary costs).

Costs of participating in CPTAC meetings. Applicants should budget for the PDs/PIs and/or alternative designated representatives (in aggregate, up to 4 members of each PGDAC) to attend semi-annual, face-to-face CPTAC investigator meetings.

R&R Subaward Budget

All instructions in the SF424 (R&R) Application Guide must be followed.

PHS 398 Cover Page Supplement

All instructions in the SF424 (R&R) Application Guide must be followed.  

PHS 398 Research Plan

All instructions in the SF424 (R&R) Application Guide must be followed, with the following additional instructions:

Research Strategy:

Instead of the standard subsections described in Application Guide, Research Strategy must consist of the subsections A-D specified below.

Sub-Section A. Overview of the Proposed Proteogenomic Data Analysis Center (PGDAC)

Present the overall vision for the proposed PGDAC including the following items:

  • Outline the overarching aims for the PGDAC.
  • Describe the rationale for how the proposed research approach will improve the understanding of cancer biology.
  • Applicant Group.
  • Provide details on collective aspects of the team (which are not covered and cannot be covered by individual biosketches).  For example, outline the proposed Team structure and explain how the group expertise contributes to achieving the objectives of the proposed studies. Also highlight how the diverse group expertise contributes to the innovation of which the Team is capable, the flexibility they possess to redirect research when scientific progress warrants it, and their ability to anticipate new directions. If applicable, provide evidence of previous successful collaborations among members of the applicant team.
  • Without repeating information from individual biosketches, summarize the group's expertise and experience in complex data analysis projects, omics-specific bioinformatics, computational data analysis, cancer biology, and clinical oncology.
  • Briefly describe the contributions of research partners from other institutions (if applicable).

If appropriate, preliminary data relevant to the proposed methods should be included in sub-sections B, C, and D.  Applicants should demonstrate an understanding and capability to meet the scientific requirements, including accuracy, reproducibility and high-throughput nature of the proposed computational analysis.  Furthermore, there should be evidence for the quality of the data that may be anticipated from the proposed computational tools when utilized by the applicant.

Sub-Section B.  Analysis of CPTAC data

Each PGDAC will analyze and integrate data generated by the CPTAC sub-programs to identify the complex pattern of changes that occur in the cancer cases studied.

Describe how the proposed PGDAC will ensure efficient “data mining” and analysis of CPTAC data (to include data and metadata generated by GCCs, PCCs, as well as data generated by other PGDACs and the PTRCs). In this context, outline, as appropriate, unique approaches related to (a) systems biology; (b) pathway analysis; and (c) data integration with visualization. In some instances, results from different analyses may identify the same biological phenomenon and provide bioinformatic “validation”, while in others they will be unique and significant so that the results can be further pursued by the research community.

Provide specific information on approaches and tools for the integration of data sets from the GCC, the PCCs, and the PTRCs. Include plans for identification of differences between tumor and normal tissues in terms of differential metabolic and signaling pathways, the links between such individual pathways, and the entire genomic/proteomic networks.  This type of evaluation should include multiple networks based on experimental and clinical data that may be linked in a manner that identifies cancer-specific proteins/genes and pathways. As appropriate, outline tools to evaluate cause-and-effect relationships between combinations of genes and pathways that may predict biological outcomes.  In addition, methods for the identification of control points within pathways or multiple pathways that correlate to any of the proteogenomic data would be relevant to this FOA. As this FOA is not limited to pathway and proteogenomic networks, applicants are encouraged to also propose other methods that could fulfill these requirements or methods that provide a unique analytical capability useful in the identification of biological mechanisms and/or protein targets for prevention, detection, or therapeutic applications.

Integrated data and their interpretation should be available in reports formatted for ease of visualization and to simplify the meaning of the data for use by non-bioinformatic end users.

It is anticipated that the PGDACs will perform analysis of CPTAC Network data as required to support CPTAC process improvements, and publications and presentations from CPTAC.  It is also expected that the PGDAC will provide statistical and analytical confirmation of relevant discoveries as appropriate based on the type of analysis performed and data generated.

PGDAC applicants should include a provision to write small software applications to wrap the data or to bridge functional gaps in the CPTAC-wide, comprehensive analysis pipeline. However, this would be a minor part of their function. The DCC will also aid in ensuring compatibility between different elements of the pipeline. 

PGDACs applicants should propose timelines and implement pipelines to analyze data generated by the GCC and the PCCs, and PTRCs. The analyses will summarize data across samples and will integrate clinical data with multiple genomic data types.  The goals of the PGDACs' analyses are to discover molecularly defined disease subtypes and therapeutic targets or diagnostic markers, identify recurrently cancer-related proteogenomic regions and cancer-related pathways, and construct models of oncogenic processes. The PGDAC pipelines will produce data that is structured and formatted. PGDACs are expected to utilize those formats already standardized by the CPTAC DCC, with extensions as needed.

Sub-Section C. Computational tool development

Tools should be targeted for the evaluation of CPTAC data sets (to include clinical data), capable of analyzing these data sets in a standardized format. The analytic pipeline needs to be sufficiently flexible to analyze data for each tumor type and across different tumor types. Tools may include systems biology approaches, data integration with visualization, integrated pathway analysis methods or other approaches that increase the ability to interpret CPTAC data at biologically and clinically relevant levels.

Novel tool development may be proposed to functionally integrate or link existing tools or types of outputs. However, tool development is not the primary goal of this FOA.

Tools may be targeted for the evaluation of cancer-type data sets as well as pan-cancer-type data sets, capable of analyzing these data sets in a standardized format.  Each PGDAC will develop a user manual which will be disseminated through the DCC.

Provide plans to improve overall performance of analysis tools during the project term and implement them into the project after validation. These improvements could include optimization of sensitivity and resolution in the detection of cancer-associated genomic and/or epigenomic and/or transcriptome and/or proteomic alterations, with specific emphasis on enhancing analysis throughput.

Applicants should propose algorithms and bioinformatics tools that are suitable for the integration of large sets of proteogenomic 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. The proposed approaches and bioinformatics tools will be shared among the PGDACs and the entire CPTAC. Upon validation, these tools will be made publicly available as an additional resource to the scientific community.

Integrated Analysis Pipeline: Applicants should outline their plans for the development of computational tools. The plans should specify the length of time required to develop the analysis pipeline as well as all relevant information regarding the development process such as: 1) steps in the development process, 2) types of data required for development and analysis, 3) length of time to complete the integrated analysis through the pipeline, 4) the plan for the integration of analysis results into disease-relevant conclusions, 5) expected types of data and reports generated by the pipeline, 6) collaborations and analysis resources required to align the required tools into an analysis pipeline, and 7) any other information relevant to the development of an analysis pipeline.

PGDACs will need to be able to adjust to new data types.  PGDACs focused on analysis will also address improvements in their analytical pipeline to increase the efficiency of analysis, adopt better algorithms and to be able to include other data types beyond those currently being generated.  The scope, quality, coverage, etc. of the data are very different and modifications will be needed.

Sub-Section D. Biomarker candidate identification

PGDAC applicants should specify their strategy for identifying biomarker candidates from CPTAC data.  Each PGDAC is to utilize or develop integrative tools/methods which analyze GCC, PCC, PTRC, and PGDAC generated data to identify cancer-related molecular alterations. These tools/methods may be applied to normalized data obtained from the DCC. This analysis should select specific proteomic and/or genomic regions of interest for further investigation by targeted proteomic assays (to be carried out by other sub-programs of CPTAC).  Each PGDAC will work with the Protein Candidate Selection Subcommittee to refine the CPTAC-wide candidate list for protein assay development (see Section VI.2)

Resource Sharing Plan: Individuals are required to comply with the instructions for the Resource Sharing Plans as provided in the SF424 (R&R) Application Guide, with the following modifications.

  • All applications, regardless of the amount of direct costs requested for any one year, should address a Data Sharing Plan.
  • Data Sharing Plan should be consistent with accomplishing the goals of the CPTAC program. Specifically:
  • Data Sharing Plan should acknowledge that all PGDAC awardees will be required to upload all of their data to the CPTAC DCC during the five-year funding period.
  • The plan should specify how and when data and algorithms will be released and shared. The sharing timing and frequency are expected to be consistent with achieving the goals of CPTAC (such as submitting all data to the CPTAC DCC within 30-60 days after completion of data generation and Level 1 data analysis, to become publicly available after appropriate Quality Assurance as determined by the CPTAC Steering Committee), and with NIH data sharing guidelines.
  • The plan should also adhere to the general proteomic data sharing principles established such as in the Amsterdam Principles for mass spectrometry (http://proteomics.cancer.gov/resources/opendatapolicy) or an equivalent set of principles for other technologies/platforms.
  • The plan should include a description of the criteria for data evaluation, submission, and storage. Applicants should describe briefly the format of the datasets, the documentation to be provided, and any analytic tools provided.  However, they must also acknowledge that a uniform data reporting standard may be implemented across the PGDAC network.  A reporting system should allow for performance evaluation, optimization, and should facilitate data mining as part of an integrated bioinformatics infrastructure.
  • The plan should assume that, similar to TCGA and other programs, CPTAC data will be subject to a period of embargo (https://cptac-data-portal.georgetown.edu/cptac/aboutData/disclaimer).
  • Other Resources Sharing: Consistent with achieving the goals of this program, all resources generated by the PGDACs (e.g., SOPs, workflows, software) will promptly become available through a CPTAC Public Resource (CPTAC Data Portal, Assay Portal and Antibody Portal; http://protoemics.cancer.gov). It is anticipated that other distribution avenues will be made available by the NCI if determined to be necessary. Resource sharing plans would be expected to describe the type(s) of resources that will become available through the proposed center.
  • Note that the NCI Program Staff may negotiate modifications to these plans prior to funding.
  • CPTAC Intellectual Property Policy: Consistent with achieving the goals of this program and maximizing the benefit of all research funded as part of the CPTAC program for the improvement of public health through discoveries of the scientific community, CPTAC Data Sharing and Data Release policies expect a broad freedom-to-operate for all users of CPTAC data (e.g., by rapidly placing all data in the public domain). In addition, computer algorithms produced specifically to analyze CPTAC data, software source code or other resources (reagents) made possible under the auspices of CPTAC are expected to be made broadly available. It is expected that any data producer in the PGDACs will make all information available, without requirement for licensing, for applications such as, but not necessarily limited to, the use of markers in developing assays or targets for therapeutic and diagnostic purposes. All PGDAC members and affiliated institutions must acknowledge agreement to the CPTAC Intellectual Property Policy. Investigators and their institutions must expressly acknowledge and agree to abide by this policy.

Appendix:  Do not use the Appendix to circumvent page limits. Follow all instructions for the Appendix as described in the SF424 (R&R) Application Guide.

Planned Enrollment Report

When conducting clinical research, follow all instructions for completing Planned Enrollment Reports as described in the SF424 (R&R) Application Guide. 

PHS 398 Cumulative Inclusion Enrollment Report

When conducting clinical research, follow all instructions for completing Cumulative Inclusion Enrollment Report as described in the SF424 (R&R) Application Guide.

3. Submission Dates and Times

See Part I. Section III.1 for information regarding the requirements for obtaining a Dun and Bradstreet Universal Numbering System (DUNS) Number and for completing and maintaining an active System for Award Management (SAM) registration. Part I. Overview Information contains information about Key Dates. Applicants are encouraged to submit applications before the due date to ensure they have time to make any application corrections that might be necessary for successful submission.

Organizations must submit applications to Grants.gov (the online portal to find and apply for grants across all Federal agencies). Applicants must then complete the submission process by tracking the status of the application in the eRA Commons, NIH’s electronic system for grants administration. NIH and Grants.gov systems check the application against many of the application instructions upon submission. Errors must be corrected and a changed/corrected application must be submitted to Grants.gov on or before the application due date.  If a Changed/Corrected application is submitted after the deadline, the application will be considered late.

Applicants are responsible for viewing their application before the due date in the eRA Commons to ensure accurate and successful submission.

Information on the submission process and a definition of on-time submission are provided in the SF424 (R&R) Application Guide.

4. Intergovernmental Review (E.O. 12372)

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.

Pre-award costs are allowable only as described in the NIH Grants Policy Statement.

6. Other Submission Requirements and Information

Applications must be submitted electronically following the instructions described in the SF424 (R&R) Application Guide.  Paper applications will not be accepted.

Applicants must complete all required registrations before the application due date. Section III. Eligibility Information contains information about registration.

For assistance with your electronic application or for more information on the electronic submission process, visit Applying Electronically. If you encounter a system issue beyond your control that threatens your ability to complete the submission process on-time, you must follow the Guidelines for Applicants Experiencing System Issues.

Important reminders:

All PD(s)/PI(s) must include their eRA Commons ID in the Credential field of the Senior/Key Person Profile Component of the SF424(R&R) Application Package. Failure to register in the Commons and to include a valid PD/PI Commons ID in the credential field will prevent the successful submission of an electronic application to NIH. See Section III of this FOA for information on registration requirements.

The applicant organization must ensure that the DUNS number it provides on the application is the same number used in the organization’s profile in the eRA Commons and for the System for Award Management. Additional information may be found in the SF424 (R&R) Application Guide.

See more tips for avoiding common errors.

Upon receipt, applications will be evaluated for completeness and compliance with application instructions by the Center for Scientific Review and responsiveness by NCI, NIH. Applications that are incomplete, non-compliant and/or nonresponsive will not be reviewed.

Post Submission Materials

Applicants are required to follow the instructions for post-submission materials, as described in NOT-OD-13-030.

Section V. Application Review Information

Important Update: See NOT-OD-16-006 for updated review language for applications for due dates on or after January 25, 2016.

1. Criteria

Only the review criteria described below will be considered in the review process. As part of the NIH mission, all applications submitted to the NIH in support of biomedical and behavioral research are evaluated for scientific and technical merit through the NIH peer review system.

For this particular announcement, note the following:

In determining the merit of applications, reviewers will assess the applicants' capabilities and plans in terms of the stated scientific, technological, and organizational requirements..

Overall Impact

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

Scored Review Criteria

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

Significance

Does the PGDAC address an important problem or a critical barrier to progress in the field? If the aims of the PGDAC are achieved, how will scientific knowledge, technical capability, and/or clinical practice be improved? How will successful completion of the aims change the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field?

Specific to this FOA:

How will the proposed activities significantly advance the knowledge of cancer cell complexities at the proteogenomic level?  How strong is the rationale that the PGDAC, as proposed, will contribute meaningfully to improved understanding of fundamental issues relevant to cancer biology?

Investigator(s)

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

Specific to this FOA:

How strong is the applicant team in terms of expertise in computational systems biology and pathway mapping capabilities? How adequate is the applicant's experience in terms of management and analysis of proteogenomic data from other institutions? How productive were the applicants in terms of the timeliness of the development, implementation, and completion of recently conducted bioinformatics research using proteogenomic data, if applicable?

Innovation

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

Specific to this FOA:

How innovative is the application in terms of processing and integrating proteogenomic data in the context of disease-relevant associations?

Approach

Are the overall strategy, methodology, and analyses well-reasoned and appropriate to accomplish the specific aims of the PGDAC? Are potential problems, alternative strategies, and benchmarks for success presented? If the PGDAC is in the early stages of development, will the strategy establish feasibility and will particularly risky aspects be managed?

Specific to this FOA:

How clear is the outlined path to ensure successful accomplishment of the specific objectives of the PGDAC (including computational tool development, analysis of CPTAC data, and identification of candidates for targeted protein assays) ? How well will the analytical approaches, data analysis methods and tools, and quality control measures yield reliable and meaningful results for the goals set in this FOA? Has sufficient evidence been provided to indicate that the applicant team can reach the specific data analysis goals during the first 3-6 months of the project to include a design document for novel analytical methods and the ability to analyze CPTAC data?

How well does the applicant's plan for the construction and sharing of analytical pipelines address the CPTAC goals? How likely is the the applicant's approach to identify clinically relevant and biologically important biomarker candidates?

How strong is the potential of the applicants for team science approaches to developing and implementing PGDAC research studies?  To what degree will the proposed PGDAC be able to participate in inter- and trans-disciplinary team-based research efforts, including potential for interactions with investigators from other sub-programs, other NCI-sponsored programs, and NCI staff members?

If the PGDAC involves human subjects and/or NIH-defined clinical research, are the plans to address 1) the protection of human subjects from research risks, and 2) inclusion (or exclusion) of individuals on the basis of sex/gender, race, and ethnicity, as well as the inclusion or exclusion of children, justified in terms of the scientific goals and research strategy proposed?

Environment

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

Specific to this FOA:

To what extent are the proposed leadership and governance structure, decision-making processes, and interactions among key investigators optimal for coordinating activities related to the PGDAC across the various disciplines and institutions?

Additional Review Criteria

As applicable for the PGDAC proposed, reviewers will evaluate the following additional items while determining scientific and technical merit, and in providing an overall impact score, but will not give separate scores for these items.

Protections for Human Subjects

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

For research that involves human subjects and meets the criteria for one or more of the six categories of research that are exempt under 45 CFR Part 46, the committee will evaluate: 1) the justification for the exemption, 2) human subjects involvement and characteristics, and 3) sources of materials. For additional information on review of the Human Subjects section, please refer to the Guidelines for the Review of Human Subjects.

Inclusion of Women, Minorities, and Children 

When the proposed project involves human subjects and/or NIH-defined clinical research, the committee will evaluate the proposed plans for the inclusion (or exclusion) of individuals on the basis of sex/gender, race, and ethnicity, as well as the inclusion (or exclusion) of children to determine if it is justified in terms of the scientific goals and research strategy proposed. For additional information on review of the Inclusion section, please refer to the Guidelines for the Review of Inclusion in Clinical Research.

Vertebrate Animals

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

Biohazards

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

Resubmissions

Not Applicable

Renewals

Not Applicable

Revisions

Not Applicable

Additional Review Considerations

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

Applications from Foreign Organizations

Not Applicable.

Select Agent Research

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

Resource Sharing Plans

Reviewers will comment on whether the following Resource Sharing Plans, or the rationale for not sharing the following types of resources, are reasonable: 1) Data Sharing Plan; 2) Sharing Model Organisms; and 3) Genomic Wide Association Studies (GWAS) /Genomic Data Sharing Plan.

Reviewers will also assess whether the proposed plans for sharing and disseminating data and tools generated by the PCCs are sufficient and consistent with the stated requirements.

Budget and Period of Support

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

2. Review and Selection Process

Applications will be evaluated for scientific and technical merit by (an) appropriate Scientific Review Group(s) convened by the NCI, in accordance with NIH peer review policy and procedures, using the stated review criteria. Assignment to a Scientific Review Group will be shown in the eRA Commons.

As part of the scientific peer review, all applications:

  • May undergo a selection process in which only those applications deemed to have the highest scientific and technical merit (generally the top half of applications under review) will be discussed and assigned an overall impact score.
  • Will receive a written critique.

Appeals of initial peer review will not be accepted for applications submitted in response to this FOA.

Applications will be assigned on the basis of established PHS referral guidelines to the appropriate NIH Institute or Center. Applications will compete for available funds with all other recommended applications submitted in response to this FOA. Following initial peer review, recommended applications will receive a second level of review by the National Cancer Advisory Board. The following will be considered in making funding decisions:

  • Scientific and technical merit of the proposed project as determined by scientific peer review.
  • Availability of funds.
  • Relevance of the proposed project to program priorities.
3. Anticipated Announcement and Award Dates

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

Information regarding the disposition of applications is available in the NIH Grants Policy Statement.

Section VI. Award Administration Information
1. Award Notices

If the application is under consideration for funding, NIH will request "just-in-time" information from the applicant as described in the NIH Grants Policy Statement.

A formal notification in the form of a Notice of Award (NoA) will be provided to the applicant organization for successful applications. The NoA signed by the grants management officer is the authorizing document and will be sent via email to the grantee’s business official.

Awardees must comply with any funding restrictions described in Section IV.5. Funding Restrictions. 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.

Any application awarded in response to this FOA will be subject to terms and conditions found on the Award Conditions and Information for NIH Grants website.  This includes any recent legislation and policy applicable to awards that is highlighted on this website.

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  and Part II: Terms and Conditions of NIH Grant Awards, Subpart B: Terms and Conditions for Specific Types of Grants, Grantees, and Activities. More information is provided at Award Conditions and Information for NIH Grants.

Cooperative Agreement Terms and Conditions of Award

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

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

Each PD(s)/PI(s) will have the primary responsibility for:

  • Overseeing, directing, and coordinating scientific and administrative activities of the PGDAC;
  • Defining research goals, determining and/or approving experimental approaches, and setting project milestones and timelines;
  • Overseeing the conduct of research at the PGDAC, including such aspects as: experimental activities, data collection, quality control, interim data and safety monitoring, final data analysis and interpretation, and preparation of results for publications;
  • Ensuring the timely sharing of PGDAC-generated data across the PGDAC and the entire CPTAC program through CPTAC DCC as appropriate;
  • Participating in the activities of the CPTAC Steering Committee as voting members;
  • Accepting and implementing all scientific and policy recommendations approved by the CPTAC Steering Committee to the extent consistent with applicable grant regulations;
  • Committing an effort to the PGDAC of at least 2.4 person-months;
  • Preparing for annual administrative site visits by NCI Program Staff;
  • Providing other information as might be requested by Project Scientist (e.g., on annual Center milestones, goals for throughput, procedures, etc.)
  • Monitoring the completion of established goals and benchmarks within the timeframe and budget proposed;
  • Submitting a list of prioritized discovered high-priority protein targets for consideration by the Protein Candidate Selection Subcommittee for subsequent confirmatory studies;
  • Coordinating and encouraging inter-network collaborations;
  • Participating in the semi-annual PD/PI meeting organized by NCI;
  • Ensuring that proper process management methods are executed for planning, monitoring, and managing the workload over the award period, and are expected to provide update reports to NCI Program Staff upon request.

Awardees will be expected to participate in an external evaluation process of the CPTAC program coordinated by NCI Program Staff.

Investigators from each PGDAC award will be expected to participate in various task-oriented working groups together with members from other CPTAC sub-programs that might be formed, as needed, e.g., as subcommittees of the CPTAC Steering Committee.

The primary PGDAC awardee institution and all other institutions participating in a given PGDAC must agree to share and release results, data, research materials, and any other resources necessary and relevant to the PGDAC’s award as appropriate. Awardees will retain custody of and have primary rights to the data and the software developed under these awards, subject to Government rights of access consistent with current HHS, PHS, and NIH policies.

NIH staff has substantial programmatic involvement that is above and beyond the normal stewardship role in awards, as described below:

Designated NCI Program Staff members will have substantial programmatic involvement as Project Scientists. Specifically, the NCI Project Scientists will:

  • Serve as voting members of the CPTAC Steering Committee and its subcommittees as appropriate;
  • In collaboration with the PDs/PIs and the CPTAC Steering Committee, ensure the CPTAC network functions as a unified whole to achieve the goals of the program;
  • Coordinate collaborative research efforts that involve multiple PCCs, PGDACs and PTRCs when necessary;
  • Monitor the operations of the CPTAC program and make recommendations on overall project directions and allocations of project funds;
  • Assist in avoiding unwarranted duplications of effort across the CPTAC awardees;
  • Review the progress of individual CPTAC awardees and specific activities shared among the awardees;
  • Assist the awardees as a resource in stimulating their broader interaction with other NCI and NIH programs to disseminate results and outcomes from the CPTAC program and effectively leverage existing NIH/NCI resources and infrastructures;
  • Coordinate the supply of specimens and reagents for analyses by the CPTAC program through the CPTAC Research Resources whenever applicable;
  • Co-organize and participate in the semi-annual meeting of CPTAC investigators;
  • Ensure the availability of data and related resources developed during the course of the CPTAC program to the scientific community at large;
  • Participate in data analyses, interpretations, and co-authorship of CPTAC publications as appropriate and jointly agreed through the CPTAC Steering Committee.
  • Ensuring that decisions, recommendations, and policies of the CPTAC Steering Committee are consistent with applicable grant regulations.

Areas of Joint Responsibility include:

CPTAC Steering Committee. CPTAC Steering Committee will serve as the primary governing body of the CPTAC program. The Committee will be jointly established by all the awarded PDs/PIs of the PCCs, the PGDACs, the PTRCs and the NCI Program Staff members. The CPTAC Steering Committee will provide strategic coordination for the activities of the PCC network and the CPTAC program overall.

Voting members of the CPTAC Steering Committee will include:

  • One representative from each PCC;
  • One representative from each PGDAC;
  • One representative from each PTRC; and
  • One representative from the NCI Office of Cancer Clinical Proteomics Research.

The CPTAC Steering Committee will elect three representatives (one each from the PCC sub-program, PGDAC sub-program, and PTRC sub-program) as its co-chairs (or alternating chairs) for a pre-determined length of time).

Non-Voting Members:

  • Additional representatives from other NCI-supported research resources serving CPTAC may also participate as non-voting members and as determined by the CPTAC Steering Committee.
  • The CPTAC Steering Committee may decide to add other non-voting members as needed, e.g., to provide specific scientific expertise and/or to include patient advocates.

CPTAC Steering Committee:

  • CPTAC Steering Committee will establish a Protein Selection Subcommittee (see below).
  • CPTAC Steering Committee may also establish other subcommittees as it deems appropriate.

It is anticipated that the CPTAC Steering Committee will formulate strategic decisions and policies for consortium-wide activities. The CPTAC awardees will be required to accept and implement these decisions and policies to the extent consistent with applicable grant regulations.

The activities of the CPTAC Steering Committee are expected to include the following:

  • Establishing operational guidelines and policies to meet the goals of the CPTAC network and monitor the implementation of these guidelines and policies;
  • Reviewing progress of the CPTAC sub-programs on a regular basis;
  • Developing quality assurance goals for all network functions, specimens, technology and data for the CPTAC network;
  • Following-up on action items from the CPTAC Steering Committee in a timely fashion;
  • Approving recommendations and development plans from the Protein Candidate Selection Subcommittee (see below);
  • Prioritizing and recommending pilot studies for execution;
  • Organizing semi-annual meetings of CPTAC investigators;
  • Coordinating the development of a standard data reporting system by the CPTAC Steering Committee (e.g., updating the reporting system currently used in CPTAC);
  • Developing operating guidelines, quality control procedures, and consistent policies for the CPTAC network.

Protein Candidate Selection Subcommittee. The members of the Protein Candidate Selection Subcommittee will include a set number of members of the CPTAC Steering Committee (or their nominees); NIH/NCI Program Staff members; and additional scientific experts as deemed necessary by the committee.

The activities of the Protein Candidate Selection Subcommittee will include the following:

  • Consolidating the lists of prioritized proteins from each CPTAC sub-program’s inventory and prioritization process, including reviewing scientific justifications for developing multiple targeted proteomic assays against the same protein originating from a given "parent gene," such as its protein variants, modified forms, etc.
  • Recommending a biological- and clinical-based selection of protein candidates for clinical research studies;
  • Recommending reagents and specimens to be used for the selected protein candidates.

Recommendations by the Protein Candidate Selection Subcommittee will be reviewed and approved by the CPTAC Steering Committee.

CPTAC External Scientific Panel. The CPTAC Steering Committee will establish a panel of external experts (i.e., individuals with appropriate expertise who are NOT affiliated with any of the CPTAC awardees). The primary role of the External Scientific Panel will be to provide independent assessment of research directions and progress of the CPTAC awardees. The External Scientific Panel will annually evaluate research conducted by the CPTAC members, including the review of the overall program metrics, progress of individual awardees, strategic plans, etc. The panel may also recommend to the Steering Committee new research opportunities to explore, adjustments in priorities, and/or approaches as well as other steps/actions to advance the overall CPTAC goals.

Dispute Resolution Process:

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

3. Reporting

When multiple years are involved, awardees will be required to submit the Research Performance Progress Report (RPPR) annually and financial statements as required in the NIH Grants Policy Statement. In addition to the annual RPPR, a detailed interim Center progress report will be required once a year. This report should be submitted directly to the NCI Project Scientist. The interim report will be required to be formatted following standardized guidelines developed by the NCI Program Staff and may be changed according to programmatic needs based on discussions among the CPTAC Steering Committee members.

A final progress report, invention statement, and the expenditure data portion of the Federal Financial Report are required for closeout of an award, as described in the NIH Grants Policy Statement.

The Federal Funding Accountability and Transparency Act of 2006 (Transparency Act), includes a requirement for awardees of Federal grants to report information about first-tier subawards and executive compensation under Federal assistance awards issued in FY2011 or later.  All awardees of applicable NIH grants and cooperative agreements are required to report to the Federal Subaward Reporting System (FSRS) available at www.fsrs.gov on all subawards over $25,000.  See the NIH Grants Policy Statement for additional information on this reporting requirement.

Section VII. Agency Contacts

We encourage inquiries concerning this funding opportunity and welcome the opportunity to answer questions from potential applicants.

Application Submission Contacts

eRA Commons Help Desk (Questions regarding eRA Commons registration, submitting and tracking an application, documenting system problems that threaten submission by the due date, post submission issues)
Finding Help Online: http://grants.nih.gov/support/ (preferred method of contact)
Telephone: 301-402-7469 or 866-504-9552 (Toll Free)

Grants.gov Customer Support (Questions regarding Grants.gov registration and submission, downloading forms and application packages)
Contact CenterTelephone: 800-518-4726
Web ticketing system: https://grants-portal.psc.gov/ContactUs.aspx
Email: support@grants.gov

GrantsInfo (Questions regarding application instructions and process, finding NIH grant resources)
Email: GrantsInfo@nih.gov (preferred method of contact)
Telephone: 301-435-0714

Scientific/Research Contact(s)

For general aspects of the entire Clinical Proteomic Tumor Analysis Consortium, contact:

Henry Rodriguez, MS, PhD, MBA
National Cancer Institute (NCI)
Telephone: 301-451-8883
Email: rodriguezh@mail.nih.gov

For issues pertaining specifically to Proteogenomic Data Analysis Centers, contact:

Chris Kinsinger, PhD
National Cancer Institute (NCI)
Telephone: 301-451-8883
Email: kinsingc@mail.nih.gov

Peer Review Contact(s)

NCI Referral Officer
National Cancer Institute (NCI)
Telephone: 240-276-6390
Email: ncirefof@dea.nci.nih.gov

Financial/Grants Management Contact(s)

Metema Nyankale
National Cancer Institute (NCI)
Telephone: 240-276-5987
Email: nyankalem@mail.nih.gov

Section VIII. Other Information

Recently issued trans-NIH policy notices may affect your application submission. A full list of policy notices published by NIH is provided in the NIH Guide for Grants and Contracts. All awards are subject to the terms and conditions, cost principles, and other considerations described in the NIH Grants Policy Statement.

Authority and Regulations

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 Part 52 and 45 CFR Part 75.

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