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Reissuance of Clinical Proteomic Tumor Analysis Consortium

Type: 
Notice
Expiration Date: 
Wednesday, June 30, 2021

The National Cancer Institute is soliciting applications for the reissuance of its Clinical Proteomic Tumor Analysis Consortium (CPTAC). This re-issuance seeks to continue building on the current achievements in clinical cancer proteogenomics discoveries and infrastructure to accelerate molecularly oriented cancer research toward basic discovery and clinical impact. FOAs are open to all qualified applicants regardless of whether or not they participated in the previous issuance of the CPTAC program.

Proteome Characterization Centers (PCCs) for Clinical Proteomic Tumor Analysis Consortium (Clinical Trial Not Allowed)
Announcement Number: RFA-CA-21-023
Letter of Intent Due Date: 30 days prior to application due date
Application Due Date: June 30, 2021
Activity Code: U24, Resource-Related Research Projects - Cooperative Agreements

Proteogenomic Data Analysis Centers (PGDACs) for Clinical Proteomic Tumor Analysis Consortium (Clinical Trial Not Allowed)
Announcement Number: RFA-CA-21-024
Letter of Intent Due Date: 30 days prior to application due date
Application Due Date: June 30, 2021
Activity Code: U24, Resource-Related Research Projects - Cooperative Agreements

Proteogenomic Translational Research Centers (PTRCs) for Clinical Proteomic Tumor Analysis Consortium (Clinical Trial Not Allowed)
Announcement Number: RFA-CA-21-025
Letter of Intent Due Date: 30 days prior to application due date
Application Due Date: July 30, 2021
Activity Code: U01, Research Project - Cooperative Agreements



NOT-CA-21-072: Pre-Application Webinar for the Clinical Proteomic Tumor Analysis Consortium (CPTAC) -- RFA-CA-21-023, RFA-CA-21-024, and RFA-CA-21-025

The NCI will conduct a pre-application webinar on Monday, May 17, 2021, from 11:30am - 1:30pm (ET) for the following Funding Opportunity Announcements (FOAs): Proteome Characterization Centers (PCCs), Proteogenomic Data Analysis Centers (PGDACs), and Proteogenomic Translational Research Centers (PTRCs). NCI program staff involved in these FOAs will provide orientation to potential applicants by explaining the goals and objectives for the FOAs. The webinar will conclude with a final, open online question and answer session, with program staff available to answer questions. Pre-registration is required to participate in the webinar. Learn more about NOT-CA-21-072 at here.

Watch the webinar at here!

Presentation slides at here.



Frequently Asked Questions

RFA-CA-21-023 (PCCs)

Question 1. What human cancer types are to be characterized by the PCCs/PGDACs in the tumor characterization program?
Answer. PCCs and PGDACs are to be agnostic to the human cancer types to be characterized/analyzed in the tumor characterization program. Specific cancer types will be made available at the time of award.

Question 2. Would applicants who may have access to biospecimens be allowed to use these samples (in addition to NCI ­supplied samples) in the generation of data under this RFA? 
Answer. NCI has limited this funding mechanism to NCI-supplied samples. Applications will not be evaluated based on the inclusion and/or sharing of additional applicant-provided samples.

Question 3. What is the purpose and timeline for PCC pilot studies?
Answer. Pilot studies are to improve technologies/platforms used in the primary research objective of the PCC, and are anticipated to have relatively short timeframes, i.e., on a yearly basis or at most two years.

Question 4. Is the total amount of material stated in the RFA (25 mg wet weight) for the human biospecimens supposed to cover both discovery and targeted proteomics on each sample, or will there be separate aliquots of 25 mg provided for each of the two analyses?
Answer. A minimum of 25 mg of wet tissue weight per sample is anticipated for both discovery and targeted proteomics. However, additional sample may be provided for samples which had more than 25 mg collected.

Question 5. Could a PCC application be a stand-alone application, or does it required that the PCC application pre­coordinate with specific PGDAC or PTRC applicants? Additionally could/should the PCC be multi-institution?
Answer. PCC applications are independent of PGDAC and PTRC applications. However, PCC applications should adhere and acknowledge data sharing plan and resource sharing plan required by this FOA. PCC applications can be single or multi­institutional applications as long as it meets the objectives and goals of the program.

Question 6. Under the list of required capabilities it says "Extensive expertise in using a variety of biological sample types, including fresh frozen tissues, formalin fixed tissues, OCT embedded tissues, and liquid biopsies.” Should a PCC demonstrate extensive experience in all of these?
Answer. Applicants are expected to demonstrate expertise in using a  variety of biological sample types, but, as indicated in the Research Objectives: Applicants seeking a PCC award must be able to perform comprehensive characterizations of the proteomic composition of human biospecimens and samples from preclinical models, including fresh frozen, formalin fixed paraffin-embedded and optimal cutting temperature (OCT)-embedded.  For clarification, applicants should describe which sample types they have experience and to what extent the expertise.


RFA-CA-21-024 (PGDACs)

Question 1. What human cancer types are to be characterized by the PCCs/PGDACs in the tumor characterization program?
Answer: PCCs and PGDACs are to be agnostic to the human cancer types to be characterized/analyzed in the tumor characterization program. Specific cancer types will be made available at the time of award.

Question 2. Is it only CPTAC generated data that PGDACs should consider? What about other TCGA datasets or local data?
Answer. PGDACs may integrate other datasets with CPTAC data, but other datasets should not be analyzed to the exclusion of CPTAC data.

Question 3. What is the role of imaging data in CPTAC?
Answer. Integrating proteomic data with imaging data (pathology and radiological images) shall be considered responsive to the RFA.


RFA-CA-21-025 (PTRCs)

Question 1. Does a PTRC have to focus on one tumor type, or can they instead focus on a druggable pathway and study drug response across different tumor sites?
Answer. It is responsive to focus on a druggable pathway and study drug response across different tumor sites.

Question 2. Are applicants allowed to partner with one or more clinical trials?
Answer. Yes.

Question 3. What qualifies as an NCI-supported trial?
Answer. “NCI-Supported” in the context of clinical trials for this FOA means all clinical trials that are funded in full or in part by NCI. This includes all NCI network trials, trials that are supported by NCI grants, and trials at the NIH Clinical Center in Bethesda, Maryland. Clinical trials that are wholly funded by private entities (and in which the data from the clinical trial belong to the private funder) are not considered to be NCI-supported even if such studies are conducted at the NCI-designated Cancer Centers and benefit from the Cancer Center infrastructure.

Question 4. Do all trials with a ClinicalTrials.gov NCT Identifier count as an NCI trial for the clinical arm of the PTRC, or do the trials ALSO have to be annotated (in clinicaltrials.gov) as having NCI listed as the sponsor?
Answer. ClinicalTrials.gov is a database of privately and publicly funded clinical studies conducted around the world. Not all trials with a ClinicalTrials.gov NCT identifier count as an NCI trial for the clinical arm of the PTRC. Please refer FAQ 3; "What qualifies as an NCI-supported trial?"

Question 5. Would an NCI-sponsored intramural trial be permissible for this RFA?
Answer. Yes. NCI intramural trials are responsive to RFA-CA-21-025. Intramural trials are to be coordinated through Dr. William Dahut, Clinical Director of NC l's Center for Cancer Research (dahutw@mail.nih.gov).

Question 6. Can PTRCs be included in the GCC agreements? (from the RFA, “Genomic Characterization Center (GCC) that will genomically characterize the same biospecimens provided by CPTAC to PCCs for proteomic characterization”)
Answer. No. This does not apply to PTRCs. In RFA-CA-21-025 under section [Overall CPTAC structure and functions/ Additional Resources Supported by NCI], it states that the GCC genomically characterize the same biospecimens provided by CPTAC to PCCs for proteomic characterization.

Question 7. Given that it will not be possible to get a commitment of biospecimens from a clinical trial until after the data are generated in the preclinical arm, how should the PTRC applicants describe getting access to clinical trial samples in the Clinical Arm of the grant proposal?
Updated Answer on June 1, 2021. In the section IV, it is stated that "If Applicant is proposing a Preclinical Research Arm, the Letter(s) should state that the proposed research questions are clinically aligned/clinically relevant to trials being conducted and for which appropriate samples (in quality and quantity) may be available." Such a letter does not need to describe secured access of the clinical trial samples if applicants propose to start with Preclinical Research Arm. If applicants propose to start with Clinical Research Arm, evidence of secured access to clinical trial samples is to be provided in the letter.

Question 8. Can NCI intramural investigators participate in RFA-CA-21-025?
Answer. It is allowable for NCI intramural investigators to participate as sub-awardees on RFA-CA-21-025. Please note that any salaries for, expenses of, and/or work done by intramural investigators is to be paid for by the intramural program. Also, intramural investigators cannot be the PI or Contact PI (if multiple PIs) on the application and award.

Question 9. Do PTRCs have to analyze tumor tissues, or can proteogenomics instead be done on a biofluid, for example looking at cell free DNA and proteins?
Answer. “Human cancer sample” refers to archived biopsy or surgical tissue from cancer patients with clinical data including clinical outcome. Focusing solely on biofluids is not responsive.

Question 10. For PTRCs, can the “drug” for which we study response/resistance be a cell-based therapy; in other words, do cell-based therapies qualify as a “drug”?
Answer. Yes, provided they are in NCI-supported trial(s).

Question 11. Are PTRCs to focus only on molecularly targeted "nextgen" cancer therapies, or would conventional chemotherapies, radiation therapy, and/or preventative vaccine trials also be considered responsive?
Answer. With the exception of vaccine cancer prevention trials, all the other aforementioned therapies are considered to be responsive.

Question 12. With respect to chemotherapies, are all of the drugs (conventional and nextgen) listed on the NCI site (http://www.cancer.gov/about-cancer/treatment/drugs) eligible for study by a PTRC?
Answer. Yes, provided they are in NCI-supported trial(s).

Question 13. Are non-NCI-supported trial samples allowed?​
Answer. Non-NCI-supported clinical trials may be used in an auxiliary role.​ However, NCI-supported clinical trial samples are required in Clinical Research Arm.

Question 14. Can a combination of NCI-supported and non-NCI supported clinical trial specimens be used to obtain sufficient sample size?​
Answer. Proposed projects are expected to be conducted in collaboration with clinical researchers and acquire human biospecimens from NCI-supported clinical trials for the Clinical Research Arm. However, as stated in the RFA-CA-21-025, other human biospecimens from non-NCI-supported clinical trials may be used in an auxiliary (supplementary) role. Please note that all PTRC investigators and affiliated institutions/organizations must expressly acknowledge and agree to abide by the CPTAC Intellectual Property Policy. Furthermore, all applicants need to address a Data Sharing Plan that is to be consistent with accomplishing the goals of the CPTAC program.

Question 15. What is being validated in clinical research arm of PTRC?​
Updated Answer on June 1, 2021. PTRCs are to understand molecular mechanisms of drug responses and resistance to therapies in a clinical context. "Validation/clinical validation" in RFA-CA-21-025 refers to approaches that "confirm and extend findings" from the preclinical research arm and continue to elucidate biological mechanisms of response/resistance using clinical trial samples.

Question 16. Who should provide the Letter(s) of Support for clinical trial sample availability and/or access?​
Answer. The Letter(s) of Support comes from clinical trial leadership. For the NCTN Groups, the principal investigator of the NCTN Operations Center grant is the Group Chair and any Letter(s) of Support must be generated through the Group’s standard operating procedures and come from the senior leadership/Group Chair’s office. The lead investigator(s) of the clinical trial would need to ask for this Letter(s) of Support from the NCTN Group leadership, but the Letter(s) of Support itself would need to come directly from the Group leadership.

Question 17. What information is required in the Letter(s) of Support for clinical trial sample availability and/or access?​
Answer. Letter(s) of Support for clinical trial sample availability and/or access should at least specify 1) Expected number of such specimens and amounts that will be available to the PTRC applicants; 2) Timing of the availability; 3) Specimen nature; and 4) Types of accompanying data. If applicant is proposing to start at the clinical research arm, letter should also indicate evidence of secured access to the clinical trial samples. For more information, please refer to Section IV of RFA-CA-21-025 and its related FAQ #7 and #16. Please note that Letter(s) of Support is not a component in review criteria for RFA-CA-21-025.

Question 18. Is Statistical Analysis Plan required for an applicant proposing to start at Preclinical Research Arm?​
Answer. No. The Statistical Analysis Plan is required for applicants proposing to start at Clinical Research Arm.

Question 19. What is meant by "genomic characterization which meets TCGA or equivalent platform and data quality standards"?​
Answer. This statement refers to quality of molecular data that is comparable, for each cancer type, to the corresponding molecular data generated by TCGA comprehensive genomic profiling studies. TCGA marker publications are found here.