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Frequently Asked Questions

Please select a FAQs category from the list below.

RFA-CA-15-021 - Proteome Characterization Centers (3)

Question: 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. As outlined in the review criteria of the RFA, applications will not be evaluated based on the inclusion and/or sharing of additional applicant-provided samples.

Question: Could a PCC application be a stand-alone application, or does it required that the PCC application pre-coordinate with specific PGDAC or PTRC applicants? Additionally could/should the PCC be multi-university (two or more; i.e. gathering of MS proteomics data across MS cores from different institutions)?
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 multi-institutional applications as long as it meets the objectives and goals of the program.

Question: What is the 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. Short timelines should allow the implementation of multiple improvements into the proteomic characterization pipeline of a grant.

RFA-CA-15-022 - Proteogenomic Translational Research Centers (13)

Question: Are applicants allowed to partner with one or more clinical trials?
Answer: 

Yes, permitting that the PTRC allows for the complete interrogation (data production and analyses) of all samples within the timeline specified in this FOA.

Question: Why only NCI-sponsored trials are allowed?
Answer: 

In order to be assured of access to clinical trial data from studies carried out under RFA-CA-15-022, NCI has limited this funding mechanism to NCI-sponsored trials.

Question: What qualifies as an NCI-sponsored trial?
Answer: 

“NCI-sponsored” in the context of clinical trials means all clinical trials either financially supported by the NCI for any part of research (excluding support for infrastructure and grants for NCI-designated Cancer Centers), or carried out under an NCI-held IND. 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: PTRCs are to focus only on molecularly targeted “nextgen” cancer therapies (e.g. specific monoclonals, TKIs, or specific inhibitor compounds such as PARP), or if conventional chemotherapies (e.g. cisplatinum, Doxorubicin, Fluorouracil), preventative vaccine trials and/or radiation therapy would also be considered responsive?
Answer: 

With the exception of vaccine cancer prevention trials, all the other aforementioned trials are considered to be responsive.

Question: 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 CPTAC PTRC?
Answer: 

Yes, provided they are in a NCI-sponsored trial. In addition, a listing of approved agents for ETCTN trials are referenced in a file located at http://proteomics.cancer.gov/aboutoccpr/fundingopportunities/current/Rei..., under Supporting Documents (File Name: Active ETCTN trials), while additional agents that include investigational agents under NCI’s Cancer Therapy Evaluation Program IND are listed at the following website http://ctep.cancer.gov/protocolDevelopment/agents_drugs.htm (File Name: CTEP Agents and Active Agreements, MS Excel)

Question: Preclinical Research Arm: Is it cell lines or mouse models?
Answer: 

It could be either or both.

Question: Data analysis: To what level of data analysis are required and how this is related to PGDAC analysis?
Answer: 

Data analyses are required for all three levels as defined by all three RFAs. PTRC awards are expected to interact with the PGDAC awardees to coordinate prioritization of protein candidates ultimately approved by the Protein Candidate Selection Sub-committee and the Steering Committee to avoid duplicative efforts for targeted assay development.

Question: The RFA states that only NCI-funded clinical trials are eligible. Is there any chance this requirement can be relaxed if non-NCI clinical samples are available?
Answer: 

No. In order to be assured of access to clinical trial data from studies carried out under RFA-CA-15-022, NCI has limited this funding mechanism to NCI-sponsored trials. “NCI-sponsored” in the context of clinical trials means all clinical trials either financially supported by the NCI for any part of research (excluding support for infrastructure and grants for NCI-designated Cancer Centers), or carried out under an NCI-held IND. 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: In Section IV. 2. PHS398 Research Plan the PTRC RFA mentions drug toxicity, whereas the rest of the RFA only discusses response/resistance. Would a study of mechanisms of toxicity to cancer therapies be considered responsive to this RFA, or only studies of response/resistance?
Answer: 

Yes – mechanisms of toxicity would be responsive.

Question: For the CPTAC-PTRCs, please clarify whether the goal is to identify predictive biomarkers of response/resistance to therapies (requiring rigorous clinical testing and appropriate statistical power), or if the goal is to elucidate biological mechanisms of response/resistance and thereby implicate potential predictive biomarkers that would require downstream clinical validation (beyond the scope of this RFA)? For example, studies focused on early clinical trials could look for potential biomarkers as an exploratory goal, but would not be sufficiently powered to validate the marker(s).
Answer: 

Section 1 of RFA-CA-15-022, states that the “purpose” of PTRCs are to apply standardized state-of-the-art proteomic and genomic approaches to clinically-relevant research projects. Projects should focus on the proteogenomic aspects in understanding drug responses and resistance to therapies in a clinical context. It is envisioned that these projects will facilitate a rational approach to target cancer related pathways and improve outcomes for patients with cancer. Concomitantly, Part 2, Section 1 of the RFA-CA-15-022 (in Research Objectives), it states that PTRCs are to “perform comprehensive proteomic and genomic characterizations in preclinical cancer models and/or clinical specimens in response to therapeutic agents under study using analytically validated, high-throughput technologies/platforms. These characterizations may enable better evaluation of novel targeted therapeutics and identification of predictive biomarkers in early stages of drug development/treatments. Therefore, elucidating biological mechanisms of response/resistance that implicate potential predictive biomarkers that would require downstream clinical validation (beyond the scope of this RFA), would be responsive.

Question: How do we team up with clinicians? Are pathologists considered as a qualified clinician PI?
Answer: 

Yes, as long as the pathologist is familiar with unmet clinical needs, clinical trials, and access to trial samples (see section SF424(R&R) Senior/Key Person Profile). In addition, a FOA Teaming Site at http://proteomics.cancer.gov has been developed to facilitate interactions between proteomicists, genomicists, and clinicians. In addition, applicants are encouraged to contact NCI’s clinical trial point-of-contacts listed in the RFA.

Question: Would an NCI-sponsored intramural trial be permissible for this RFA?
Answer: 

Yes.  NCI intramural trials are responsive to RFA-CA-15-022.  Intramural trials are to be coordinated through Dr. William Dahut, Clinical Director of NCI’s Center for Cancer Research (dahutw@mail.nih.gov)

Question: For PTRCs, please clarify whether in hematological or solid tumor clinical trials, elucidating biological mechanisms of action and/or the proteogenomic analysis of the therapy used (e.g. therapeutic agents) without investigation of individual patients’ tumor is considered responsive?
Answer: 

No.  To be responsive to RFA-CA-15-022, elucidation of biological mechanisms of response/resistance/toxicity of therapeutic agents, whether conventional chemotherapy, targeted therapies (either cell-based, such as CAR T-cell therapy; or non-cell based, such as antibodies, small molecules, etc.), radiation therapy or others, applications are to include proteogenomic analysis of the tumor (solid or liquid sample) from clinical trial patients.  {In the context of this FOA, human specimens refer to individual patient’s tumors/cells from clinical trials and any additional tumors/cells used in an auxiliary role to be analyzed in the Clinical Research Arm}.

RFA-CA-15-023 - Proteogenomic Data Analysis Centers (3)

Question: 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: How closely should applicants connect to “existing” PCCs?
Answer: 

All PCCs must recomplete to become a PCC for CPTAC 3. There is no guarantee that any current CPTAC PCC will again become a CPTAC PCC in the reissuance.

Question: Should proposals be limited to data that is currently supported by CPTAC and TCGA? Specifically - what might the role of image data be?
Answer: 

A de-identified pathology report and pathology analysis of frozen sections will be available for each CPTAC sample. Integrating proteomic data with these and other imaging modalities shall be considered responsive to the RFA.