Solicitation for NCI Genomic Characterization Centers

Amendment No.: 1 to RFP N02CO87001-94 Date of Issuance: 12/20/2018 The above numbered Request For Proposal (RFP) is amended as set forth below. The hour and date specified for receipt of offers remains unchanged: 3/18/2019 at 4:00 PM Wash. DC local prevailing time. Offerors MUST acknowledge receipt of the amendment prior to the hour and the date specified in the solicitation or as amended, by separate letter, telegram, or email which includes a reference to the RFP and Amendment number. For your convenience, the Proposal Intent Response Form is provided in SECTION J - List of Attachments of this RFP, for this purpose. FAILURE OF YOUR ACKNOWLEDGMENT TO BE RECEIVED AT THE PLACE DESIGNATED FOR THE RECEIPT OF OFFERORS PRIOR TO THE HOUR AND DATE SPECIFIED MAY RESULT IN REJECTION OF YOUR OFFER. This Amendment provides responses to questions received under RFP N02CO87001-94: Note of clarification: Indefinite Delivery, Indefinite Quantity (IDIQ) contracts are used when the Government cannot determine the precise quantities of products or services that will be required during the contract period of performance. Under this particular requirement the base awards will be for a five-year period of performance. Once the quantity of supplies/services are determined, a Task Order (TO) for services will be competed in their respective (DNA, RNA or Protein) pools and a TO award will be made after an evaluation of the proposals received. For this RFP N02CO87001-94 please provide separate responses to the Base SOW AND all of the TO SOWs (DNA, RNA or Protein) pools for which your firm would like to be considered for an award. Question 1: Article B.2. Prices/Costs says maximum of $49,832,452 for successful performance of the contract. Is that the maximum budget amount that can be requested; and, is it for one task order or all three; and, is that including indirect costs? Answer: Under Article B.2. Prices/Costs the $49,832,452 is the maximum dollar/ceiling amount (inclusive of indirect costs) for all potential task order awards made under all contract awards resulting from this solicitation for Indefinite Delivery Indefinite Quantity (IDIQ) type contracts. As noted in the Additional Business Proposal Instructions, proposed fixed per-unit prices shall include all direct and indirect costs. Question 2: On page 57 item #4 Small Business Subcontracting Plan states "if the proposed contract exceeds a total estimated cost of $700K for the entire period of performance, the offeror shall be required to submit an acceptable subcontracting plan..." - Is that $700K for one task order or total for all 3, including indirect costs? Answer: Any contracts awarded under this RFP will have a ceiling amount of $49,832,452, which exceeds the $700K subcontracting plan threshold. Therefore, offerors (except for small businesses) must submit a subcontracting plan with their proposal submission that uses the ceiling amount as the total estimated cost of the contract. Question 3: Can a non-US organization apply for this RFP? Answer: Yes, a non-US organization may submit a proposal under this Request for Proposal (RFP) if they can perform all tasks within the statement(s) of work. Question 4: The question came up about whether there is any notion of what kind of output would be needed. I know there is a reference in the RFP to having a capacity for 100 genomes per month, but the actual contracts could be for far less, correct? Answer: Correct. No minimum volume is guaranteed by the base contract or any individual task order. Actual amount of work load may be more or less than the minimum capacity for 100 genomes per month. Question 5: What is the source for tumors? Answer: All tumor or normal samples are of human origin. Question 6: The RFA lists Baylor as a current contract through 8/19 - what is this for? Answer: The Request for Proposal (RFP) N02CO87001-94 lists Baylor as the incumbent currently performing work under a subcontract from Leidos Biomedical Research which is the current prime contract holder for this requirement. This arrangement is not being replicated; contracts awarded as a result of this RFP will not be subcontracts under the Leidos contract. (It also should be noted that this requirement is a RFP which would result in a contract award; RFA is a Request for Application and is used only for grant awards.) Question 7: The scope looks like DNA, RNA and protein are covered in the RFA, perhaps a call might be helpful. Answer: This is a Request for Proposal (RFP) and phone calls to discuss the tasks under the Statements of work (SOW) are not authorized. Any discussions and or questions related to the NCI's Genomic Characterization Center's project must go through the Office of Acquisitions office and must be in writing. All questions need to be directed to Contracting Officer via email provided under the RFP post. Question 8: The RFP list Baylor University - is this Baylor College of Medicine? Answer: Yes. Question 9: The overall document alludes to the fact that the cancer genomics program at NCI is planning to continue with a number of components, as it has in the past such as the Genome Data Analysis Centers (GDAC). We're wondering whether there is an RFA that is currently posted for the GDAC, or whether this is something that we should expect in the future? We're also hoping to know whether we missed the announcement about GDAC. Answer: This Request for Proposal (RFP) No. N02CO87001-94 is for the NCI's Genomic Characterization Centers (GCCs) project, as specified in the RFP and explains the work to be done under each Statement of Work (SOW). This RFP is for production of genomic data under a contract mechanism. It is not for data analysis such as the Genome Data Analysis Centers (GDAC), which is performed under a separate cooperative agreement grant mechanism. Question 10: For all task order statements of work, the Characterization Platform requirements refer to DNA/RNA/protein "extracted from...samples". Will the GCCs be receiving from the BPC DNA/RNA/protein, or will GCCs receive samples in form of FFPE/Fresh-Frozen/samples of limited size and be required to extract DNA/RNA/protein? Answer: For DNA and RNA sequencing, GCCs will be receiving DNA or RNA molecular analytes from the BPC. For protein characterization, GCC will receive samples relevant to their analysis platforms. Question 11: For the task order statement of work for DNA samples, the Characterization Platform requirements do not list whole genome bisulphite sequencing as one of the platforms. The "Additional Business Proposal Instructions" do list this protocol. Can you provide the performance criteria for whole genome bisulphite sequencing? Answer: The DNA pool SOW has platform "Whole Genome Methylation Sequencing". Offerors should propose relevant methods and parameters to be used. Question 12: For the task order statement of work for RNA samples, the Characterization Platform requirements list FFPE samples, fresh frozen samples, and minimal quantity samples for all three platforms. The "Additional Business Proposal Instructions," only include FFPE and fresh frozen in the pricing table. Can you confirm which sample types will be required for the RNA platforms? Answer: Both FFPE and fresh frozen samples should be considered for pricing. Minimal quantity cases can be from either FFPE or fresh frozen samples. The contract does not ask a pricing on minimal quantity samples, but rather the ability to develop a protocol to deal with those situations. Question 13: The Pricing Table instructions indicate that for protocols where the Number of Cases is 0, it is because the protocol is not required in the "Task Area Statement of Work." Should this read "Task Order Statement of Work?" Assuming yes, the task order DOES list those protocols - please confirm that offerors should provide pricing for all protocols for which they wish to be considered for service, even where the number of cases currently shows 0. Answer: The offeror should provide pricing for all protocols for which they consider providing service, even where the number of cases currently shows 0. Question 14: Can offerors for service for DNA or RNA samples offer only some of the characterization protocols, or must offerors be willing and able to provide service in all platforms and protocols in the statement of work? Answer: Offerors are not required to address all the platforms in the characterization pool Task Order SOW. However, ability to perform multiple platforms listed in a characterization pool Task Order SOW will be considered favorably. Question 15: The task order statement of work lists Whole Genome Sequencing low coverage depth at 15X, but the pricing table includes 15X, 30X, 60X and 80X for both tumor and normal samples. Can you confirm that all coverage options are required for all sample types (FFPE, Fresh-frozen, limited input) for both tumor and normal? Answer: The task order statement of work lists WGS low coverage depth and WGS high coverage depth. Offerors should provide pricing on all services to be provided in the pricing table. Question 16: In the price list table for DNA, the number of cases for the selected platforms is 1,200. Can you confirm whether this is 600 cases, each with a tumor and a normal for a total of 1,200 samples? Or is it 1,200 cases each with a tumor-normal pair, for a total of 2,400 samples? Answer: It is 1,200 cases each with a tumor-normal pair, for a total of 2,400 samples for DNA. Please note that the numbers in pricing table are just estimate for cost calculation. Proposals should not take the numbers as a firm commitment from NCI. Cases may also come with different configuration in specific projects. For example, some may be collections of primary tumors, recurrences, metastasis, while others may be single tumors only. Question 17: For RNA work, please confirm whether the work would be on tumor samples only, or on a tumor-normal pair. Answer: Both situations are possible. In the pricing table, only tumor samples are listed. Question 18: For DNA work, please confirm whether sample type "limited input" is a requirement for deep sequence targeted validation. Answer: "Limited input" is unlikely to be used for deep sequence targeted validation but is possible. Question 19: The characterization pipelines listed in the Attach3BaseIDIQ(allpools) SOW document do not correspond to the numbered lists of characterization platforms listed in the documents Attach5DNApoolSOW and Attach6RNApoolSOW. Section B.2 in Base IDIQ(allpools) for instance, references single cell DNA and single cell RNA sequencing (among other things), neither of which are listed as characterization platforms in the DNA or RNA SOW's. Are we correct in assuming that for either document our application only needs to encompass a subset of the characterization pipelines/platforms within each Task Area of interest? That is, for DNA can we, for instance, apply to perform only WGS, WES and WGMetSeq? Answer: Yes. Offerors do not have to propose on all platforms. We ask for information on new technologies, like single cell sequencing, so that offerors can discuss their capabilities, but we do not ask for a firm fixed unit price for these new technologies. Question 20: I know that NCI intends to award up to 10 contracts, but do you know how many it expects to award for each pool (DNA, RNA, and protein)? Answer: The number of awards made in each pool will depend upon the number and type of qualified proposals received across all pools. Question 21: Is there somewhere online I might find a list of the organizations who have been funded from this program in the past? Answer: This is an existing requirement currently supported through subcontracts that were awarded under the Federally Funded Research and Development Center (FFRDC) contract number HHSN261200800001E, the Frederick National Laboratory for Cancer Research, operated by Leidos Biomedical Research, with a period of performance of 09/26/2008 - 08/30/2019. The contract is entitled "Operations and Technical Support Services at NCI-Frederick" at the FFRDC. Leidos subcontract numbers and periods of performance are listed below: - The Broad Institute of MIT and Harvard = 15X054, 6/24/2015 - 8/30/2019 - MD Anderson Cancer Center = 15X140, 6/19/2015 - 8/30/2019 - University of North Carolina = 16X250, 11/17/2016 - 8/30/2019 - Stanford University = 17X029, 1/1/2017 - 8/30/2019 - Baylor University = 17X184, 10/25/2017 - 8/30/2019