Solicitation for NCI Genomic Characterization Centers
Amendment No.: 2 to RFP N02CO87001-94
Date of Issuance: 2/15/2019
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.
This Amendment provides responses to questions received under RFP N02CO87001-94:
*Note: Please carefully review the RFP Section L - INSTRUCTIONS, CONDITIONS, AND NOTICES TO OFFERORS, specifically (II. TECHNICAL PROPOSAL) I., II. and III. on page 45 of the RFP with regards to responding to the IDIQ Base Contract SOW and the Task Order SOWs. Attachment 3 is for the Base IDIQ SOW and Attachments 5 - 7 are the DNA, RNA and Protein Task Order SOWs. Please carefully review ALL attachments to the RFP.
Question 1: Is there a posting of the projects the CCG is working on that might give some idea of the type of work to expect?
Answer 1: The CCG website: https://www.cancer.gov/about-nci/organization/ccg/research
Question 2: Is it possible that some projects envisioned by the CCG might want CLIA lab capability?
Answer 2: It is not required for offerors to have capability of CLIA certified service in this RFP.
Question 3: I unfortunately missed the kick off Webinar. Was that recorded and still available?
Answer 3: There was no kick-off webinar for RFP No. N02CO87001-94. Please carefully read the Request for Proposals (RFP) and all attachments, as well as Amendment 1 for complete information.
Question 4: If a small business wishes to submit a proposal, what % of the contract dollars are they allowed to subcontract with another firm - large or small? Since this solicitation is not a set-aside for small business, would subcontracting with large firms be allowed as a small business and if "yes" what are the restrictions? Also, what are the restrictions for small to small business subcontracting?
Answer 4: Please reference FAR Part 52.219-14 Limitations on Subcontracting.
Question 5: How can a small business become part of the subcontracting plan for a large firm that is competing for this solicitation? In other words, if a small business wishes to be included for a larger firm's proposal, is there a way to be considered as a subcontractor to meet their SB and/or WOSB requirements before the contract is awarded?
Answer 5: Please reference FAR Subpart 44.2 - Consent to Subcontracts - a large business would have to competitively select the small business.
Question 6: Are prime contractors required to identify subcontractors (WOSB, HUBzone, 8a etc) and submit the subcontracting agreements along with the proposal or only state the dollar and percentage amounts they plan to subcontract in attachment #16 of this solicitation?
Answer 6: Prime contractors that are not small businesses must submit a Small Business Subcontracting Plan. Please reference the RFP under BUSINESS PROPOSAL INSTRUCTIONS section, subpart "Subcontractors" for specific details when proposing subcontractors and complete Attachment 16.
Question 7: Can foreign entities be subcontractors for either parts or all tasks listed in the SOW for DNA, RNA, and Protein. Do they have to be listed and active in SAM.gov?
Answer 7: Yes, foreign entities can be subcontractor as long as they can perform the work within the SOW (DNA, RNA and or Protein). Yes, all prime contractors and subcontractors performing work for the Government have to be registered and active in SAM (https://www.sam.gov/SAM/).
Question 8: Can a small business submit a proposal for subcontracting with a potential prime contractor (unknown) that is yet to be awarded for this RFP due on March 18, 2019?
Answer 8: See response to question 5 above.
Question 9: I was writing to get some clarification on what content should appear in the Base IDIQ Technical Proposal vs. the Task Order Technical Proposals. Would you be able to provide some guidance on how the Technical sections should differ for each? Also, should we repeat whole sections (e.g. - Organizational Experience, Personnel, Facilities) in both the Base IDIQ Proposal and Task Order Proposals?
Answer 9: Offerors should address individual Statements of Work (SOWs) separately. Please be sure to review each SOW. Generally speaking, your proposal responding to the Base IDIQ SOW should explain and demonstrate your firm's ability to perform all the requirements of that SOW. Likewise, your proposal(s) addressing a Task Order should address very specifically the requirements of that SOW. To the extend necessary to do this, yes, your proposals may repeat certain information. In addition, overall sequencing capabilities and qualifications should go into the Base response and individual Task Order response(s) should address approaches to specific characterization requirements.
Question 10: In fulfilling the task orders in the RFP can a US company use a global supply chain, for example can DNA be extracted in the US and samples sequenced in a different country?
Answer 10: Foreign subcontractors must be registered and active in SAM and go through a review/approval process to be a subcontractor under a Government contract. In terms of the example provided, it is not correct since Molecular analyte will be provided by a different NCI contract. Therefore, DNA extraction is out of the scope of this RFP.
Question 11: Is there an obligation to be FedRAMP and FISMA compliant? If yes, at time of contract do we need to be FedRAMP and FISMA compliant.
Answer 11: Neither FISMA nor FedRAMP are applicable to this RFP. However, the SOW does require offeror to treat all produced molecular characterization results as protected information and abide by NIH patient and data protection policies.
https://grants.nih.gov/grants/policy/data_sharing/data_sharing_guidance.htm ;
https://www.cancer.gov/grants-training/policies-process/nci-policies/genomic-data/about-policy
Question 12: In considering data delivery and cost implications it would be helpful to understand if transferring data from an AWS S3 bucket is a viable option to the NCI Data Sharing Portal?
Answer 12: The data transfer option/s are implemented and controlled by NCI Genomics Data Commons (GDC) in a separate contract. This GCC RFP is not able to make assumptions on GDC's data submission options. GCC centers are required to comply with data submission standards published by GDC. Those standards might vary in the future due to systematic enhancements, and the GCCs need to modify their submission pipeline accordingly.
Question 13: In the Additional Instructions Technical Proposal Instructions, it states we need to obtain a document for IRB approval or waivers to perform relevant work. We are a CLIA/CAP certified lab, can you supply us with a template and or requirements to secure the waiver? Our understanding is the BPCs will be providing de-identified data and we will put an MTA in place.
Transition Plan
The Offeror shall include a Draft Transition-In Plan comprised of the following:
Additional Technical Proposal Instructions Page 4 of 5
The Offeror shall include a start-up plan of how the Contractor shall commence operations, including specifically the scale up of staffing (including key personnel) and operational resources as well as obtaining required certifications and the incorporation of data, SOPs, and materials and other transition information. The offeror shall include in the plan a timeline to obtain document for IRB approval or waivers to perform relevant work.
Biospecimen Processing Center (BPC): The BPC serves as the tissue processing center and provides the biomolecules for GCCs. Standard operating procedures will be used for clinical data collection, sample collection, pathological examination, biomolecule (e.g., DNA and RNA) extractions, quality control, laboratory data collection, and biomolecule distribution to the GCCs. The samples are required to have patient informed consent for the public release of data or an IRB waiver. (https://cancergenome.nih.gov/abouttcga/policies). All GCC awardees will be required to work with the BPC to establish legal framework document entitled Material Transfer Agreement (MTA) for the transfer of analytes.
NIH recognizes that data sharing may be complicated or limited, in some cases, by institutional policies, local IRB rules, as well as local, state and Federal laws and regulations, including the Privacy Rule (see HHS-published documentation on the Privacy Rule at http://www.hhs.gov/ocr/). The rights and privacy of people who participate in NIH-funded research must be protected at all times; thus, data intended for broader use should be free of identifiers that would permit linkages to individual research participants and variables that could lead to deductive disclosure of the identity of individual subjects.
Answer 13: The program does not have requirement for documentation of local IRB approvals or waiver. We just need to know that offerors have a viable plan to comply with all local regulations to start the work of contract. The second italic sentence in BPC paragraph above is a description for BCP contract which is different than GCC contract. In addition, this GCC RFP has no requirement for CLIA certification since data are generated for general research purposes.
Question 14: This is a follow-up to my initial call and message left on your voicemail. We are in the process of securing our SAM registration and hope to have that soon. To that end, and given that this is an IDIQ opportunity, will we also need to be established via GSA as a primary contractor in the appropriate Schedule? I did see that because of the amount, up to $49,832,452, there will need to be a subcontracting plan in place by the primary contractor, so we could also consider that course as well. Would we still need a SAM number for that, or would it be required of the primary contractor only?
Answer 14: All prime and subcontractors must be registered and active in SAM to perform work under any contract with the government. For this project it is not required that the prime or any subcontractors be registered/established under the GSA.
Question 15: Would you be sending us gDNA (extracted from FFPE samples and fresh frozen samples) as the starting material for DNA sequencing protocols?
Answer 15: Yes.
Question 16: There are several data QC metric items from each sequencing protocols. Do we need to meet ALL the QC metrics requirements? If not, what is/are the most important item(s) to meet? I'm asking this question because some data QC items are contradicted each other and some items we cannot guarantee.
Answer 16: Yes. All QC metrics are required. If some metrics are overlapping, then the intersection of higher standards should apply.
Question 17: For the Whole Genome Sequencing, I believe low depth coverage is for 15X coverage; high depth coverage is for 30X (non-tumor samples) and 80X (tumor samples). Would you please provide data QC metrics for WGS 60X, which are not included in the DNA Pool SOW?
Answer 17: The QC metrics for 60X WGS is extrapolated below using 30X and 80X. WGS 60X is not part of the specific Task Order so it is not in the DNA Pool SOW. It may be used in future task orders.
1) Average coverage of bases will be 60X or greater for tumor.
2) >85% of bases in genome will have >30x for tumor.
Question 18: Would you please specify library kits that you prefer to use for all protocols under DNA and RNA sequencing? (WGS, WES, WGMetSeq, total RNAseq, Transcriptome sequencing, micro RNA sequencing)?
Answer 18: The RFP does not have recommendations on specific library kits. The offerors are expected to propose their complete pipelines to meet requirements in the SOWs.
Question 19: For the deep sequence targeted validation, we will need custom library kit to sequence. Will you be sharing the kit design number, or will you be providing the custom kit for deep targeted sequencing?
Answer 19: The deep sequencing library design will be project specific. The information is not available at this time.
Question 20: Would you be sending us total RNA (extracted from FFPE samples and fresh frozen samples) as the starting material for RNA sequencing protocols?
Answer 20: Yes.
Question 21: For RNA sequencing, ‘number of mapped reads' is per sample total reads? 150 Million reads under the QC metrics will be 75M from read1 and read2 from the paired-end read setting. Can you confirm this is what you are looking for?
Answer 21: Yes, ‘number of mapped reads' refers to total reads per sample. If 100% of mapped reads are properly paired reads, then the calculation of read 1 and read 2 is 75M.
Question 22: For RNA sequencing, ‘maximum number of genes not detected' and ‘percentage of miRNA detected' are not being guaranteed as these are very different from the type of sample source. Are these the requirements that we need to meet?Answer 22: Yes, these metrics are expected. Our current studies showed that large percent of genes and miRNA are expressed in interested tumor samples. In case of sample sources with limited gene and miRNA expressions in future task orders, the metrics will be adjusted.
Question 23: What is the preferred data deliver method among external hard drive, server upload, or cloud (client account) upload?
Answer 23: This RFP does not specify a preferred data deliver method. Offerors should comply with the data submission instructions provide by NCI-GDC (https://gdc.cancer.gov/submit-data). The delivery method might change with time and the offerors need to be able to adapt to those changes.
Question 24: In the DNA SOW on page 4 of Attach5DNApoolSOW.pdf the WGS Low coverage quality control metrics (d) are
#1 Average coverage of bases 15X or greater, and #3. At least 30 Gb or greater.
The genome is 3 Gb, so if we are allowed to provide 30 Gb or greater, this would deliver Average coverage of 10X. To deliver Average coverage 15x, you would need at least 45 Gb. Similarly, on page 5, the WGS High coverage quality control metrics (d) are #1 Average coverage of base 30X/80X for normal/tumor, but #3 says at least 220 Gb sequence per sample [this must mean patient consisting of tumor and normal?]. 30X requires ~90Gb, and 80X requires ~240Gb. If there was a T/N pair, it would require 330Gb, or if tumor only at least 240 Gb. The WGS parameters are somewhat at odds. Should we take #1 (target coverage) or #3 (target base count) as the relevant minimum standard. There is a significant difference with regard to pricing. Or should we price it both ways?
Answer 24: For DNA WGS quality control metrics, offeror should take #1 (depth-of-coverage) and #2 (breadth-of-coverage) as absolute minimum requirements and price tasks accordingly. #3 only suggests an " at least" measure of sequence quantity and is not a QC standard on its own. As offeror pointed out, sequence quantity numbers are usually larger when requirements #1 and #2 are achieved. Under WGS high coverage quality control metrics, "at least 220 Gb sequence per sample" is for tumor/normal pair.
Question 25: The document Attach3BaseIDIQ(allpools)SOW describes 3 Task Areas. In Task Areas 1 & 2, Single cell DNA and RNA sequencing is mentioned; however, in the corresponding Attach5DNApoolSOW and Attach6RNApoolSOW, there is no mention of the criteria for single cell sequencing. We can provide those data types. Should we include those in our proposal?
Answer 25: The document Attach3BaseIDIQ(allpools)SOW is the statement of work for the Base IDIQ contract. It has a broad scope of work anticipated to cover all potential future task orders related to this project. The documents, Attach5DNApoolSOW, Attach6RNApoolSOW and Attach7ProteinpoolSOW are the first set of Task Orders to be awarded under the Base IDIQ contract. Not all items in Base IDIQ are subscribed in these task orders. While single cell DNA and RNA sequencing are not part of the current task orders, it is possible that these platforms will be called in task orders for future projects. Offerors should include responses to single cell DNA and RNA sequencing in the proposal to the Base IDIQ SOW if offerors want to propose the capability. Offerors should address task order requirements in the proposals to individual task orders should they choose to respond.
Alexis Hudak, Contract Specialist, Phone (301) 624-8753, Email alexis.hudak@nih.gov - Matthew Packard, Contracting Officer, Phone (301) 624-8742, Email packardm@mail.nih.gov
