Amendment_0003_for_RFP_N02CO87001-94.pdf

OFFICE OF ACQUISITIONS

NATIONAL CANCER INSTITUTE

REQUEST FOR PROPOSAL NUMBER: N02CO87001-94

Amendment No.: 0003

Date of Issuance: 2/27/2019

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.

*NOTE: Amendment 0003 hereby DELETES B – Project Objectives AND C – Government Notice for Handling Proposal under Attachment 13 – Technical Proposal Instructions.

This Amendment provides responses to questions received under RFP N02CO87001-94:

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? Q. Will the samples be marked by the BPC as being from FFPE, fresh-frozen, or minimal DNA?

Answer 1: The CCG website: https://www.cancer.gov/about-nci/organization/ccg/research and Yes, they will be marked.

Question 2: Please define “minimal DNA”. How is the amount/quality determined?

Answer 2: There is no specific definition for “minimal DNA”. Offerors can propose a protocol to deal with low amount of analyte input for specific platforms.

Question 3: RNApoolSOW - Page 5 - "Read 1/Read 2 Ratio: 1:1 with a maximum 20% deviation" - Could we get some more information about this? Is this a count of how many read1s we have compared to read2s?

Answer 3: Yes. It is a metrics for paired-end sequencing.

Question 4: RNApoolSOW - Page 5 - "Maximum Number of genes not detected: 4000" - In any RNA sample there would always be more than 4000 genes that aren't expressed, so maybe there is a specific set of genes that is being used here that should always be expressed/looked for. If this is a known/expected set of genes, could we get that list to assess our ability to achieve this metric?

https://www.cancer.gov/about-nci/organization/ccg/research

Answer 4: This metric is an estimate based on data from over 10,000 tumor samples in TCGA projects. In case of sample sources with limited gene expressions in future projects, the metrics can be adjusted.

Question 5: RNApoolSOW - Page 6 - "Percentage of miRNA detected: >85%". Does this refer to "Percent of reads aligning to miRNA > 85%"? As with the RNAseq, there will always be a number of miRNAs that are not expressed. Is a list of known/expected items for detection available?

Answer 5: This metric is an estimate based on data from 11000 tumor samples in TCGA project. In case of sample sources with limited gene expressions in future projects, the metrics can be adjusted.

Question 6: For the exome sequencing, is there a preference for exome versions (e.g. exons only or with UTRs) and/or vendor specific products (e.g. Agilent SureSelect All Exon V6+UTR, IDT xGen Exome Research Panel, Twist Human Core Exome)?

Answer 6: The RFP does not specify a preference for exome versions and/or vendor specific products. The offerors should propose a complete technical approach to meet the requirements.

Question 7: Q. Is Transcriptome (mRNA-seq) from FFPE? Could the FFPE sample type requirement be an error? Capturing mRNA transcripts using polyA-selection from highly degraded RNA is not advised unless 3’ gene expression is the only requirement.

Answer 7: Current projects use TotalRNAseq for expression analysis of FFPE samples. FFPE samples requirement appears under all platforms in the statement of work as most of projects going forward will be based on FFPE cases. If there is no valid technology available under the specific platform, offerors can skip the task.

Question 8: DNApoolSOW – Page 6 – lists “Whole Genome Methylation Sequencing (WGMetSeq) as a characterization platform, with quality control metrics, turnaround time, and minimal operational capacity. Attachment9 Additional Business Proposal Instructions – page 2 – lists both Whole Genome Bisulfite Sequencing and Whole Genome Methylation Sequencing as part of Task Area 1 – DNA sequencing. Can information be provided about the requirements and expectations for bisulfite sequencing, including quality control metrics, turnaround time, and minimal operational capacity?

Answer 8: The method for Whole Genome Bisulfite Sequencing (30X coverage) is an item in pricing table for methylation sequencing. As the technology of bisulfite sequencing is evolving, details of specifications are not put in the statement of work. Offerors can propose specific technical approach to Whole Genome Bisulfite Sequencing (30X coverage).

Question 9: Attachment 10 – Technical Proposal Cost Information/Summary of Labor and Direct Costs. Do we need to supply this table for each offering (i.e., 30X WGS, WES, Transcriptome sequencing) or just one representative table?

Answer 9: Offerors should submit one Attachment 10 per Task Order response.

Question 10: Are there any required meetings or expected travel? If so, how many attendees and meetings?

Answer 10: There is no travel required for meetings. All meetings will be conducted as tele-conferences.

Question 11: Within PDF attachment 5DNApoolSOW on page 8 under Objective 5: Support informatics and data delivery, could you clarify on what bioinformatics deliverables/file formats are desired for WGS and WES services?

Answer 11: Bioinformatics deliverables/File formats are defined by NCI-GDC (https://gdc.cancer.gov/submit-data). Offerors should comply with all requirements of data submission instructions provide by NCI-GDC. The delivery requirements in GDC also might change with time and the offerors need to be able to adapt to those changes.

Question 12: Within PDF attachment 5DNApoolSOW on page 4 under Whole Genome Sequencing, it states “Produce WGS for both frozen and FFPE cases with the following requirements: i. Quality control metrics: 1. Average coverage of bases will be 15x or greater…...” Could you please clarify coverage expectations? For example, is it correct that coverage will be calculated as an average over a batch of samples? Or would you prefer for each individual research sample will be sequenced (WGS) to a guaranteed minimum of > 15-fold coverage?

Answer 12: The average coverage of bases should be calculated for each individual sample.

Question 13: Will the coverage calculation be based on all high-quality informative sequence reads, including those from molecular duplicates generated by the Illumina NovaSeq cluster creation process (NovaSeq platforms can generate up to 20% duplicate reads during cluster creation)?

Answer 13: The specifics for implementing the metrics should be developed in the technical proposal by the offerors to allow generation of high-quality data. The duplicate reads topic raised for NovaSeq can be addressed in offerors response.

Question 14: The RNA SOW requires a minimum of “150 Million reads”. Because we plan to use paired-end sequencing, we would like to clarify if the requirement should be interpreted as “75 million pairs”, or “150 million reads”.

Answer 14: Yes, it can be interpreted as “75 million pairs”, or “150 million reads”.

Question 15: The RNA SOW requires “Maximum number of genes not detected: 4000”. Please clarify the method and level of detection under which a gene is considered “not detected”, and how many genes (or which annotation) should be considered for this metric.

Answer 15: The method to determine gene detection in RNAseq is part of the offorors proposal.

The reference should be public accepted annotation for “protein coding genes” in human genome.

Question 16: If a subject requests erasure of their genomic data, will this be communicated to the Contractor through the Biospecimen Processing Center?

Answer 16: Yes, an email of Patient Withdrawal Notification will be communicated to the Offeror through a separate NCI contractor.

https://gdc.cancer.gov/submit-data

Question 17: If a subject requests erasure of their genomic data, will the Biospecimen Processing Center provide the Contractor with a sample ID or other information that will allow the Contractor to execute upon this request?

Answer 17: Yes, an email of Patient Withdrawal Notification will be communicated to the Offeror with appropriate ID and other information that will allow the Offeror to execute upon this request.

Question 18: Will the Biospecimen Processing Center provide the Contractor with a completed NIH Extramural Institutional Certification covering all samples?

Answer 18: The studies for all samples should already be registered in NCBI dbGaP database with completed Institutional Certification by the study authorities. The offerors for GCC contract will not involve in the Institution Certification process.

Question 19: According to the Attachment 9-Additional Business Proposal Instructions, the Kick-off meeting must be treated as a Statement of Work, and therefore a response is required in the business proposal. However, the RFP-Page 45 refers to the Kick-off meeting in the Technical Proposal. Could you please clarify?

Answer 19: The Kick-Off Meeting proposal is requested as a separate Task Order response with a Technical Proposal and Business Proposal including the offeror’s fully loaded labor-hours budget by labor category for the Kick-Off Meeting. Offerors shall only include information in the response to the Kick-Off Meeting Task Order that is specifically relevant to the kick-off meeting.

Question 20: If a response to the Kick-off meeting Statement of Work is required in both technical and business proposals, we understand the cost related items must only be discussed in the business part. Would you please confirm?

Answer 20: The Kick-Off Meeting proposal is requested as a separate Task Order response with a Technical Proposal and Business Proposal including the offeror’s fully loaded labor-hours budget by labor category for the Kick-Off Meeting.

Question 21: Is there a page limit required for the response to the Kick-off Meeting Statement of Work?

Answer 21: The page limit is 50 pages per task order response as specified in the Additional Technical Proposal Instructions. Offerors shall only include information in the response to the Kick-Off Meeting Task Order that is specifically relevant to the kick-off meeting.

Question 22: Is the budget narrative required for the task orders cumulatively or separately per task order (Attachment 9-Additional Business Proposal Instructions)?

Answer 22: Offerors should provide a separate Budget Narrative for each task order they propose.

Question 23: Should the Program Management Plan, Transition Plan, Organizational Experience, Team and Key Personnel, and Facilities and Equipment sections (all listed in Attachment 13-Additional Technical Proposal Instructions) be included in all responses to the specific TO SOWs or just in the response to the Base IDIQ SOW?

Answer 23: The plans should be included in relevant responses to address specific requirements in the SOW.

Question 24: Are NIH biosketches acceptable for the resumes section?

Answer 24: Yes, so long as they are detailed/specific based on the technical evaluation criteria specifics. Please reference the technical evaluation criteria attachment.

Question 25: According to the RFP-Pages 44 & 56, and the Attachment 13-Additional Technical Proposal Instructions, it seems that two different outlines are provided for the cover pages. Please confirm the outline. Additionally, there are two statements referred to in the RFP- Pages 37 & 56, respectively “A statement specifying the extent of agreement with all terms, conditions, and provisions included in the solicitation and agreement to furnish any or all items upon which prices are offered at the price set opposite each item” and “By submitting this proposal, the offeror, if selected for discussions, grants the contracting officer or an authorized representative the right to examine, at any time before award, any of those books, records, documents, or other records directly pertinent to the information requested or submitted”. Which statement should be included? Please clarify.

Answer 25: The outline beginning on p. 44 refers to the Technical proposal, and the outline on

p. 56 refers to the Business proposal. The Technical proposal outline is supplemented by the Additional Technical Proposal Instructions included as Attachment 13 to the RFP. Therefore, your Technical proposal should conform to both the requirements of Section L of the RFP and Attachment 13.

Regarding the statements on pages 37 & 56 cited above, both statements apply, and offerors must respond to both in their proposal. In response to the requirement on p. 37, offerors must include a statement that specifies the extent to which they agree with all terms of the solicitation.

In response to the statement on p. 56, offerors may simply indicate that they will comply with the statement.

Question 26: It is unclear as what is meant in Attachment 13 - Additional Technical Proposal Instructions by B - Project Objectives. Would you please clarify?

Answer 26: For the sake of clarity, Amendment 0003 hereby deletes B – Project Objectives under Attachment 13 – Technical Proposal Instructions.

Question 27: Please clarify what you are referring to in the Attachment 13 - Additional Technical Proposal Instructions, section C-Government Notice for Handling Proposal?

Answer 27: For the sake of clarity, Amendment 0003 hereby deletes C – Government Notice for Handling Proposal under Attachment 13 – Technical Proposal Instructions.

Question 28: In the list of attachments (RFP - page 34), the Attachment 15-Proposal Summary and Data Record (NIH 2043) is listed as a business proposal attachment. However, it is later listed in the Attachment 13-Additional Technical Proposal Instructions as a form to include following the technical cover page. Would you please clarify where it is to be included in both proposal?

Answer 28: Please provide a response to Both Attachment 15 – Proposal Summary And Data Record AND Attachment 13 – Additional Technical Proposal Instructions. Both need to be completed.

Question 29: It is understood that letters of commitment are required in case subcontractors are involved. Are letters of support required or permitted? If no, would it be favorable to include them for subcontractors, consultants, and the personnel involved?

Answer 29: Letters of support are permitted.

Question 30: We understand SOPs are required in the Base IDIQ (Attachment 13-Additional Technical Proposal Instructions). However, our institutional SOPs are extensive. Would the full SOPs be accepted as appendixes in the technical proposal?

Answer 30: Yes. They are accepted as appendixes.

Question 31: Is the budget narrative required for the task orders cumulatively or separately per task order (Attachment 9- Additional Business Proposal Instructions)?

Answer 31: Offerors should provide a separate Budget Narrative for each task order they propose.

Question 32: What would fall in the Data Other than Certified Cost and Data section (RFP -page 57)? Would you mind providing an example?

Answer 32: Please reference FAR Part 15.403-3 (Requiring data other than certified cost or pricing data).

Question 33: In Attach9AdditionalBusinessProposalInstructions.pdf Page 2: Pricing Table – Task Area 1: Genome Characterization Center for DNA Sequencing Protocol: Whole Genome Bisulfite Sequencing (30X coverage) Can you provide the definition for Whole Genome Bisulfite Sequencing (30X coverage)? Attach5DNApoolSOW (2).pdf does not have its definition. How is it different from Whole Genome Methylation Sequencing (WGMetSeq)?

Answer 33: Whole Genome Bisulfite sequencing is a specific platform for Whole Genome Methylation Sequencing. As the technology of whole genome methylation sequencing is evolving, details of specifications are not put in the statement of work. The method for Whole Genome Bisulfite Sequencing (30X coverage) should be part of the technical proposal that offerors develop. Whole Genome Bisulfite Sequencing (30X) is a specific item on the pricing table for offerors.

Question 34: In Attach9AdditionalBusinessProposalInstructions.pdf Page 2: Pricing Table – Task Area 1: Genome Characterization Center for DNA Sequencing Protocol: Deep Sequence Targeted Validation (Validation) Could you please clarify if we need to provide the price of validating a panel only or the total pricing of both panel validation and 1200 sample test?

Answer 34: The RFP asks for fixed unit price per sample for relevant molecular characterization. All cost are inclusive in the fixed unit price. In case of volume, there is no guaranteed number of samples in ID/IQ contract.

Question 35: In Attach9AdditionalBusinessProposalInstructions.pdf Page 4: Pricing Table – Task Area 2: Genome Characterization Center for RNA Sequencing Protocols of both Transcriptome Sequencing (mRNASeq) from FFPE samples and Transcriptome Sequencing (mRNASeq) from fresh Frozen samples Their Number of cases are 0, which is not commensurate with “Minimum operational capacity:

100 cases/month; 1200 cases/year: the work described in the Attach6RNApoolSOW (1).pdf.

can we assume 600 samples each?

Answer 35: The numbers of cases in the pricing table corresponds to the work described in the sample Task Order Statement of Work (SOW). This Task Order SOW does not request all protocols to be performed, therefore the number of cases is 0. However, offerors who wish to propose their services for this protocol shall provide their price in the pricing table for potential future task orders. There is no guaranteed volume of samples in this ID/IQ contract. “Minimum operational capacity” is only a measure on operation capacity at proposed facility. It is not a description of task quantity in the statement of work.

Question 36: Can you confirm that a foreign institution with SAM registration – Federal Assistance awards only is eligible to apply and host the funds?

Answer 36: All contractors must be registered and active in SAM and must be registered for ALL Award types, not just Federal Assistance awards only.

Question 37: I was wondering when the RFP will be available in eCPS?

Answer 37: The RFP is now visible in the electronic Contract Proposal Submission (eCPS) system at (https://ecps.nih.gov/), as well as, the Federal Business Opportunities (FBO) website.

All proposal packages related to RFP N02CO87001-94 must be submitted through the eCPS.

https://ecps.nih.gov/