Q301--Genome Sequencing (VA-22-00058417)

RFP 36C24E22R0020 QUESTIONS WITH VA ANSWERS (No additional questions will be answered. Proposals due date has been extended to 9/7/22 at 4:30PM).

1. I have one more question for you related to this solicitation. Since this is our first foray into federal contracting, we do not have entities from whom we can seek references from previous contracts. We do however, have numerous references in the private sector and academia for whom we have provided services in the past. Would it be appropriate to have prior customers complete the Past Performance Survey, or should this only be completed by entities falling under a prior federal contract? See Evaluation Factor 2 - Relevant past performance history: The offeror must provide past performance proposal that describes in great detail up to three (3) recent and relevant contracts of similar scope and nature. It does not specify federal.

If the latter is the case, would it be appropriate to have a subcontractor with whom we may seek to have a teaming agreement in place for this solicitation provide these surveys from their previous federal contract work? No, it would not be appropriate to have a subcontractor provide surveys from their previous federal contract work.

2. My company is planning on submitting an offer for the VA genome sequencing solicitation. One point that I did want to ask about is the stated requirement for the laboratory to be both GLP and CLIA. Customarily, a laboratory that has CLIA certification and additionally is accredited by an agency such as the College of American Pathologists is considered to be of higher standards of practice than a non-clinical laboratory that is only GMP-compliant. I don't actually personally know of a CLIA lab that holds GLP - especially as a small business. My question is this - is it an absolute requirement that the laboratory possess both a GLP certificate and CLIA certificate, or would CLIA suffice for this requirement? Either the GLP (Good Laboratory Practice) OR CLIA certification (or both) are sufficient to meet the requirements for this contract.

3. There's verbiage in the solicitation that has me questioning if this is intended for the Veteran Set Aside group. As marked it says 100% Small Business. Would you mind confirming that the solicitation is for Small Business as indicated, please? It is a 100% small business set aside with SDVOSBs/VOSBs getting a competitive advantage in accordance with VAAR 852.215-70 & VAAR 852.215-71.

4. Is current GLP certification required to be eligible or is adhering to GLP standards adequate if the laboratory is CAP/CLIA certified? Would approvals from other agencies (e.g. FDA) be considered as evidence of quality? If GLP is required, would completion of GLP certification within the first budget period be adequate? Either GCP certification OR CLIA certification is acceptable. Certification must be in place at the time of response to the RFA.

5. The solicitation specifies options for deliverables (FASTQ, BAMs, and/or Variant Call files (VCFs)) based on task order requirements, but a single price per tier is requested independent of deliverable. VCF generation is the more extensively processed data form of these options and thus requires greater computational resources than do FASTQ or BAM generation. Therefore, the cost to generate the VCF is typically higher. For the purpose of calculating the cost per sample, should we assume VCFs will be required for each sample? Only FASTQs. No VCFs

6. The solicitation states that the contractor must adhere to the FAR 52.219-14 Limitations on Subcontracting: Services (except construction), it will not pay more than 50 percent of the amount paid by the Government for contract performance to subcontractors that are not similarly situated entities. Any work that a similarly situated entity further subcontracts will count towards the prime contractor's 50 percent subcontract amount that cannot be exceeded. When a contract includes both services and supplies, the 50 percent limitation shall apply only to the service portion of the contract

For providing the service of WGS detailed in this solicitation, would the cost of supplies purchased by the subcontractor be excluded from the services subcontract total for the purposes of calculating the 50% limit? No supplies should not be excluded.

7. Is there a specified turnaround time required to return completed data from time of sample intake? There is no specified turnaround time expected. Response to the RFA can indicate the expected turnaround time.

8. Should we include payment terms in the proposal or will this be discussed after award? i.e. Milestone/time-based, sample completed based etc. Billing occurs monthly in arrears, based on number of samples received and processed.Â

9. Have any samples been processed to date? If yes,

What kit was used for library preparation and do you want to retain the kit for consistency? Not necessarily state of the art is requested

What sequencing depth (coverage) was provided? At least 30X or 100X

Was analysis conducted? If the question is QC, yes

Will you provide QC values and/or data for any further analysis (if needed)? No, this would not be needed.

Where were they processed? VA Laboratory

10. When will samples begin arriving at Lab for processing? Within one month of contract execution.

11. Do all samples need to be processed in the same facility as long as all protocols are followed and security measures are in place? Samples are to be processed within the same facility and cannot be sub-contracted out to other locations or facilities.

12. Is the rate of 3300 (30X) and 900 (100X) per month expected to begin immediately or will some leeway be given to initiating the project (1-2months to implement and accelerate processes) )1-2 month ramp up is acceptable.

13. Will samples be sent in batches of 4200 samples or larger batches and the lab will be expected to process 4200/month as outlined in the RFP?

14. Are samples coming from one location or several? Will this change over time? ? Samples will come from one or two VA lab locations. No.

15. Is CLIA certification mandatory or preferred? If mandatory, will proposal be considered if the lab is able to obtain CLIA prior to processing samples in house? Either GCP or CLIA certification is required. This must be in place at the time of response to the RFA.

16. If CVE SDVOSB certification is pending and will be completed prior to the initiation of the project, will it still be considered a factor in one s proposal? No, must be verified in Vetbiz as SDVOSB at time of submission and upon award.

17. Do you require a specific sequencing instrument? (Novaseq, NextSeq, etc.)Â Illumina Short Read, Novaseq or more recent

18. Do you require a specific extraction kit? Â N/A unless in the future we ask them to extract DNA from sample

19. Do you require a specific library preparation kit? No specific requirement other than state of the art

20. Do you prefer/require a PCR-Free WGS kit? No

21. What percentage of samples do you expect to require analysis (mapping, variant calls, etc.)Â NA

22. Is there an anticipated minimum number of samples per month of each type of sequencing being requested? There is no minimum number of samples per month, however, VA will likely focus more on 30x. As stated in the RFP, A requirements contract provides for filling all actual requirements for services during a specified contract period with time or duration to be scheduled by placing task orders (TO) with the contractor. The Government s realistic estimate for anticipated need over the course of the contract is stated in the RFP. This estimate was developed using historical data from the previous contract and projected needs at the time of the RFP. However, these are only estimates and task orders will be awarded based on actual needs.

23. The contract states that up to a maximum of 3300 30X WGS and 900 100X WGS sequences could be requested in each calendar month, so does that mean that the minimum of each type per month would be 1? The minimum could be 0 for either type.

36C24E22R0020 RFP