36C24E22R0020 0001.docx

5. PROJECT NUMBER (if applicable)

CODE

7. ADMINISTERED BY

2. AMENDMENT/MODIFICATION NUMBER

CODE

6. ISSUED BY

8. NAME AND ADDRESS OF CONTRACTOR

4. REQUISITION/PURCHASE REQ. NUMBER

3. EFFECTIVE DATE

9A. AMENDMENT OF SOLICITATION NUMBER

9B. DATED

PAGE OF PAGES

10A. MODIFICATION OF CONTRACT/ORDER NUMBER

10B. DATED

BPA NO.

1. CONTRACT ID CODE

FACILITY CODE

CODE

Offers must acknowledge receipt of this amendment prior to the hour and date specified in the solicitation or as amended, by one of the following methods:

The above numbered solicitation is amended as set forth in Item 14. The hour and date specified for receipt of Offers

E. IMPORTANT:

is extended,

(a) By completing Items 8 and 15, and returning __________ copies of the amendment; (b) By acknowledging receipt of this amendment on each copy of the offer submitted; or (c) By separate letter or electronic communication which includes a reference to the solicitation and amendment numbers. FAILURE OF YOUR ACKNOWLEDGMENT TO BE RECEIVED AT THE PLACE DESIGNATED FOR THE RECEIPT OF OFFERS PRIOR TO THE HOUR AND DATE SPECIFIED MAY is not extended.

12. ACCOUNTING AND APPROPRIATION DATA

(REV. 11/2016)

is required to sign this document and return ___________ copies to the issuing office.

is not, A. THIS CHANGE ORDER IS ISSUED PURSUANT TO: (Specify authority) THE CHANGES SET FORTH IN ITEM 14 ARE MADE IN THE CONTRACT ORDER NO. IN ITEM 10A.

15C. DATE SIGNED

B. THE ABOVE NUMBERED CONTRACT/ORDER IS MODIFIED TO REFLECT THE ADMINISTRATIVE CHANGES SET FORTH IN ITEM 14, PURSUANT TO THE AUTHORITY OF FAR 43.103(b).

RESULT IN REJECTION OF YOUR OFFER. If by virtue of this amendment you desire to change an offer already submitted, such change may be made by letter or electronic communication, provided each letter or electronic communication makes reference to the solicitation and this amendment, and is received prior to the opening hour and date specified.

C. THIS SUPPLEMENTAL AGREEMENT IS ENTERED INTO PURSUANT TO AUTHORITY OF:

D. OTHER

Contractor

16C. DATE SIGNED

14. DESCRIPTION OF AMENDMENT/MODIFICATION

16B. UNITED STATES OF AMERICA

Except as provided herein, all terms and conditions of the document referenced in Item 9A or 10A, as heretofore changed, remains unchanged and in full force and effect.

15A. NAME AND TITLE OF SIGNER

16A. NAME AND TITLE OF CONTRACTING OFFICER

15B. CONTRACTOR/OFFEROR

STANDARD FORM 30

PREVIOUS EDITION NOT USABLE

Prescribed by GSA - FAR (48 CFR) 53.243 (Type or print) (Type or print) (Organized by UCF section headings, including solicitation/contract subject matter where feasible.)

(Number, street, county, State and ZIP Code) (If other than Item 6) (Specify type of modification and authority) (such as changes in paying office, appropriation date, etc.)

(If required)

(SEE ITEM 11)

(SEE ITEM 13)

(X)

CHECK

ONE

13. THIS ITEM APPLIES ONLY TO MODIFICATIONS OF CONTRACTS/ORDERS,

IT MODIFIES THE CONTRACT/ORDER NO. AS DESCRIBED IN ITEM 14.

11. THIS ITEM ONLY APPLIES TO AMENDMENTS OF SOLICITATIONS

AMENDMENT OF SOLICITATION/MODIFICATION OF CONTRACT

(Signature of person authorized to sign) (Signature of Contracting Officer) None 00240E US Department of Veterans Affairs Veterans Health Administration Regional Procurement Office (RPO) East 323 North Shore Drive, Suite 500 Pittsburgh

PA

15212-5319 00240E US Department of Veterans Affairs Veterans Health Administration Regional Procurement Office (RPO) East 323 North Shore Drive, Suite 500 Pittsburgh

PA

15212-5319 To all Offerors/Bidders

36C24E22R0020

X x X ** HOUR & DATE for Receipt of Offers is EXTENDED to:

x The purpose of this amendment is to extend the proposal due date until Wednesday September 7th at 430PM EST & to post vendor questions with answers to the solicitation. No additional questions will be answered.

Lynn Portman 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.

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

0. 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

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

0. Was analysis conducted? If the question is QC, yes

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

0. 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.) Illumina Short Read, Novaseq or more recent

18. Do you require a specific extraction kit? 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.) 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.