36C10G21R0015 0001.docx

Amendment 0001 Tumor Normal Matched Genomic Testing Services Solicitation Number 36C10G21R0015 Question and Response

5. PROJECT NUMBER (if applicable)

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7. ADMINISTERED BY

2. AMENDMENT/MODIFICATION NUMBER

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8. NAME AND ADDRESS OF CONTRACTOR

4. REQUISITION/PURCHASE REQ. NUMBER

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9A. AMENDMENT OF SOLICITATION NUMBER

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10A. MODIFICATION OF CONTRACT/ORDER NUMBER

10B. DATED

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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

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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)

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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)

36C10G U.S. Department of Veterans Affairs OPAL | Strategic Acquisition Center

10300 Spotsylvania Ave | STE 400 Fredericksburg VA 22408-2697

36C10G U.S. Department of Veterans Affairs OPAL | Strategic Acquisition Center

10300 Spotsylvania Ave | STE 400 Fredericksburg VA 22408-2697 To all Offerors/Bidders

36C10G21R0015 08-03-2021

X

Amendment 0001 is issued to provide responses to vendor raised questions. Delete Attachment F - Past Performance Questionnaire and replace in its entirety with Attachment F rev 1 - Past Performance Questionnaire.

Delete Attachment C - Schedule of Service and replace in its entirety with Attachment C rev 1 - Schedule of Service.

All changes to documents are highlighted in yellow. All Other Terms and Conditions Remain Unchanged.

Zachary Wilcox Contracting Officer

See attached document: Attachment C rev 1- Schedule of Services.

See attached document: Attachment F rev 1 - Past Performance Questionnaire.

Amendment 0001 Tumor Normal Matched Genomic Testing Services Solicitation Number 36C10G21R0015 Question and Response

Question 1. Our team has reviewed the solicitation terms (Clause C.15 SAC 18-01) and we understood that we would need to make a service level agreement (SLA) reimbursement of 3% of sales resulting from this VA contract back to the SAC on an ongoing basis. The Quarterly sales report (attachment A) is used to provide accounting of sales to the SAC and to calculate the amount of SLA reimbursement for submission. Then we use Pay.gov site to submit quarterly SLA payments per instructions in attachment D. Therefore, can you please confirm that we don’t need to submit attachment A and D as a part of the RFP process?

Response1. Yes. These are submitted on the Governments quarterly basis by the awardee following an award.

Question 2. When should we expect the first sample to arrive?

Response 2. This is dependent upon clinician and patient sample being collected. No timeframe can be supplied at this time, but awardee should be capable of receiving samples and testing at time of award.

Question 3. We understand that all the raw data including FASTQ, BAM, VCF files will be delivered directly to the VA. Please confirm if our understanding is correct.

Response 3. Yes, your understanding is correct. In addition to raw data, finished data (defined as data that will populate the final issued patient report) including (but not limited to) PDF, structured results (XML, JSON, or .txt files) shall be returned to the National Oncology Program.

Question 4. Do physicians at the VA like to see a subset of research data output (neoantigen load, mutational signatures, tumor escape, HLA, LOH, oncoviral detection, gene expression markers) through a portal?

Response 4. Yes, ability to view and interact with this information via a portal is preferred.

Question 5. Is a genetic counselling service required for physicians or for patients?

Response 5. A genetic counseling service is not a requirement of this RFP however if this is an available service, a description can be included in the proposal.

Question 6. For a small business, would it be permissible to subcontract for other ancillary services?

Response 6. Yes, subject to approval by the VA Contracting Officer.

Question 7. For a small business, would it be permissible to subcontract interpretation by personnel who are not employees of the prime contractor?

Response 7. Although this is not the preferred approach, it will be considered if needed but remains subject to credential review and approval by the National Precision Oncology Program leadership.

Question 8. We interpret that we will need to provide germline variants as incidental findings from a tumor-normal test. Are you also expecting a standalone germline diagnostic test to be run, either in general or on a reflexive basis depending on incidental findings?

Response 8. The requirement in the RFP is for reporting of incidental findings from a tumor normal test. A separate standalone germline test is not required, but if the contractor has the ability to do so, it should be stated in the proposal.

Question 9. The language in the past performance document has a couple of items we wanted some clarification on. Under Information Request there is a listing for Closed Circuit Televisions? Is that a mistake I assume? Then there is no address as to where to send the form in the section that reads Send Questionnaire to?

Response 9. Under Information Request the listing should have read “Tumor Normal Matched Testing Services” and the questionnaires should be returned by POCs directly via email to lawrence.toperoff@va.gov and zachary.wilcox@va.gov. See Amendment A00001 that deletes Attachment F- Past Performance Questionnaire in its entirety and is replace with Attachment F rev 1 – Past Performance Questionnaire.

Question 10. Can you also confirm the processes that the offeror would send the PPQ to the POCs of the contracts you are submitting. Do the POCs send their response back to the contracting officer at the VA? If so, is there a process where we can confirm that the forms have been returned to the VA?

Response 10. See response to question 9 above. You can ask your references if they have returned their Past Performance Questionnaire to the VA.

Question 11. Given the RFP due date is about 2 weeks away can we have an extension to respond?

Response 11. No extension will be granted.

Question 12. Do you have an expected implementation date?

Response 12. Implementation is expected to occur upon date of award.

Question 13. What is the expected ramp up to 3,000 assays?

Response 13. See response to Question 2 above.

Question 14. What is the contract fee, if any? Attachment D Response 14. Contract Fee is the Department of Veterans Affairs Service Level Agreement (SLA) Fee of 3 percent. Attachment D is the process to submit the vendor payment on a Government Quarter after award.

Question 15. For attachment F, are we using the correct form, as it references closed circuit televisions? Attachment F

Response 15. See response to Question 9 and 10 above. Attachment F rev 1 – Past Performance Questionnaire is provided in this amendment to the solicitation.

Question 16. In attachment C, can you please define MSVP? Attachment C

Response 16. Medical Surgical Prime Vendor (MSPV) Consumables Program.

Awardee may be requested to utilize Prime Vendor (PV) contracts for distribution and supply management services for products clinically deemed eligible for stock and issue by VA personnel. VA facilities routinely order from the MSPV Product List.

Attachment C – Schedule of Service is deleted in its entirety and replaced by Attachment C rev 1 – Schedule of Service with any reference to MSPV to be deleted from Attachment C.

Question 17. In Attachment D (strategic acquisition center, sales reporting), are you requesting sales volume specific to the VA or to our overall organization? Attachment D

Response 17. Sales volume specific to the VA for sales made under this specific award.

Question 18. Can you provide your definition of “match tumor normal”?

Response 18. A matched tumor normal is when a sample of healthy tissue from the same individual (normal) is obtained and tested in addition to a tumor sample. The normal sample is used in order to distinguish germline mutations from somatic mutations in the patient, resulting in a report that integrates these results. Any germline findings revealed through testing of the normal sample should also be reported per ACMG recommendations.

Question 19. Can you share your data return specifications, specifically is there a cloud storage destination, third party database application, or secure file transfer method you would like us to utilize?

Response 19. Once award is made, the method of delivery will be determined in conjunction with the Government and the awardee, however, a cloud-based data return is preferred.

Question 20. Is there a data schema the VA would like us to follow for the structured data (XML, JSON) or will we collaborate to assimilate Caris data into your existing repositories if selected?

Response 20. The Government and the awardee will collaborate to design a data schema for the structured data upon award.

Question 21. Do we need an offeror code for this RFP? If yes, please send one to me.

Response 21. To be awarded a contract and do business with the U.S. Federal Government a vendor must be self-registered in The System for Award Management (SAM.gov) prior to an award being made.

Question 22. Do the Past Performance documents need to also be submitted by us since they are being sent directly to you as well from our partners?

Response 22. No. See response to Question 10 above.

Question 23. Please confirm that we can submit past performance qualifications for services performed by wholly owned subsidiaries?

Response 23. Of the 3 past performance questionaries only 1 may be from a wholly owned subsidiary.

Question 24. Does germline testing need to be available as an option or always reported as part of the tumor profiling report?

Response 24. Germline testing should always be reported with the tumor results, unless it is determined that a germline specimen is unavailable Question 25. Someone in the lab asked whether there will be a return of nucleic acid?

Response 25. Yes, return of residual nucleic acid to the National Oncology Program Office is required.

Question 26. We have a BAA with the [Specific Named] Foundation for a program we are doing with the DOD. Can that be used?

Response 26. No. A Business Associate Agreement (BAA) must be in place with the Department of Veterans Affairs.

Question 27. Is there a time frame for responses?

Response 27. The solicitation closes on September 1, 2021 at 15:00 (3 pm) Eastern Time for offers to be received by email.

Question 28. What is the estimated timeline for notification if contract is awarded?

Response 28. It is anticipated that award will be made approximately 45 days after date and time of closing. The awardee is notified upon the Government award on the same day or not later than the next business day.

Question 29. What is the estimated timeline for receipt of first sample?

Response 29. See response to Question 2 above.

Question 30. Germline testing:

1. What is the intended use for germline testing results? Guiding treatment decisions such as the use of PARP inhibitors in some specific types of cancer (DNA repair gene alterations) or determine genetic predisposition to specific syndromes and cancers?

1. If the latter, are all 59 genes described in ACMG guidelines required (we have panel that covers 27 genes out of 59).

1. What is the level of germline interpretation required, is ClinVar alone acceptable?

1. Is an integrated somatic + germline report required, or can we submit separate clinical reports?

Response 30.

a. The intended use for germline testing results is to guide treatment decisions and to determine genetic predispositions.

b. All ACMG recommended genes are preferred, however smaller panels will be considered. Please include details in the proposal.

c. No, ClinVar alone is not acceptable. Germline results must be interpreted using a variety of sources and by individuals with molecular genetics experience per ACMG standards.

d. An integrated somatic + germline report is required.

Question 31. RNASeq: what are the requirements for the RNASeq pipeline and reporting?

0. Is targeted RNASeq aligned with the DNA somatic panel accepted or whole transcriptome is a requirement?

0. What must be included in the RNASeq report and what is the required format?

Response 31.

a. Whole transcriptome is preferred but not required.

b. RNASeq, at a minimum, must report on gene fusions and splice variants.

Question 32. Regarding the 2-week turnaround time: does this only pertain to somatic (FFPE/cfDNA) and germline (blood) testing or also for testing beyond that such as RNASeq, and non-NGS confirmatory testing?

Response 32. The two week turn around time pertains to NGS testing. Non-NGS confirmatory testing turn around time may extend beyond this time and will be discussed upon contract award.

Question 33. What are the acceptable methods for secure electronic transfer of raw data files, such as BAMs and VCFs?

Response 33. See response Question19 above.

Question 34. Is NY and CAP accreditation required at the time of proposal submission?

Response 34. Yes. NY and CAP accreditation are required at the time of proposal submission.

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