36C24E25Q0045 0002.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) 240E

06-23-2025

00240E Veterans Health Administration Regional Procurement Office East Building 32 Suite 1A1111 1010 Delafield Road Pittsburgh PA 15215-1802

00240E Veterans Health Administration Regional Procurement Office East Building 32 Suite 1A1111 1010 Delafield Road Pittsburgh PA 15215-1802 To all Offerors/Bidders

36C24E25Q0045

X

X

** HOUR & DATE for Receipt of Offers is EXTENDED to: 06-26-2025 11:59 EDT See CONTINUATION Page

-01- The purpose of this modification is to provide additional responses for questions asked in preparation of submissions and to extend the solicitation response date no later than 11:59a, Thursday, 6/26/2025.

All other terms and conditions of solicitation are in effect.

Millicent Covert Contracting Officer

RFQ 36C24E25Q0045

Advanced Genetic Sequencing Solicitation Clarification and Question & Answer, PART 2 **Quote submission is extended to no later than 11:59AM EST, Thursday, June 26, 2025.** Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered nonresponsive.

Response to Question 1: Scope, Library Prep, and Sequencing Capacity We appreciate your request for clarification and have refined the expectations to ensure alignment with the full Statement of Work (SOW). The following applies:

1. Workflow Scope – Full Single-Cell RNA-seq Services Required The requirement includes complete execution of the Parse Biosciences single-cell RNA-seq pipeline, starting from fixed single-cell suspensions. This encompasses:

- Sample intake and QC

- Cell barcoding and library preparation using Parse WT or MEGA kits

- Library quality control

- High-throughput sequencing on NovaSeq X Plus PE150 (25B lanes)

- Full bioinformatics pipeline (alignment, clustering, DEG, pathway analysis)

Pre-made libraries are not in scope, and the contractor must have demonstrated experience handling Parse Biosciences workflows end-to-end, including immediate sequencing upon library completion without outsourcing.

2. Library QC and Kit Considerations Library QC is embedded within the full workflow and must be included in the price per library. The contractor should have:

- Infrastructure and staffing to process up to 20 libraries/year in multiple independent batches (2–6 per shipment)

- Access to and experience with Parse WT and MEGA kits, with the ability to scale per batch and adjust based on submission schedule without delays or combining batches

3. Sequencing Specifications and Lane Requirements Sequencing must reach 30,000–50,000 PE150 reads per cell in line with Parse’s UMI-based design. The contractor should be able to independently:

- Assess and balance sample pools

- Perform high-throughput sequencing using NovaSeq X Plus

- Deliver per-library and per-cell metrics, not only per-lane summaries

Contractor must control both library prep and sequencing in-house, ensuring minimal sample handoff and continuity of sample metadata.

Response to Question 2: Misalignment Between Pricing Table and Deliverables We acknowledge that the originally provided table structure may have introduced ambiguity. To ensure it accurately reflects the technical and operational deliverables, we recommend the pricing table be realigned to match the complete workflow.

Recommended Table Format (Reflecting SOW)

Summary of Key Requirements To ensure scientific success, the vendor must:

- Handle full Parse Evercode single-cell RNA-seq pipeline internally

- Have proven experience with Parse kits (WT, MEGA) and NovaSeq X Plus

- Support batch-level flexibility (2–6 samples), not pooled 20-sample prep

- Deliver complete sequencing + bioinformatics per sample

- Ensure end-to-end traceability and QC without third-party outsourcing

RFQ 36C24E25Q0045

Advanced Genetic Sequencing Solicitation Clarification and Question & Answer, PART 2 **Quote submission is extended to no later than 11:59AM EST, Thursday, June 26, 2025.** Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered nonresponsive.

See attached document: Attachment 2 - Price Cost Schedule_updated.