36C26225Q0827 0001.docx

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AMENDMENT OF SOLICITATION/MODIFICATION OF CONTRACT

(Signature of person authorized to sign) (Signature of Contracting Officer) 06-25-2025 36C262 Department of Veterans Affairs NCO 22 - Network Contracting 3601 S. 6th Avenue Tucson AZ 85723 36C262 Department of Veterans Affairs NCO 22 - Network Contracting 3601 S. 6th Avenue Tucson AZ 85723 To all Offerors/Bidders

36C26225Q0827

X X X X The purpose of this amendment is to answer questions and as a result update the statement of work as well. Please see following pages.

Koby Thiel Contracting Specialist Q: Is this a new contract or was there a previous contract?

A: This is a new requirement. There is not an incumbent or previous contract number.

Q: The specification states…”analysis from CD Genomics to determine clonal expansion.” Please note that CD Genomics is a vendor and competitor. Is the intent of this posting to sole source to CD Genomics, or is this intended for fair and open competition?

A: This was a mistake. This is being competed as full and open competition as a total small business set-aside. This has been corrected, please see correct SOW below.

Q: Section 4 and subsequent sections notes genomic DNA (gDNA or DNA) for bulk TCR processing. Using DNA for TCR profiling is old technology and the industry now standardizes on RNA for TCR analysis. Is DNA the stringent requirement, or is RNA an acceptable alternative? Another way to ask the question is if the VA scientists want to know what TCR markers “can be” expressed (which would be DNA analysis), or which markers are ”actually” expressed (which would require RNA analysis).

A: Our primary goal is to quantify absolute T cell clone counts and assess repertoire diversity (i.e., clonality), for which DNA-based TCR sequencing is more appropriate. Genomic DNA provides a stable and comprehensive readout of all rearranged TCRs, regardless of expression level, making it ideal for estimating total T cell diversity and tracking clonal expansions. While RNA-based TCR profiling captures only actively transcribed TCRs and is valuable for assessing functional expression, it introduces expression bias and is typically more expensive particularly in bulk formats—without offering significant advantages for the specific aims of this study. Single-cell RNA sequencing would provide additional insight into expression and pairing but is currently cost-prohibitive at the scale we require. We consider DNA the most cost-effective and technically appropriate method for this phase of the project, and we plan to conduct follow-up studies using single-cell RNA sequencing to explore TCR expression dynamics and chain pairing in more detail.

Q: Please define “sufficient depth to enable high resolution TCR repertoire profiling”. What is the minimum sequencing depth required per sample – for either DNA or RNA?

A: Minimum: ~100,000–200,000 reads/sample. Preferred: 500,000–1,000,000 reads/sample Q: On the pricing chart, it notes a QTY of 250 samples. Will all 250 samples be provided as a single batch, or multiple batches over the year? If multiple batches, what will be the minimum batch size and # of batches per year?.

A: All 250 samples will be provided as a single batch.

Q: How much material (purified nucleic acid) will be provided per sample?

A: 1.0 - 3.0 µg of DNA at a concentration of 20-60ng/µL in 50 µL of TE buffer.

Q: Under Qualification requirements: What does it mean to “have access to an Illumina PE150 system”? Is that a requirement to use an Illumina sequencing platform, within the contractor lab, with a PE2x150bp flow cell for this project?

A: Yes. It is indeed a requirement for the contractor lab to use an Illumina sequencing platform capable of performing paired-end 150 bp sequencing for this project.

UPDATED STATEMENT OF WORK

1. Contract Title T-Cell Receptor Sequencing For an Ongoing Research Study

2. Background TCR sequencing principle is to extract RNA or DNA from T cells and sequence TCR gene. TCR sequencing (TCR-Seq) technology enables accurate profiling of the TCR repertoire and is used to analyze the diversity, clonal distribution, in which also serves as a biomarker for monitoring and provides valuable insights into immune responses.

3. Objective For an ongoing Southern Arizona VA Healthcare System (SAVAHCS) stroke study, where the primary objective is to determine clonal expansion, a DNA-based approach is crucial for capturing stable T-cell clone populations. TCR provides an understanding of T cells which provide technical support for study immune related diseases, drug efficacy prediction, immune drug targets, tumor immunotherapy, and other developments.

4. SCOPE:

Obtain customized Mouse T-CELL RECEPTOR sequencing (gDNA) analysis from the contractor to determine clonal expansion.

The contractor will provide the subject matter expertise, technical skill and knowledge to conduct TCR sequencing to detect structural variants of DNA on samples. They will perform T- cell receptor immune sequencing from mouse derived DNA including amplification of TCR genes followed by library preparation. Using Next-generation sequencing (NGS) platform(s) they will create a high-resolution image of the TCR repertoire to potential uncover the changes in clonal populations in the provided biological sample.

4.1 SPECIFIC REQUIREMENTS:

Requirements: Genomics data analysis service which includes comprehensive T Cell Receptor Sequencing (TCR-Seq) services, encompassing both wet lab work and bioinformatics analysis. This includes:

Analyze and provide:

• Mouse TCR-seq (gDNA): Library Preparation-Mouse TCR α/β Profiling Sequencing-Illumina PE150 Standard Data Analysis.

Deliverables:

Qualification Requirements

4.2.1. Any work other than as specified in the contract shall be identified as a non-priced task, and if determined by the Contracting Officer (CO) to be within the overall scope of the contract, work shall be added by a modification to the contract. Any work requested that is identified as outside the scope of the contract shall be addressed by the facility as a separate procurement.

5. Security Requirements The C&A requirements do not apply, and Security Accreditation Package is not required.

This service does not involve Contractor connection of one or more contractor-owned IT devices (such as laptop computer or remote connection from a contractor system) to a VA internal trusted (i.e., non-public network) therefore Information Technology (IT) Security certification and accreditation (authorization) (C&A) requirements do not apply per VA Handbook 6500.6.

Contractor shall obtain all necessary licenses required to perform this work. Contractor shall take all precautions necessary to protect persons and property from injury or damage during the performance of this contract. Contractor shall be responsible for any injury to himself/herself, his/her employees, or others, as well as for any damage to personal or public property that occurs during the performance of this contract that is caused by him/her or his/her employees’ fault or negligence. Contractor shall maintain personal liability and property damage insurance prescribed by the laws of the Federal Government.

The Government reserves the right to accept or reject Contractor’s employee for the rendering of services. Complaints concerning Contract Personnel’s performance or conduct will be dealt with by the Contractor and COR with the final decision being made by the Contracting Officer.

9. Insurance Coverage The Contractor agrees to procure and maintain, while the contract is in effect, Workers Compensation and Employee’s Public Liability Insurance in accordance with Federal and State of Arizona laws. The Contractor shall be responsible for all damage to property, which may be done by him, or any employee engaged in the performance of this contract.

The Government shall be held harmless against any or all loss, cost, damage, claim expense or liability whatsoever, because of accident or injury to persons or property of others occurring in the performance of this contract.

Before commencing work under this contract, the Contracting Officer shall require the Contractor to furnish certification from his/her insurance company indicating that the coverage specified by FAR 52.228-5 and per FAR Subpart 28.307-2 has been obtained and that it may not be changed or canceled without guaranteed thirty (30) day notice to the Contracting Officer.

Contractor is required to provide copies of proof of Workers Compensation and Employee Public Liability Insurance within fifteen (15) calendar days after notification of contract award.

10. Invoicing and Payment Overtime & Holiday Pay Any overtime and/or holiday pay that may be entitled to the Contractor’s employees shall be the sole responsibility of the Contractor and shall not be billed to nor reimbursed by the Government.

Contractor will bill and be paid for actual services provided by Contractor personnel. Contractor will not be paid for “availability” or “on-call” services unless otherwise provided herein.