A11 - Sources Sought_Final.docx

Sources Sought Notice

Title of Project: scRNA Sequencing Service of Influenza Vaccine Study Samples

Introduction. This is a Sources Sought notice. This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this notice is to obtain information regarding the availability and capability of qualified sources; Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. The NAICS code for this Sources Sought Notice is: 541380 Testing Laboratories and Services.

Background. The Centers for Disease Control and Prevention (CDC) is charged with influenza pandemic preparedness and response, with one of the primary goals being developing and assessing effective influenza vaccines. The immune response elicited by a vaccine is characterized by the induction of protective immunological memory. Although the precise mechanisms underlying this response are not yet fully understood, modern techniques such as bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) have greatly enhanced our understanding of the immune response following vaccination.

Purpose and Objectives. This initiative seeks to provide the Influenza Division with library construction and NGS services for RNA sequencing. Samples from various infected, vaccinated, and/or control cohorts will be provided to the Contractor for bulk RNA sequencing and scRNA-seq. Combining the results of both bulk RNA sequencing and scRNA-seq allows for the identification of key genes, cell types, and molecular pathways involved in the protective immune response elicited by vaccines. In turn, these insights will inform the development of more effective vaccines and therapeutic strategies for combating influenza and other infectious diseases.

Project Scope.

The scope is limited to the activities required for sequencing of samples provided by the Government. This primarily includes library construction and Next-Generation Sequencing (NGS) services for both bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq). The Scope of Work includes processing up to 450 mammalian and viral RNA samples for bulk RNA sequencing, ensuring a minimum coverage of 20 million 150bp paired-end reads per sample, and performing bioinformatics analysis on the generated data. For scRNA-seq, the Contractor is responsible for sequencing up to 225 Government-prepared libraries, guaranteeing over 300 million 150bp paired-end reads per sample. The Contractor must also provide quality control reports prior to sequencing to confirm sample integrity.

Turnaround time (TAT) is a critical aspect of this project. For bulk RNA-seq, the maximum TAT specified is 35 business days for every batch of 48 samples post-quality control completion. In contrast, scRNA-seq requires a TAT of 14 business days for batches on flow cells with up to 16 lanes and 28 business days for those with up to 32 lanes. All sequencing must achieve at least a Phred quality score greater than Q30 (>99.9% base call accuracy), or similar metric, with detailed quality control analyses provided before each batch's sequencing commencement.

The Contractor will utilize high-throughput NovaSeq-X Series technology or an equivalent platform capable of producing extensive read outputs while maintaining quality standards. Bioinformatics analysis conducted by the Contractor will include alignment, raw read counts in FPKM, expression estimates, gene body coverage, splicing annotation, hierarchical clustering, PCA analysis, and heatmap correlation assessments.

See a draft Statement of Work (SOW) attached to this announcement.

Anticipated period of performance. The period of performance will be one years.

Capability Statement/Information Sought. PAGE LIMIT 10 PAGES.

Interested firms are requested to submit a capability statement, which shall include documentation of the ability to perform the requirements and information on previous successfully completed contracts for the same type of work. The capability statement shall specifically address the criteria listed below ONLY. Please note that capability statements that only include marketing material will not be considered or reviewed.

a. Your opinion about the difficulty and or feasibility of the potential requirement(s) or proposed acquisition, possible solutions and approaches that may currently exist in the marketplace, and information regarding innovative ideas or concepts;

b. Your staff expertise, including your availability, experience, and formal and other training; include a discussion on your proven track record for the type of work as per the SOW;

c. Your current in-house capability and capacity to perform the work; specifically, the Contractor must demonstrate a robust infrastructure capable of handling high-throughput sequencing operations, including access to advanced platforms such as the NovaSeq-X Series or validated equivalents. The capability statement should detail the Contractor's laboratory facilities, equipment availability, and maintenance protocols that ensure uninterrupted operation and adherence to the specified turnaround times (TAT). Furthermore, it is essential for the Contractor to exhibit an established process for quality control using systems like Agilent TapeStation or equivalent technologies that guarantee sample integrity before sequencing. The Contractor should also provide evidence of sufficient bioinformatics support with proven expertise in data analysis as outlined in the scope of work, including but not limited to alignment, FPKM raw read count assessment, expression estimates, gene body coverage analysis, splicing annotation, hierarchical clustering, PCA analysis, and heatmap correlation. Capacity assessments should include personnel allocation plans and workflow management strategies that can accommodate up to 450 bulk RNA samples and 225 scRNA-seq libraries within the project's TAT requirements. Documentation of previous experience managing similar scale projects with high-quality deliverables will substantiate the firm's ability to meet the Government's needs effectively. Completed projects in the last 5 years of similar size and scope;

d. Corporate experience and management capability;

e. Provide any examples of prior completed Government contracts, reference, and other related information;

f. Recommendations for a different NAICS code. If so, please explain?

Information Submission Instructions: Please include a cover page with the following business information. The cover page does not count against the page limit for the capability statement.

1. Company name and address;

2. UEI number and CAGE Code, as registered in the System for Award Management (SAM) at http://www.SAM.gov/;

3. Do you have a government-approved accounting system? If so, please identify the agency that approved this system;

4. Business Size and Type of Business (e. g., small business, 8(a), woman owned, veteran owned, etc.).

5. Technical point of contact including name, title, address, telephone number, and email address of the individual(s) who can verify the demonstrated capabilities identified in the response;

6. Contracts’ point of contact including name, title, address, telephone number, and email address;

7. In your opinion, can this work fit under a GSA Schedule? If so, which GSA Schedule? Please provide the schedule number.

Page Limitation: Capability Statements shall be limited to TEN (10) single-spaced pages not including cover page. Pages shall be formatted as follows: MS Word, 8 ½ x 11, 12 pitch, Times New Roman font with one (1) inch margins.

Response Due Date: Submit capability statements via email to Kahala McCaskey, Contract Specialist at zch2@cdc.gov. Should you have any questions concerning this sources sought, please direct your questions in writing to the Contracting Specialist Kahala McCaskey at zch2@cdc.gov. The government will not respond to oral questions. Responses must be submitted no later than 1:00 pm, Eastern Standard Time (EST) by Thursday, June 20th, 2024. Capability statements will NOT be accepted after the due date. No telephonic or facsimile responses will be accepted.

The Government will not provide feedback on capability statements and we will not return capability statements received.

Disclaimer and Important Notes. This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization’s qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published on sam.gov. However, responses to this notice will not be considered adequate responses to a solicitation.

Confidentiality. No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).

Response is strictly voluntary. It is not mandatory to submit a response to this notice to participate in any formal RFP process that may take place in the future. However, it should be noted that information gathered through this notice may significantly influence our acquisition strategy. All interested parties will be required to respond separately to any solicitations posted as a result of this Sources Sought notice.

We appreciate your interest and thank you in advance for responding to the Sources Sought.