Q301--Intent to Sole Source to University of Florida Research - Metagenomic Sequencing Analysis for Gut Microbiomes - MADISON VA

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Contract Opportunity

The Veteran s Administration (VA) Office of Research and Development, Regional Procurement Office East in Pittsburgh, PA intends to negotiate on a sole source basis with the University of Florida based in Gainesville, FL on behalf of the Madison WI VA Healthcare System. The requirement is to provide research assistance for a planned VA medical study. The study focuses on the successful execution and completion of the Department of Veterans Affairs BCCMA-funded research project, #1I01CX002471-01A2 : BCCMA: Targeting Gut Microbiome in Veterans Deployment related Gastrointestinal and Liver Diseases: CMA5-Functional metagenomics in GWI-related gut dysfunction, The requirement is for metabolomics analysis lab support services to characterize metabolites present in the samples. Metabolomics identifies the end products of bacterial fermentation of foods in the gut and allows the VA to understand the function of the gut microbiome. This understanding is necessary for deciphering the mechanistic relationship between the gut microbiome and gulf war illness. The methods proposed for metabolomics are commonly accepted methods in the scientific literature and provides a deep level analysis of the mechanistic relationship of the human microbiome and host diseases. This analysis will enable the project Principle Investigator (PI) and research team to assess whether elements of the human gut microbiome are related to symptoms of Gulf War Illness in Veterans.
The contractor shall have previous experience conducting similar analyses in other patient populations, which will be leveraged for the results of Veteran participants. Presently, the parent project has accumulated the pilot data for sequencing (Aims 1 and 2) and will also enroll additional subjects and collect samples throughout the project period.

The specific work to be performed includes:

Samples will be shipped in batches to the contractor for testing. Metagenomic sequencing, bile acid laboratory testing, and fatty acid laboratory testing will be performed on week 1-3 samples (N=207) using the Illumina NovaSeq 6000 at the contractor s Genomics Center. Libraries will be prepared using local procedures and prep kits. Samples will be sequenced using 2x250 bp reads on the S4 flow cell with an estimated 30 million reads per sample. Metagenomic sequencing will provide species level taxonomic data as well as provide data on the functional potential of the gut microbiome of subjects. Data, including raw reads data, will be transferred to Madison VA for analysis and storage. Samples will be exhausted at the contractor s facility and destroyed according to local policies and procedures after sequencing is completed.

5.1 Task 1 The contractor shall provide necessary supplies to library prep and preliminary processing at the laboratory and will consult with personnel at Madison VA to ensure correct and standardized procedures.

5.1.1 The contractor shall advise personnel at Madison VA on all necessary equipment for the services performed and processing procedures.

5.1.2 The contractor shall also provide support to the Madison VA personnel for the duration of the contract in order to maintain sample quality and integrity.

5.1.3 The contractor shall verify sample quality upon receipt of sample shipments from Madison VA by examining package shipper integrity, proper temperature controls, integrity of sample vials, and verifying number and type samples against the manifest accompanying the shipment.

5.2 Task 2 The contractor shall provide results from comprehensive laboratory testing and/or metagenomics sequencing analyses of previously and to be collected stool and serum samples from participants of the parent project.

5.2.1 Duplicate testing of any leftover samples may be performed upon request of Madison VA in the event of failed sequencing run, or other confounding event, to receive results.

5.2.2 Testing for bile acids may be performed at the request of Madison VA team on all samples, or a subset of samples, per the study protocol. Testing will be performed by contractor according to procedures approved by Madison VA. Results will be transferred via approved methods after each batch of laboratory testing for bile acids is completed.

5.2.3 Testing for fatty acids may be performed at the request of Madison VA team on all samples, or a subset of samples, per the study protocol. Testing will be performed by contractor according to procedures approved by Madison VA. Results will be transferred via approved methods after each batch of laboratory testing for fatty acids is completed.

5.3 Task 3 The contractor shall provide regular progress reports (at a minimum of every 90 days) to research personnel at Madison VA.

5.3.1 Progress reports will include itemized lists of: Sample number, receipt date, type of testing performed, analysis date, and date results will be sent to Madison VA research personnel.

5.3.2 Communication and questions regarding contractor progress will be transmitted to the Madison COR and Madison VA research personnel via email.

5.3.3 Delays in timeline to generate results, or other barriers to complete any work, will be explained via progress reports and emails by contractor and solutions will be offered to complete the required services

The requirement will take place at the contractor s facility with information received from the Madison, VA. The sole source is pursuant to FAR 6.302-3 (a)(2)(ii) Industrial Mobilization, Engineering, Developmental or Research Capability or Expert Services per 41 USC §3304(a)(3). This notice of intent is not a request for competitive proposals, however; any responsible source who believes it is capable of meeting the requirement may submit a capability statement and supporting documentation to the contracting office no later than Thursday, May 29, 2025, (10:00 AM, EST). Interest/capability statements may be sent to Michael Haydo at Michael.haydo@va.gov. No telephone responses will be accepted. A determination not to compete the proposed requirement based upon the responses to this notice is solely within the discretion of the Government.

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