A-- Microbiome Studies/Research (VA-19-00057012)

Page 3 of 3 THIS IS A NOTICE OF INTENT, NOT A REQUEST FOR A QUOTE/ PROPOSAL. A SOLICITATION DOCUMENT HAS NOT BEEN ISSUED AND PROPOSALS HAVE NOT BEEN REQUESTED. The Department of Veterans Affairs, VHA Regional Procurement Office -East, intends to enter into on a sole source basis, under the authority of 41 U.S.C. 253 (c) (1) and FAR 6.302-1(a) (2) (ii), a contract, entitled " Microbiome Sequencing in Systemic Lupus Erythematosus (SLE) Disease This contract is necessary to perform the process of DNA amplification by PCR and subsequent sequencing. However, Molecular Research LP, of Shallowater, Texas is the only Company that can successfully sequence DNA isolated from plasma. We previously sent samples to other companies, and they were unable to successfully sequence the DNA isolated from plasma. This notice of intent is not a request for competitive quotes/ proposals. However, if there are sources other than Molecular Research LP, able to perform the requirement, they must respond by submitting a capability statement within 5 business days of publication of this synopsis. Quotes/Proposals received within 5 business days of publication of this synopsis will be considered solely for the purpose of determining whether to conduct a competitive procurement. A determination by the Government not to compete this proposed requirement based upon responses to this notice is solely within the discretion of the Government. Deliveries should be by made by electronic mail (e-mail), hand carried or sent via other mail or package delivery services. NO COLLECT CALLS OR FACSIMILE TRANSMISSIONS WILL BE ACCEPTED. This acquisition will be processed under FAR Part 12 - Acquisition for Commercial Items and will be made pursuant to the authority in FAR 13.106-1(b)(2) and 13.501-(a)(1) to use simplified procedures for commercial acquisitions. The North American Industry Classification System Code is 541715 Research and Development in the Physical, Engineering and Life Sciences (except Biotechnology and Nanotechnology) business size standard is 1,000 employees. Only one award will be made as a result of this solicitation. This will be a firm fixed price type contract for Base year and (4) one year Options of the requested services. Any interested party that believes it can meet the above requirement may submit a capability statement. All information furnished must be in writing and must contain sufficient detail to allow determining if the interested party can meet the above criteria, meaning experience and expertise. The capability statement must be received in the Contracting Office mentioned below on or before 10:00 APM EST on July 29, 2019. All questions must be submitted in writing and can be emailed to Wileen Stokes, Contract Specialist, at contact@example.gov. In the event this procurement is solicited in the future on a competitive basis, in order to receive an award, contractors must have valid registration and certification in the System for Acquisition Management (SAM) www.sam.gov. Please reference solicitation No. 36C24719Q0806 on all correspondence. Contracting Office Address: VHA Regional Procurement Office-East W.J.B Dorn VA Medical Center, Bldg.#100 6439 Garners Ferry Road Columbia, SC 29209 Place of Performance: Ralph H. Johnson VA Medical Center 109 Bee Street Charleston, SC 29401 Primary Point of Contact: Wileen Stokes, Contracting Officer contact@example.gov Statement of Work Title: Microbiome Sequencing in Systemic Lupus Erythematosus (SLE) Disease Background Systemic lupus erythematosus (SLE) is a chronic inflammatory autoimmune disease characterized by loss of tolerance to self-antigens leading to the hallmark production of autoantibodies. However, the etiology of SLE remains largely unknown with many studies suggesting a role for genetic, hormonal, immunologic, and environmental factors. There is growing evidence to suggest that autoimmune diseases such as SLE may arise or worsen due to increased intestinal permeability allowing passage of antigens into the systemic circulation. Translocation of microbes or microbial components into the systemic circulation can result in consequences including alteration of microbiota composition and immune system activation. In SLE disease, the extent of intestinal permeability and microbial translocation and their effect on SLE disease development is yet to be defined. We hypothesize that increased gut permeability resulting in increased magnitude of microbial translocation and alteration of microbiota composition are catalysts for development of SLE disease. Determining the microbiota composition in SLE disease requires DNA extraction of microbes or microbial products from either stool or plasma samples. After DNA extraction, the 16S rRNA gene, a highly conserved region found in bacteria, is amplified through a polymerase chain reaction (PCR) and then sequenced. The produced sequences undergo bioinformatics preprocessing and quality control before they are finally annotated to different microbial species or taxa. To begin the process of identifying microbes or microbial products present in the gut or plasma of SLE patients, bacterial DNA is extracted from plasma or stool using the QIAamp UCP Pathogen Mini Kit produced by Qiagen. This process of bacterial DNA extraction is completed in the lab of Dr. Gary Gilkeson. Following bacterial DNA extraction, the extracted DNA is amplified through a molecular biology process called polymerase chain reaction (PCR). Briefly, the process of PCR involves three main stages. The first stage is denaturation, or separating of double stranded DNA into single strands through high heat. After denaturation is annealing which involves lowering the reaction temperature to allow DNA primers to attach to the template DNA. The last stage is elongation, when the temperature is increased and a new strand of DNA is made by Taq polymerase enzyme. Following amplification by PCR, sequencing of the DNA is performed to identify the various bacteria or bacterial products present in the plasma or gut. The contractor, Molecular Research (MRDNA), will perform the process of DNA amplification by PCR and subsequent sequencing. For PCR, the 16S rRNA gene V4 variable region PCR primers 515/806 (or other primers selected) with barcode on the forward primer will be used in a 30 cycle PCR (5 cycle used on PCR products) using the HotStarTaq Plus Master Mix Kit (Qiagen, USA) under the following conditions: 94°C for 3 minutes, followed by 28 cycles of 94°C for 30 seconds, 53°C for 40 seconds and 72°C for 1 minute, after which a final elongation step at 72°C for 5 minutes is performed. After amplification, PCR products are checked in 2% agarose gel to determine the success of amplification and the relative intensity of bands. Multiple samples are pooled together (e.g., 100 samples) in equal proportions based on their molecular weight and DNA concentrations. Pooled samples are purified using calibrated Ampure XP beads. Then the pooled and purified PCR product is used to prepare DNA library by following Illumina TruSeq DNA library preparation protocol. Sequencing is then performed on Illumina s MiSeq following the manufacturer s guidelines. Following the sequencing, sequence data is processed using MR DNA analysis pipeline. Briefly, the sequencing analysis pipeline involves joining sequences, depleting barcodes and removing sequences with less than 150 base pairs and sequences with ambiguous base calls. Sequences are then denoised, OTUs generated and chimeras removed. Operational taxonomic units (OTUs) are defined by clustering at 3% divergence (97% similarity). Final OTUs are taxonomically classified using BLASTn against a curated database derived from GreenGenes, RDPII and NCBI (www.ncbi.nlm.nih.gov, DeSantis et al 2006, http://rdp.cme.msu.edu). The raw DNA sequences generated from the sequencing as well as the data generated from the analysis pipeline will be sent back to the Gilkeson lab, where we will perform further downstream analyses to identify microbes and microbial products specific to SLE disease. The expected timing for the sequencing service is base year plus four option years of performance. Objectives Perform DNA amplification and 16S sequencing from extracted DNA samples sent from the Gilkeson lab Provide raw sequencing reads and analysis pipeline data from the 16S sequencing back to the Gilkeson lab Scope The scope of work includes PCR amplification and subsequent 16S rRNA gene sequencing of the provided DNA samples, and provision of the sequencing reads and generated analysis data back to the Gilkeson lab upon completion of the sequencing. Statement of Required Goods or Deliverables The contractor, Molecular Research (MRDNA), must deliver the raw sequencing reads and the data analysis files for each sample received upon completion of the 16S sequencing. The raw sequencing data with the reads for each sample can be sent through email with a link containing the location of the raw sequences in Illumina s BaseSpace Sequence Hub Data Storage. The data analysis files and folders can be sent through email. Tasks The contractor, Molecular Research (MRDNA), shall perform the tasks stated in the objectives. Training No training is required for this scope of this work. Government-furnished property There is no government-furnished property being supplied for this proposed scope of work. Security Requirements There are no security requirements associated with the proposed scope of work. Period of Performance or Required Delivery Date The expected timing for the sequencing service is base year plus four option years of performance. The receipt of the order by the stated delivery date is essential in order to have sufficient time for data analysis and dissemination of the results to the general public through peer-reviewed publications.