SPECIAL NOTICE
66 -- NOTICE OF INTENT TO SOLE SOURCE TO COREBIOME INC
- Notice Date
- 6/4/2018
- Notice Type
- Special Notice
- NAICS
- 541990
— All Other Professional, Scientific, and Technical Services
- Contracting Office
- Agricultural Research Service - Western Business Service Center
- ZIP Code
- 00000
- Solicitation Number
- 1232SD18P0360
- Archive Date
- 6/12/2018
- Point of Contact
- WASHINGTONI NLN,
- E-Mail Address
-
washingtoni.NLN@ars.usda.gov
(washingtoni.NLN@ars.usda.gov)
- Small Business Set-Aside
- N/A
- Description
- The USDA ARS - WBSC intends to award a sole source Firm Fixed Purchase Order (PO) to COREBIOME, INC, 25 Langford Park, St. Paul, MD 55108-1910. This order will purchase CoreBiome BoosterShot TM Shotgun Sequencing & DNA Extraction in support of the ongoing research at USDA ARS, Western Health Nutrition Research Center (WHNRC), Obesity and Metabolism Unit (OMU), 430 West Health Sciences Drive, Davis, CA. The Firm Fixed PO will include the following: 1. CoreBiome Extraction • MoBio PowerFecal DNA isolation kit 2. CoreBiome BoosterShot TM Shotgun Sequencing • Library preparation and QC from extracted DNA. • Whole-genome shotgun sequencing using Illumina NextSeq 1x145 single-end reads • Mean read depth of 0.5 million sequences per sample. Not all QC-validated samples will achieve the mean depth: o ≥ 95% of samples > 0.25M reads (50% of specification), excludes samples failing prior QC 3. CoreBiome Core Analysis Online Report • Raw FASTQ data • Trimmed, adaptor-removed FASTA data • Quality-control dashboard • Strain- and species-level taxonomic assignments via alignment to a curated reference database. • Direct functional profiling via alignment to a curated reference database, reported as KEGG orthology groups, modules, and pathways where available. • Best-practice diversity analysis and data visualization CoreBiome created a process called BoosterShot TM. BoosterShot TM is "shallow shotgun" sequencing method using illumina techology used to profile the composition of the microbiome, providing species-level or strain-level resolution. Based on the algorithms developed in the lab of computational biologist Dr. Dan Knights at the University of Minnesota, BoosterShot TM uses very shallow (low-coverage) shotgun sequencing to recover the full species-level taxonomic and functional repertoire. BoosterShot TM gives far superior taxonomic and functional profiles to 16S sequencing because their software is able to use 10% or more of observed sequences as species level markers, achieving rich coverage of microbiome composition even at very low sequencing depths. Overall Performance of BoosterShot TM - Sequencing output and Sensitivity: BoosterShot TM is built on a foundation of standard shotgun nextgeneration sequencing, powered by proprietary library creation, sequencing, and advanced informatics. Sequencing executed on the Illumina HiSeq platform in single-end, 1x100-bp sequencing mode at a depth of approximately 250,000-500,000 sequences per sample. In a typical human gut microbiome sample BoosterShot TM recovers approximately 50,000 species-level markers, for detection of species at an abundance of 0.04%. This is similar sensitivity to BenchMark TM, but with better taxonomic and functional resolution. Analysis: CoreBiome provides customers with full primary data analysis and annotation, including species-level and putative strain-level taxonomy tables, KEGG metabolic pathway and module tables predicted the Knights Lab's SHOGUN tool (expected to have substantially higher accuracy than PICRUSt predictions from 16S sequencing), beta diversity analyses (Bray-Curtis distance at different taxonomic levels, strain-level weighted and unweighted UniFrac distances), and alpha diversity analysis (Shannon, Simpson, Chao1, and whole-tree phylogenetic diversity). Customers also have access to raw demultiplexed sequencing data. USDA ARS, WHNRC is attaining the BoosterShot TM Sequencing & DNA Extraction in support of their primary goal of the Obesity and Metabolism Unit (OMU), which is to identify the sources of variation that predispose a person to increased adiposity and body weight. One critical source is the composition and function of the gut bacteria. The sequencing project proposed is aimed at understanding the functional composition of the microbiota (the bacteria themselves and the genes they contain) which are related to physiological traits like adiposity and body weight. BoosterShot TM combines "shallow shotgun" gene sequencing methods with specific analytical algorithms to both profile the composition of the microbiome while providing functional annotation of gene functions. The BoosterShot TM methods will provide the Dr. Bennett's lab (OMU scientist) an efficient method to accomplish his research goal. Pursuant to the authority of 41 U.S.C. 253(c)(1) and FAR 6.302-1, Only One Responsible Source and No Other Supplies or Services Will Satisfy Agency Requirements. The award date will be on or about June 12, 2018; and this Notice of Intent is not considered as a Request for Quotation (RFQ) nor is it a Request for Proposals (RFP). No solicitation document is available and telephone requests will not be honored. Interested persons may identify their interest and capability to respond to this requirement. A determination, by the Government, to compete this proposed PO based on responses to this notice is solely within the discretion of the Government. The Government will consider all responses received by 10:30AM PST, June 11, 2018. Information received will be considered solely for determining whether to conduct a competitive procurement. Inquiries will only be accepted via email to the Primary Point of Contact: Washingtoni.NLN@ars.usda.gov.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/notices/62ddac6b58a1d369807cffbfea8e7c17)
- Place of Performance
- Address: USDA ARS, Western Health Nutrition Research Center (WHNRC), Obesity and Metabolism Unit (OMU), 430 West Health Sciences Drive, Davis, CA., United States
- Record
- SN04942373-W 20180606/180604230636-62ddac6b58a1d369807cffbfea8e7c17 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
(may not be valid after Archive Date)
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