Attachment 1 - Statement of Work.pdf
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- Attached to
- Processing Experimental Samples
- Solicitation number
- 12305B24Q0072
About this file
This document is a Statement of Work (SOW) for a federal contract opportunity issued by the USDA-ARS Diet Genomics and Immunology Laboratory (DGIL) at the Beltsville Human Nutrition Center (BHNRC) in Maryland. The requirement is for whole-genome shotgun sequencing services for 137 intestinal content samples and short chain fatty acid (SCFA) determination in 94 of these samples. The contractor must perform DNA extraction, library preparation, sequencing, and bioinformatic analysis, including microbiome analysis and functional profiling. The government will provide the 137 intestinal content samples. The contract has a 4-month period of performance and the deliverables include quality control data, sequencing data, and SCFA analysis results. The federal contract opportunity is Solicitation Number 12305B24Q0072, a 100% small business set-aside with a NAICS code of 541990 and a small business size standard of $19.5 million. Offers are due by April 17, 2024, and the evaluation will be based on best value considering price, technical capability, and past performance.
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Other files
| File | Type | Posted |
|---|---|---|
| AMEND 0001 Attachment 3 - Questions and Answers.pdf | ||
| WD 2015-4281.pdf | ||
| Attachment 2 - Contract Terms and Coniditons.pdf |
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STATEMENT OF WORK (SOW)
GENERAL INFORMATION:
1.0 Background:
The USDA-ARS Diet Genomics and Immunology Laboratory (DGIL) at Beltsville Human Nutrition Center (BHNRC) in Maryland requires whole-genome shotgun sequencing services for 137 intestinal content samples and short chain fatty acid (SCFA) determination in 94 of these samples.
2.0 Scope of Work:
The requirement is to generate Shotgun metagenomic sequencing using libraries derived from intestinal contents DNA and bioinformatic report that includes quantification of microbes and associated functions. In addition, determination of SCFA concentration is also required for part of the same intestinal content samples used for sequencing.
CONTRACTOR REQUIREMENTS:
3.0 Technical Requirements/Tasks:
• The contractor will perform DNA extraction and library preparation for 137 intestinal content samples providing quality control data.
• Sequencing of libraries will be performed using Illumina platform with 2 x150 base pair-end reads and the Illumina Novaseq2 instrument for whole-genome shotgun sequencing with a mean depth of at least 9 million sequences per sample.
• Contractor will process and analyze 94 intestinal content samples for measuring short chain fatty acid (SCFA) concentration including: acetic, propionic, butyric, valeric, isovaleric, caproic and heptanoic acids using Gas Chromatography with flame Ionization detector (GC-FID) instrument.
• Contractor will generate Bioinformatic report including microbiome analysis of alpha and beta diversity, determination of most abundant taxonomic groups as well as the functional profile in each sample using SUPERFOCUS platform and UNIREF including different gene ontologies for functional assessment.
4.0 Government Furnished:
The government will provide 137 intestinal content samples individually labeled to the Contractor for shotgun metagenomic sequencing and for determination of SCFA in 94 of these samples.
5.0 Schedule / Deliverables
• Schedule o To be completed within 4 months after the contract is established.
• Deliverables o The contractor will provide quality control data from extracted DNA along with the fastq files generated after sequencing.
o Contractor will provide sequences with a mean read depth of at least 9 million per sample with at least 90% of the samples achieving 3.8million reads excluding samples failing prior to quality control.
o Contractor will provide SCFA finalized data in the form of chromatograph with concentration of peaks for each of the seven SCFA analyzed.
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