Genome Sequencing Analysis
Note, This Solicitation is being posted in Draft Format initially, to allow for contractor questions and comments. The solicitation will be released no later than the response date of the government answers to contractor questions.
The US Army Medical Research Acquisition Activity (USAMRAA) is seeking potential sources capable of providing the following R&D services: Wound Microbiome Project - Chronic Wound Metagenomics and Metatranscriptomics Studies. This R&D effort will be in support of the U.S. Army Institute of Surgical Research (USAISR) in San Antonio, TX.
The goal of this study is to apply a high-resolution metagenomics strategy in conjunction with metatranscriptomics approach towards tissue specimens from chronic human wound debridement to understand the microbial ecosystem (virulence profile) present in healing-impaired wounds at the genomic and transcriptomic level. Next, the microbial profile of these chronic wound specimens, which are classified as ulcer pressure, diabetic foot ulcer, and venous leg ulcer, will be computationally correlated with the wound etiology and other clinically relevant metadata (e.g., comorbidity). Better defining the microbial composition and genotypic profile of chronic wound residents including bacteria, fungi, and viruses (microbial metagenome) via high-throughput deep sequencing will aid in defining the molecular crosstalk and interplay between different chronic wound inhabitants that result in changes in survival, fitness, or virulence; thus providing the foundation for understanding the homeostatic state and mechanisms contributing to development of chronic wounds. Moreover, identifying the genotypic features of a diverse collection of chronic wounds can ultimately lead to novel therapeutic strategies (e.g., probiotics). Metatranscriptomics profiling of the microbiota that reside in different types of chronic wounds will provide the mechanistic insight to better understand the functional characteristics of the human wound microbiome and its susceptibility to treatment.
The tasks may include but are not limited to:
1. Metagenomics Study - Use the latest deep-sequencing high-throughput NGS technology, conduct whole-genome shotgun sequencing (WGS) technology to capture and characterize microbial residents of chronic wounds including fungi, bacteria, and viruses (ssDNA and dsDNA). The details of the capabilities and approaches for library preparation and NGS sequencing will be provided by the vender and discussed with ISR investigators.
2. DNA Library Preparation
3. Whole-Metagenome Sequencing
4. DNA Bioinformatics Analysis
5. Metatranscriptomics Study - Capture transcripts produced by bacteria and fungi while also detecting the presence of RNA viruses. Use RNA-Seq technology to generate a total transcriptome profile (metatranscriptome) of wound specimens to investigate dynamics of gene expression, overall pathway landscape, and the metabolome profile of the wound's microbial community. The details of the capabilities and approaches offered for library preparation and RNA-sequencing will be detailed and provided by the vender and discussed with ISR investigator.
6. cDNA Library Preparation
7. RNA Bioinformatics Analysis
David R. Daniel, Contract Specialist, Phone 301-619-2845, Email david.r.daniel27.civ@mail.mil
