SOLICITATION NOTICE
R -- Extraction of Bacterial DNA and RNA from Human Oral Swabs and Characterization of Human Microbiome
- Notice Date
- 8/26/2013
- Notice Type
- Presolicitation
- NAICS
- 541380
— Testing Laboratories
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 9609 Medical Center Drive, Room 1E128, Rockville, Maryland, 20852, United States
- ZIP Code
- 20852
- Solicitation Number
- NCI-130126-HN
- Archive Date
- 9/10/2013
- Point of Contact
- Huy Nguyen, Phone: 2402765570, Seena Ninan, Phone: 240-276-5419
- E-Mail Address
-
anh-huy.nguyen@nih.gov, ninans@mail.nih.gov
(anh-huy.nguyen@nih.gov, ninans@mail.nih.gov)
- Small Business Set-Aside
- N/A
- Description
- Contracting Office Address: Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 9609 Medical Center Drive Room 1E154 Bethesda, MD 20892 Description: The National Cancer Institute (NCI), Division of Cancer Epidemiology & Genetics (DCEG), Genetic Epidemiology Branch (GEB) plans to procure on a sole source basis with the University of Maryland (UMD) for the extraction of Bacterial DNA and RNA from Human Oral Swabs and Characterization of Human Microbiome. The products herein are being procured in accordance with the simplified acquisition procedures as authorized by FAR Part 13.106-1(b)(1). The North American Industry Classification System code is 541380 and the small business standard is $14 million dollars. Only one (1) award will be made as a result of this solicitation. This will be awarded as a Firm Fixed Price (FFP) type contract. It has been determined there are no opportunities to acquire green products or services for this procurement. Human microbial communities (microbiotas) play an important role in the human health. The oral microbiotas are centrally related to nutrition, metabolism, immunity, inflammation, and endocrine balance. The oral cavity has the most diverse microbial communities among all the surveyed human body sites. In part, this is because microbiotas in the different sites of the same oral cavity vary widely. Recent studies indicated that the difference in microbial profiles between buccal mucosa and gingival plaque is as distinct as the difference between tongue and stool. Cigarette smoking is associated with serious health outcomes including cancer, cardiovascular disease and chronic lung disease. However, precisely how cigarette smoking leads to these health outcomes is still incompletely understood. One emerging hypothesis is that cigarette smoking might promote the colonization and overgrowth of certain human associated microbial species, which may lead to inflammation and adverse health outcomes including cancer. Cigarette smoking exposure increases the risk of several infectious diseases. Cigarette smoking has also been shown to promote the colonization of pathogens such as Porphyromonas gingivalis, Campylobacter retus, Prevotella intermedia, Tannerella forsythia, Treponema denticola and Fusobacterium nucleatum. Recently it was demonstrated that cigarette smoking could impair epithelial innate immune responses to microbial products, perhaps setting stage for microbial overgrowth and invasion. Knowledge about the effects of smoking on oral microbiotas is lacking. In this study, the NCI will survey the effects of cigarette smoking on oral microbiotas across 10 different oral sites (mouthwash, saliva collection and 8 different oral swabs from tongue dorsum, hard palate, buccal mucosa, keratinized gingiva, palatine tonsils and throat, supragingival plaque, subgingival plaque). These oral samples were collected from 25 heavy smokers and 25 never smokers. This study will provide information to determine whether cigarette smoking affects oral microbiotas and the degree of these effects on oral microbiotas across the 10 oral sites. The study will indicate promising oral sites for further studies of the relationship between cigarette-smoking and oral microbiotas. It will also provide information to determine whether buccal cells collected in the PLCO cohort can be used for further studies about the interrelationship between cigarette smoking, oral microbiota and tobacco-related cancer. In addition, initial estimates and variances of microbial composition, diversity and relative abundance will provide information required for designing future studies. The NCI has a project that requires bacterial DNA and RNA extraction from human oral and nasal swabs, PCR and sequencing for 16S rRNA bacterial genes, and bioinformatics analysis of the human microbiome. The project includes 9 different oral and 1 nasal swab collected from each subject. The DNA extraction for bacterial DNA and RNA for swab samples requires special protocols to maximize bacterial DNA and RNA extraction, while at the same time minimizing human DNA and RNA extraction. The NCI also require DNA and RNA extraction simultaneously from each swab. Also, nasal swabs require protocols different from oral swabs in order to obtain sufficient DNA and RNA to successfully conduct the analyses. It is important to note that ordinary protocols for DNA and RNA extraction are inadequate because in contrast to conventional genomic analyses, microbiome studies focus on nucleic acids from microbial origin. The UMD has already developed and conducted necessary quality control on the protocols especially for NCI samples to extract bacterial DNA and RNA from human oral and nasal swabs. As one of the leading institutes in human microbiome, the UMD has in depth experience in bacterial DNA and RNA extraction from swab samples (e. g. oral swabs, anal swabs, vagina swabs), PCR and sequencing of human microbiome and follow-up bioinformatics support. The UMD is the only known laboratory in the USA with the capability to provide all the services using the required protocols required by the NCI. The Contractor shall perform the following: 1)Total DNA from 500 oral samples 2)Total RNA extraction from 450 oral samples (The mouthwash samples are not included.) 3)PCR amplification of the 16S rRNA gene using primers F319-R806 for 500 samples 4)PCR products quantification and pooling 5)lllumina sequencing library construction 6)Sequencing of Illumina MiSeq (250 bp paired-end reads) 7)Initial ioinformatics analysis - Quality analysis/control (remove low quality/short reads,reads containing homopolymeric repeat and chimeric reads). 8)provide total DNA, RNA and denoised 16S rRNA gene sequence data The total DNA, total RNA, DNA sequences, and the analyzed sequences will be delivered to the NCI COR within a month of completion. The Period of Performance is twelve months from the contract award date. This is not a solicitation for competitive quotations. However, if any interested party believes they can meet the above requirement, especially small businesses, they may submit a tailored statement of capabilities via fax or email. In addition, all responsible sources may submit a bid, proposal, or quotation which shall be considered by the NCI. All information furnished must be in writing and must contain sufficient detail to allow the NCI to determine if it can meet the above unique specifications described herein. All information must be received in the NCI contracting office on or before 11:00 AM EST on September 09, 2013. All questions must be in writing and can be faxed (240) 276-5401 or emailed to Anh-Huy Nguyen, Contract Specialist at anh-huy.nguyen@nih.gov. A determination by the Government not to compete this proposed contract based upon responses to this notice is solely within the discretion of the Government. Information received will be considered solely for the purpose of determining whether to conduct a competitive procurement. In order to receive an award, contractors must have valid registration and certification in the System for Award Management (SAM) www.sam.gov. No collect calls will be accepted. Please reference solicitation number NCI-130126-HN on all correspondences.
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