SOLICITATION NOTICE
B -- MITOCHONDRIAL GENE CHIP STUDY
- Notice Date
- 7/1/2010
- Notice Type
- Combined Synopsis/Solicitation
- NAICS
- 541711
— Research and Development in Biotechnology
- Contracting Office
- Other Defense Agencies, Uniformed Services University of the Health Sciences, Directorate of Contracting, 4301 Jones Bridge Road, Bethesda, Maryland, 20814-4799
- ZIP Code
- 20814-4799
- Solicitation Number
- PSY0CSTS004
- Archive Date
- 7/29/2010
- Point of Contact
- Christina Johnson, Phone: 3012953069
- E-Mail Address
-
cjohnson@usuhs.mil
(cjohnson@usuhs.mil)
- Small Business Set-Aside
- Total Small Business
- Description
- The Uniformed Services University of the Health Sciences (USUHS), located on the National Naval Medical Campus in Bethesda, MD has a requirement to solicit offers to award a firm-fixed price contract to an organization to conduct a mitochondrial gene chip study. This study involves identifying biomarkers for post-traumatic stress disorder (PTSD) diagnosis and treatment in a military population. In this study, USUHS will extract blood ribonucleic acid (RNA) samples from our war-fighters with and without PTSD. All RNA samples will be sent to the contractor for microarray, bioinformatics and systems-biology analyses of gene expression profiles, canonical pathways and molecular networks. Further details are provided in the attached statement of work to inform interested offerors of an overview of the services to be performed. This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes are being requested and a written solicitation will not be issued. This is a request for quotes (RFQ) for a commercial item in accordance with FAR Part 12-Acquisition of Commercial Items and FAR Part 13-Simplified Acquisition Procedures. It is the responsibility of the contractor to monitor FedBizOpps for any amendments to the solicitation. This RFQ incorporates all provisions and clauses in effect through Federal Acquisition Circular 05-41. This solicitation is set-aside for small businesses and the applicable NAICS code for this requirement is 541711 - Research and Development in Biotechnology with a size standard of 500 employees. Statement of Work (SOW) USUHS will be responsible for extracting and purifying high quality RNA samples from peripheral white blood cells derived from our war-fighters with and without post-traumatic stress disorder (PTSD). USUHS will provide the contractor with the medical records of all subjects from whom the RNA samples were derived for supervised microarray clustering analysis in order to associate particular expression patterns with PTSD and its subtypes. All RNA samples (n=30 cases of PTSD subjects and n=30 cases of control subjects) will be sent to the contractor for microarray, bioinformatics and systems-biology analyses of gene expression profiles, canonical pathways and molecular networks in order to identify non-invasive diagnostic biomarkers in the peripheral cells. The tasks to be performed are detailed below: Task-1: Month 1-3: The contractor will start to prepare all reagents and supplies and to prepare 200 hMitChip3 cDNA microarrays. This task includes: (i) to purchase microscope glass slides and chemicals; (ii) to make solutions and buffers; (iii) to coat 400 glass slides chemically for high affinity to DNA; (iv) to allow the newly coated glass slides to age for two weeks; (v) to calibrate GeneMachine OmniGrid 100 Microarrayer using test slides; (vi) to individually select and label 300 evenly-coated and dust-free slides from 400 chemically-coated microscope slides; (vii) to print third generation human mitochondrial focused cDNA microarrays (hMitChip3), of which each gene chip contains 1,136 mitochondria-focused genes and positive and negative controls; each gene is in triplicate (technical triplicate) for authentic expression profiling. Briefly, hMitChip3 consists of the 37 mitochondrial DNA-encoded genes, 1098 nuclear DNA-encoded and mitochondria-related genes, and 225 controls, each in triplicate. The completion of this task will provide hMitChip3 gene chips for the following tasks. We will print 1,360 hMitChip3 cDNA probes each in triplicate on each of 300 glass slides selected; (viii) to allow the printed slides aging for two weeks; (ix) to view each slides under microscope in order to select 200 best ones for this project; (x) to block the high affinity DNA binding sites on these 200 slides selected; and (xi) to test quality of hMitChip3 by microarray labeling and hybridization using test RNA samples. The completion of this task will provide 190 hMitChip3 gene chips for the designed microarray experiments, that is, 30 cases of PTSD and 30 cases of control subjects, each in triplicate microarray experiments as stated below. Task-2: Month 3: The contractor will perform quality control and quality assurance experiments on RNA samples by confirming quantity (1.0 g/l, 5.0 g total RNA per samples for triplicate microarray experiments) and quality (OD260 vs. OD280: 1.8-2.0) of RNA samples from USUHS provided. The completion of this task will give the number of high quality RNA samples for the following tasks. Task-3: Months 4-6: The contractor will perform microarray labeling of RNA samples derived from Task-2 using 1.0 g total RNA per label-amplification. The labeling will be followed by microarray hybridization with hMitChip3 gene chips derived from Task-1, and microarray image scanning, processing, and data extraction. Each RNA sample will be subject to triplicate microarrays for authentic expression profiling. Therefore, this task guarantees to generate at least 180 high quality microarray images and raw. It is conceivable that microarray labeling and hybridization might need to be repeated for a few RNA samples if quality does not meet our published criteria. The completion of this task will generate all necessary microarray images and raw data for further analysis. Task-4: Months 7-8: The contractor will perform the following: (i) to construct microarray database including 180 individual database files and a master database file that is hyperlinked with all 180 individual database files, gene ontology pathway database and pharmGKB database, as well as the USUHS-provided medical records of all subjects from whom the RNA samples were derived; (ii) to perform microarray data filter, exclusion, inclusion, normalization and calculation on each individual raw data; (iii) to perform unsupervised and supervised microarray data clustering analysis; and (vi) to extract significantly differentially expressed genes between relevant clinical phenotypic characteristics using appropriate statistical tests. The completion of this task will generate publishable tables displaying data normalization, differentially expressed genes with statistics (fold change, moderated t-test p-value, and FDR), and publishable figures displaying dendrograms and heatmaps of samples and genes in relationship to PTSD and its subtypes. Task-5: Months 8-9: The contractor will identify biochemical and molecular pathways and networks, biomarkers, and drug targets from the list of significantly differentially expressed genes. The hMitChip3 bioinformatic tools included data analysis procedures and customized database for interpretation of results. The database associated 645 molecular functions with 946 hMitChip3 genes, 612 biological processes with 930 genes, 172 cellular components with 869 genes, 107 biological chemistry pathways with 476 genes, 23 reactome events with 227 genes, 320 genetic disorders with 237 genes, and 87 drugs targets with 55 genes. The completion of this task will yield publishable tables and figures including functional and disease categories of differentially expressed genes, canonical pathways and a major pathway with dysregulated genes, molecular networks with key functions and dysregulated genes. Based on sample size, this might lead to the identification of non-invasive diagnostic fingerprints. Before publication, USUHS will validate microarray results by conducting qRT-PCR analysis of at least 20 differentially expressed genes, particularly focusing on those with diagnostic values detected by the microarray technology in all RNA samples used. Then, we will be able to publish our results. CONTRACTOR'S RESPONSIBILITIES The contractor shall provide all the research support to ensure successful completion of contract requirements. Also, the contractor will send a briefing to the USUHS contact person (given at time of award) by the end of month 3 and 6, and the final report within two weeks from the end of month 9. GOVERNMENT'S RESPONSIBILITES The Government will deliver the following to the contractor: 1. extracted blood ribonucleic acid (RNA) samples 2. medical records of all subjects (war-fighters) PERFORMANCE PERIOD: All work is expected to take nine months from start of contract to delivery of data, data analysis, figure, tables and chips. Price: The contractor should provide pricing as set up below: Contract Line Number (CLIN), description, and unit of issue). Quotes are to include unit price and extended prices for each Task 1-5. CLIN 0001 Mitochondrial Gene Chip Study 1.00 jb tiny_mce_marker________________ Evaluation Factors The government will award a firm-fixed-price (FFP) contract resulting from this solicitation to the responsible offeror whose offer conforms to the combined synopsis/solicitation, and is most advantageous to the government, based on price and the technical factors listed below. Technical - Technical acceptability will be determined solely on the content and merit of the submitted in response this synopsis as it compares to the details outlined in the statement of work provided above. Therefore, it is essential for the offerors provide sufficient documentation, etc., in order for the Government evaluation team to make an adequate technical assessment of the proposal as meeting technical acceptability. Corporate Experience: Describe your organization's technical and scientific expertise as it relates to the topics described in the referenced synopsis. Additionally, address the professional qualifications and experience of key staff who may be assigned in the production of the materials and delivery of services. Past Performance: Please provide five references to be contacted by USU personnel. Include company name, description, point of contact, phone number, e-mail optional, contract value, and period of performance. The following provisions and clauses apply to this contract: • 52.212-1 Instructions to Offerors-Commercial Items • 52.212-2 Evaluation-Commercial Items • 52.212-3 Offeror Representations and Certifications-Commercial Items • 52.212-4 Contract Terms and Conditions-Commercial Items • 52.212-5 Contract Terms and Conditions Required to Implement Statutes or • Executive Orders-Commercial Items • 52.219-6 Notice of Total Small Business Set-Aside • 52.222-3 Convict Labor • 52.222-19 Child Labor-Cooperation with Authorities and Remedies • 52.222-21 Prohibition of Segregated Facilities • 52.222-26 Equal Opportunity • 52.222-35 Equal Opportunity for Special Disabled Veterans, Veterans of the • Vietnam Era, and Other Eligible Veterans • 52.222-36 Affirmative Action for Workers with Disabilities • 52.222-37 Employment Reports on Special Disabled Veterans, Veterans of the • Vietnam Era, and Other Eligible Veterans • 52.225-1 Buy America Act-Supplies • 52.232-36 Payment by Third Party Full-text versions provisions and clauses can be accessed electronically at https://acquisitioin.gov/far/index.html. To be eligible for contract award, a contractor must be registered with the Central Contractor Registration (CCR) database. For instructions on registering with the CCR, please see the CCR web site at http://www.ccr.gov. All offerors are required to submit a completed copy of the Federal Acquisition Regulations (FAR) Provision 52.212-3, Offeror Representations and Certifications - Commercial Item, with their offer. Also, list your DUNS number and Cage Code Number. Questions must be submitted via e-mail to cjohnson@usuhs.mil by July 9, 2010. Questions will not be answered over the phone and questions submitted after this date will not be answered. All quotes are due July 14, 2010 at 3:00 PM EST. Quotes may be e-mailed to cjohnson@usuhs.mil, faxed to 301-295-1716, or mailed. Your offer must reference: PSY0CSTS004.
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- SN02195191-W 20100703/100702000157-d088f52286ce51c82c243f3ee6914b1d (fbodaily.com)
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