SOLICITATION NOTICE
B -- Analysis of Gene Polymorphisms
- Notice Date
- 5/9/2007
- Notice Type
- Solicitation Notice
- NAICS
- 541710
— Research and Development in the Physical, Engineering, and Life Sciences
- Contracting Office
- RTP Procurement Operations Division (D143-01) Research Triangle Park, NC 27711
- ZIP Code
- 27711
- Solicitation Number
- PR-NC-07-10520
- Response Due
- 5/24/2007
- Archive Date
- 6/23/2007
- Small Business Set-Aside
- Total Small Business
- Description
- THIS IS A COMBINED SYNOPSIS/SOLICITATION FOR COMMERCIAL SERVICES 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. PROPOSALS ARE BEING REQUESTED AND A WRITTEN SOLICITATION WILL NOT BE ISSUED. The solicitation number is PR-NC-07-10520, and the solicitation is being issued as a 100% small business set-aside competition Request for Quotation (RFQ). The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 05-16. The associated North American Industry Classification System (NAICS) Code 541710, which has a size standard of 500 employees to qualify as a small business, is applicable. A firm fixed-price contract is anticipated to result from the award of this solicitation. This procurement is for the analysis of gene polymorphisms. A. Background Information. A population-based case-control study of air pollutants and asthma in Wayne County, Michigan completed the field collection of data and samples in January 2007. Two hundred (200) blood samples were collected and white blood cells (WBC) isolated from 100 asthmatic and 100 non-asthmatic children aged 9-12 as part of the Mechanistic Indicators of Childhood Asthma Study (MICA). These individuals answered questions related to medical history, smoking in the home, diet, and residential mobility. In addition, a number of effect modifiers, such as IgE allergen sensitivity, will be measured in the biological fluids. The rationale for selection of the 11 specific genes (see table at EPA website http://www.epa.gov/oam/rtp_cmd) and relevant Single Nucleotide Polymorphisms (SNPs) is provided in the way of relevant studies in which associations between asthma and specific genotypes were evaluated. The interpretation of several of the studies referenced is limited by incomplete knowledge regarding the biological function of the various alleles. Specific genotypes may influence disease risk by modifying the effects of environmental exposures. The SNPs were selected by querying public databases for polymorphisms showing variation in African American (AA) samples, since that race represents approximately 85% of the individuals selected in the study. For genes with no AA variable SNPs in the databases, we selected based on studies reported in the literature. To rank the available SNPs within each gene, we used a simple "weight of evidence" summation that weights the information sources according to the following inequality: African American sample > African sample > mixed-race sample including some African Americans. In the table, the SNPs are organized by gene. The polymorphisms listed are base substitutions, except for two common asthma-associated deletions (in GSTM1 and GSTT1). For GSTT1, only four polymorphisms showing sufficient variation were shown in AA populations. There are at least 5 polymorphisms for all other genes, as shown in the table. Genotyping for all of the specific SNPs in the table is required. B. Purpose and Objectives. The objective of this contract is to extract DNA from blood collected from 200 participants and determine the presence of SNPs at five specified locations in each of 11 genes (see table). The prevalence of linkage disequilibrium (LD) across SNPs needs to be assessed. Other data analyses commonly used for quality control to identify systematic genotyping errors or find evidence of population stratification in unrelated individuals are required. C. Contractor Requirements. The contractor shall perform the following tasks: TASK 1: The contractor shall extract DNA from 200 samples (White blood cell pellets to be provided). The contractor shall quantify genomic DNA concentration in units of nanograms per microliter. The concentrations of the DNA samples shall be such that when the samples are loaded, 1-10 ng of DNA is used per reaction. The contractor shall provide a report with the quantity of DNA and the DNA concentration for each sample to complete this Task. TASK 2: The contractor shall conduct genotyping PCR analyses for the 11 genes listed and up to 5 SNPs per gene, except for GST T1 (which has 4 SNPs), specified in the table. Genotyping shall be performed in duplicate for 10 percent of the DNA samples. The use of duplicate sample analysis allows the investigator to ensure that identical genotypes are being generated by the analysis of ?identical? samples. Should significant differences exist between values obtained for duplicates, further investigation shall be performed to evaluate the source of these unexpected variations. The use of previously genotyped materials may also be used to ensure that the experimental genotyping assay is accurate and reproducible. TASK 3: The contractor shall test for departure from Hardy-Weinberg Equilibrium (HWE) using the standard ?2 goodness-of-fit test. Testing for departure from HWE in control (non-asthmatic) samples is a preliminary test of association that is used to inform subsequent analyses. Departure from HWE is used for quality control to identify systematic genotyping errors. Departure from expected HWE also provides evidence of population stratification in unrelated individuals, indicating that analysis will have to account for uncertainty in the self-reported race of sample individuals. The prevalence of linkage disequilibrium (LD) across SNPs shall also be assessed. This is a standard preliminary step in genetic association analysis that assures assumptions of independence are not violated. If present, LD affects all subsequent analyses. In the event of missing or incomplete data, LD can be used to analytically overcome these issues. Tabular summaries of pair-wise (SNP-SNP) LD should display both the r2 and D' measures. A Haploview-formatted input file, freely available from http://www.broad.mit.edu/mpg/haploview/, shall also be provided by the contractor to allow the visualization of LD patterns in the data. The contractor shall provide to the EPA project officer the results of the analyses in a written report (see Deliverables Section, below). The contractor shall provide the results of all applicable information from the analysis of calibration standards and standard reference materials. The contractor shall properly store and return any unused DNA or DNA in solution at the completion of all analyses and the acceptance of the final report. The contractor shall be responsible for the disposal of all expendable materials (pipette tips, reaction wells, centrifuge tubes, etc.) used in the analysis work. D. Government Responsibilities. The government researchers will be responsible for providing the 200 samples, consisting of White Blood Cell (WBC) pellets isolated from blood samples provided by the MICA Study participants. Since the samples will only be identified by a code number, the EPA Project Officer will provide a list of samples according to the sample identifiers to allow the contractors to verify the number of samples. E. Deliverables. Task 1: The contractor shall provide a report with the quantity of DNA and the DNA concentration for each sample. The contractor shall quantify genomic DNA concentration in units of nanograms per microliter. The concentrations of the DNA samples shall be such that when the samples are loaded, 1-10 ng of DNA is used per reaction. Task 2: The contractor shall provide a report with the preliminary SNPs determinations and a description of the duplicate analyses and other quality control measures that were taken to ensure the reproducibility of the assay. Task 3: The contractor shall provide to the EPA Task Officer the results of the sample analyses in spreadsheet form (Microsoft Excel 2003 or later) and in a final report when all genotyping and subsequent data analyses are complete. The spreadsheet shall contain at least one worksheet that presents the final, quality-assured data in tabular format having individual samples in rows and genotypes at each SNP in columns. The report shall include all relevant calibration and quality control results (specified in Section C, above). The contractor shall also provide spreadsheets of the preliminary SNP-SNP linkage disequilibrium assessment (discussed in Section C, above). Upon acceptance of this report by the EPA Project Officer, the contractor shall return any unused DNA or DNA in solution from the samples provided by the EPA researchers. The table referenced above is available at the EPA Procurement website as part of the Statement of Work. The PERIOD OF PERFORMANCE will be 12 months from date of award. The following FAR provisions apply to this solicitation: 52-212-1, Instructions to Offerors?Commercial Items; 52.212-2, Evaluation--Commercial Items. Evaluation criteria to be included in paragraph (a) of provision 52.212-2 are as follows: A. Technical Criteria: 1. The demonstrated ability to determine the presence of Single Nucleotide Polymorphisms (SNPs) at specified locations. This ability shall be demonstrated by listing contracts where similar genotyping assays were performed and in which SNP analyses were conducted. 2. Demonstrated expertise in searches (literature and database) relevant to DNA alterations (point mutations, deletions, substitutions, etc.) that might indicate disease susceptibility. 3. The demonstrated ability to perform the data analyses listed in the Statement of Work, such as assessing the prevalence of linkage disequilibrium (LD) across SNPs and other data analyses commonly used for quality control to identify systematic genotyping errors or find evidence of population stratification in unrelated individuals are required. B. Past Performance: Submit a list of 3 customers for whom like or similar services have been performed. Include specific points of contact and phone numbers. Past Performance will be evaluated on 1) quality of service; 2) timeliness of performance (ability of adhere to deadlines); and 3) overall customer satisfaction. C. Price. Award will be made to the responsible offer or whose offer is determined the best overall value to the government, price and other factors considered. For this procurement Technical Criteria and Past Performance when combined are significantly more important than Price. All offerors are to include with their offers a completed copy of provision 52.212-3, Offeror Representations and Certifications--Commercial Items. The following FAR clauses apply to this acquisition: 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 and the following additional FAR clauses which are cited in Clause 52.212-5: 52.219-6 Notice of Total Small Business Set-Aside; 52.222-3 Convict Labor; 52.222-21, Prohibition of Segregated Facilities; 52.222-26, Equal Opportunity, 52.222-35, Affirmative Action for Special Disabled and Vietnam Era Veterans; 52.222-36 Affirmative Action for Handicapped Workers; 52.222-37, Employment Reports on Special Disabled Veterans and Veterans of the Vietnam Era; 52.225-13 Restrictions on Certain Foreign Purchases; 52-232-33, Payment by Electronic Funds Transfer-Central Contractor Registration. All technical questions are to be forwarded via email to the Contracting Officer at the following email address: hill.jennifer@epa.gov. Offerors should review the Statement of Work and other information posted with this Request for Quotation on EPA's website at the following address: http://www.epa.gov/oam/rtp_cmd. Click on the CURRENT SOLICITATIONS section and click on the solicitation for viewing applicable documents. Near the top of the page COMMERCIAL BUY CLAUSES AND FORMS sections are provided for your convenience. Please submit two copies of the technical proposal and price proposal to Jennifer B. Hill, Contracting Officer, U.S. Environmental Protection Agency, RTP Procurement Operations Division (D143-01), Research Triangle Park, NC 27711 if using the US Postal Service. Courier delivery address is U.S. Environmental Protection Agency, Attn: Jennifer B. Hill, RTP Procurement Operations Division (D143-01), 4930 Old Page Road, Durham, NC 27703. All offers are due by May 24, 2007, 12:00 p.m., ET. No telephonic or faxed requests will be honored.
- Web Link
-
The Environmental Protection Agency
(http://www.epa.gov/oam/solicit)
- Record
- SN01291035-W 20070511/070509222004 (fbodaily.com)
- Source
-
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