MODIFICATION
A -- Phylogenetic Microarray Services
- Notice Date
- 3/25/2011
- Notice Type
- Modification/Amendment
- NAICS
- 541711
— Research and Development in Biotechnology
- Contracting Office
- RTPPODUS Environmental Protection AgencyRTP Procurement Operations Division(E105-02)4930 Old Page RoadDurhamNC27703USA
- ZIP Code
- 00000
- Solicitation Number
- RFQ-RT-11-00065
- Response Due
- 4/11/2011
- Archive Date
- 5/11/2011
- Point of Contact
- Jacqueline Sayles
- E-Mail Address
-
Sayles.Jacqueline@epa.gov
(sayles.jacqueline@epa.gov)
- Small Business Set-Aside
- N/A
- Description
- NAICS Code: 541711 and the Small Business Size Standard of 500 employees.The United States Environmental Protection Agency (EPA) intends to negotiate a sole source purchase order with Second Genome, formerly known as (Phylotech, Inc.) of San Francisco, California. The EPA requires a commercial laboratory with the demonstrated ability to analyze complex environmental samples in order to fully describe the prokaryotic diversity in the samples. The commercial laboratory must be able to fully describe both bacterial and archaeal populations present in environmental samples as well as the relative abundance of numerically dominant taxa using demonstrated controls. The EPA believes that Second Genome, formerly known as (Phylotech, Inc.) is the only commercial provider that can meet these requirements by using phylogenetic microarrays that simultaneously target multiple variable regions of the 16S rRNA gene (i.e. PhyloChip). Samples will he collected and processed for this project by EPA personnel. The samples will he collected from different environ mental sites and different matrices, primarily groundwaters and sediments. Samples will be collected using aseptic techniques, stored in coolers, and transported to the EPA laboratory for further processing. Water samples (100 -1000 ml) will be filtered onto 0.02 um polycarbonate membranes, which will be stored at -80?C until ready for extractions. DNA will be extracted from filters and sediments (0.25-0.5-mg) by EPA personnel using commercially available DNA extraction kits (e.g., PowerSoil, MoBio; FastDNA, Invitrogen). Concentration of DNA will be estimated using spectrophotometric methods (Nanadrop). DNA aliquots will be transferred into sterile tubes and stored frozen at -20?C until they are shipped to the contractor. DNA concentration of the samples will he at least 10 ng/p.1 and the minimum amount of DNA shipped per sample will be 100ng. The contractor shall analyze each of the samples provided by EPA in accordance with the contractor's SOPs and the following requireme nts. Environmental DNA extracts shall be used in gene amplification reactions (i.e., PCR) performed by the contractor. The contractor shall perform the PCR step using primers and thermal conditions recommended for the microarray detection system. EPA is requiring gel documentation for samples that do not successfully amplify for troubleshooting purposes. Completed gels shall be visualized and an image file saved. PCR products shall then be used in microarray studies using a chip containing oligonucleotides targeting the 16S rRNA gene of a wide variety of prokaryotic microorganisms (i.e., PhyloChipTm). The microarray system should use different regions of the 16S rRNA gene, including hypervariable regions, such that the system can identify the highest numbers of operational taxonomic units for bacteria and archaea and classify organisms at the genus level. The oligonucleotide sequences will be provided by the contractor and not by EPA and shall have been validated prior to th e initiation of the project using different molecular approaches. The contractor shall determine which microorganisms are present and their relative abundance in each DNA extract and provide reports that will include diversity analysis, heat maps of OTUs, clustering analysis, and information of closely related sequence in publicly available databases. The contractor should be able to use mathematical algorithms that can identify similarities and differences between complex microbial communities and examples of bacterial and archaeal groups for each of these categories. The period of performance is expected to begin April, 2011 and last for 24 months. All interested parties who believe they can provide the required analysis should fully explain and demonstrate their capabilities and qualifications in writing within 15 days from the date of this announcement. To demonstrate the qualifications to meet the government?s requirements, the respondent should provide citations of peer reviewed journal articles which would affirm the respondent?s ability to fulfill the specific requirements as described in this notice, or provide information on customer(s)s for whom the respondent has performed similar analytical services to those described in this notice, including a name of a point of contact for the customer and telephone number that EPA may contact to confirm the respondent?s capabilities to meet these specific analytical requirements. Literature generally describing a respondent?s ability to perform microarray services would not, in and of itse lf, satisfactorily demonstrate the respondent?s ability to meet the specific requirements described above. The intent of this synopsis is to determine if any response(s) exist. A Request for Quotation (RFQ) is not available at this time. Consequently, any response(s) failing to provide the aforementioned documentation, but instead choosing to submit a routine letter requesting a copy of the RFQ will not be honored. If no affirmative responses are received within 15 days of this notice to determine whether an alternative qualified source is capable of meeting the specific Government?s needs as described herein, a purchase order will be issued to Second Genome, formerly known as (Phylotech, Inc.) Submit your response via email to savles.iacqueline@epa.gov Telephone calls will NOT be accepted. A draft statement of work can be found at: http://www.epa.gov/oamrtpnc/q1100065/index.litm
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/EPA/OAM/CMD/RFQ-RT-11-00065/listing.html)
- Record
- SN02410217-W 20110327/110325235244-0a11fc4a3a2ff3371b9e2d10debf38db (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
(may not be valid after Archive Date)
| FSG Index | This Issue's Index | Today's FBO Daily Index Page |