SPECIAL NOTICE
66 -- NOTICE OF INTENT TO SOLE SOURCE PYROSEQUENCING PYROMARK Q48 AUTO PREP SYSTEM
- Notice Date
- 4/5/2017
- Notice Type
- Special Notice
- NAICS
- 334516
— Analytical Laboratory Instrument Manufacturing
- Contracting Office
- Agricultural Research Service - Western Business Service Center
- ZIP Code
- 00000
- Solicitation Number
- AG-4431-S-17-0014
- Archive Date
- 4/27/2017
- Point of Contact
- Shalunda S. Mix, Phone: 662-686-5346
- E-Mail Address
-
shalunda.mix@ars.usda.gov
(shalunda.mix@ars.usda.gov)
- Small Business Set-Aside
- N/A
- Description
- The USDA, ARS intends to award a sole-source commercial item procurement to QIAGEN Inc, 19300 Germantown Road, Germantown, MD 20874-1415, as they are the sole source for this type of pyrosequencing system pursuant to the authority of 41 U.S.C. 253(c)(1) and FAR 6.302-1, Only One Responsible Source and No Other Supplies or Services Will Satisfy Agency Requirements. The award will be for a PyroMark Q48 Autoprep system needed for quantitatively measuring the proportions of specific single nucleotide polymorphisms (SNPs) in mixed DNA populations. The following items and specifications will be included in the purchase: The Pyrosequencing PyroMark Q48 Autoprep system must include (but not limited to) one PyroMark Q48 Autoprep instrument, one PyroMark Assay Design SW 2.0, one PyroMark Q48 installation, and one PyroMark Q48 Autoprep starter kit. This instrument will be used to analyze communities of fungi. The instrument must also be able to: 1) Quantify multiple SNPs in a single assay utilizing established pyrosequencing protocols. 2) Quantify frequencies of insertions and deletions (InDels) including multiple base InDels - using instantaneous measurement of light generated by sequence by synthesis reactions. 3) Automatically provide allelic frequency information and distinguish among frequencies differing by 10% (better resolution is preferred). 4) Provide a minimum of 8 base pair genotyping and SNP scoring. 5) Provide highly accurate SNP scoring (>99% accuracy). 6) The technology must provide ease of use so that new users can be rapidly productive and be flexible so that assays used to investigate communities of aflatoxin-producing fungi can be altered to meet the needs of the research program and requirements of regulatory agencies (i.e. EPA). Additional Requirements: Automated genotyping of multiple alleles (including SNPs and InDels) with calculated allele frequencies and plate statistics; Easy to use reports and export of data in multiple standard formats including Excel, tab-delimited, XML, FASTA, and text; Barcode options for data and sample tracking. The system must be complete and dedicated for high-accuracy genotyping and include analysis instrument, operator's computer, dedicated software for instrument control and data analysis, as well as optimized reagents, sample preparation tools, and accessories for DNA analysis (genotyping). Training and startup assistance must be included. The System must determine genotypes using sequence data, including negative controls, by matching expected versus actual sequence data generating positive and negative internal standards. The instrument should perform solid phase sequencing and detect which nucleotide is incorporated into the DNA sequence by detection of light emitted by an enzyme reaction during sequence synthesis. This sequencing technology generates a short read DNA sequence that enables very accurate SNP and InDel analysis. The design of assays and primers for assays should be flexible and avoid constraints experienced by single base extension technology. The methodology should be able to perform sequencing directly after purification of PCR products without running another reaction other than the actual run, and no gel electrophoresis should be required. It is preferred that real-time data output be easily accessible by the operator. It is preferred if the instrument can sequence 48 unique samples in the same run with real-time detection of nucleotide incorporation for instant data evaluation. The operating system should run on Microsoft Windows 7 or higher, and utilize standard Windows functions to maintain the uniformity of the existing computer technology. It is preferred that the instrument keeps log files that record all aspects of the system activities. The log files must be linked to individual sample data and operator name and be readily accessible to the operator. There should be an automatic Quality Assessment of data (Passed, Check, and Failed) minimizing manual checks. The instrument should be able to run both pre-programmed dispensation programs and programs created by the end-user for novel uses. The instrument must be flexible to conform to new procedures. Must communicate with standard TCP/IP protocol and be readily connected to standard Ethernet network environments for data transfer, backup, and printing. Also, there should be the capability to set-up analyses and evaluate run data on independent office computers by data exchange with a shared database on a network server/computer. It is preferred that the instrumentation has streamlined software design, from set-up to evaluation, with intuitive user interface minimizing hands-on time and time needed for education of new users. The PyroMark Q48 Autoprep System is the only sequencing-by-synthesis platform that meets the above requirements and combines: 1) innovative chemistry that allows synthesis of the true sequence being analyzed in real time, 2) high sequence fidelity, 3) flexibility in assay setup in a single run that confers ability to detect and quantify multiple types of genetic variation simultaneously, 4) ability to perform up to 48 different assays in a single pyrosequencing run, including mutation assays, DNA methylation assays and de novo sequencing assays on the same plate, and 5) Built-in quality controls that ensures data are delivered with the context of the DNA sequence, allowing for a quality check of the surrounding sequence to ensure that the correct DNA region has been analyzed. The PyroMark Q48 Autoprep instrument, PyroMark Assay Design SW 2.0 software, and PyroMark Q48 Autoprep starter kit must be bundled for the PyroMark Q48 Autoprep system to be functional. The components are not sold separately. The PyroMark Q48 Autoprep system is proprietary to QIAGEN Inc, and QIAGEN Inc. is the only company that is capable of bundling the components of the PyroMark Q48 Autoprep system seamlessly and delivering the system at the quote price. Also, purchasing the equipment directly from QIAGEN Inc. would significantly reduce cost of installation and maintenance. Pursuant to the authority of 41 U.S.C. 253(c) (1) and FAR 6.302-1, Only One Responsible Source and No Other Supplies or Services Will Satisfy Agency Requirements. The equipment will be located at the USDA, ARS, Aflatoxin Reduction Laboratory, in Tucson, AZ. The Government intends to award a firm-fixed-price purchase order on or about April 13, 2017. This Notice of Intent is not considered a Request for Quotation (RFQ), nor is it a Request for Proposals (RFP). No solicitation document is available, and telephone requests will not be honored. Interested persons may identify their interest and capability to respond to this requirement. A determination by the Government not to compete this proposed contract based on responses to this notice is solely within the discretion of the Government. The Government will consider all responses received by 12 PM Central Standard Time, April 12, 2017. Information received will be considered solely for determining whether to conduct a competitive procurement. Inquiries will only be accepted via email/ mail to the Contracting Officer at the following address: Contracting Office Address: USDA-ARS-WBSC Shalunda Mix 141 Experiment Station Road Stoneville, MS. 38776-0225 shalunda.mix@ars.usda.gov
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/notices/5851a4ccdc87288dc79b508bfd3ec275)
- Place of Performance
- Address: USDA, ARS, Aflatoxin Reduction Laboratory, 1140 E. SOUTH CAMPUS DR., TUCSON, Arizona, 85721, United States
- Zip Code: 85721
- Zip Code: 85721
- Record
- SN04461787-W 20170407/170405235811-5851a4ccdc87288dc79b508bfd3ec275 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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