SOLICITATION NOTICE
B -- CUSTOM DESIGNED GRAPE ARRAY SERVICES
- Notice Date
- 9/18/2009
- Notice Type
- Presolicitation
- NAICS
- 541711
— Research and Development in Biotechnology
- Contracting Office
- Department of Agriculture, Agricultural Research Service, North Atlantic Area, Area Office, 600 East Mermaid Lane, Wyndmoor, Pennsylvania, 19038, United States
- ZIP Code
- 19038
- Solicitation Number
- AG-3615-S-09-0015
- Point of Contact
- Lisa M. Botella, Phone: 215-233-6551, Rebecca L. Coulter, Phone: 607-255-2448
- E-Mail Address
-
lisa.botella@ars.usda.gov, rebecca.coulter@ars.usda.gov
(lisa.botella@ars.usda.gov, rebecca.coulter@ars.usda.gov)
- Small Business Set-Aside
- N/A
- Description
- The USDA, Agricultural Research Service (ARS), intends to negotiate solely with Illumina, Inc., in San Diego, California to custom design a 10,000 SNP Genotyping array for non-human species; specifically, a representative sample of the grapevine Germplasm repository of the USDA. The process of domestication has fundamentally altered human life and much of the planet’s environment and domesticated species are currently of enormous economic and cultural importance. Scientific insights into the origins and consequences of domestication are essential for a thorough understanding of the unique evolutionary history of domesticated species and for ensuring a safe and secure food supply. Identifying genes responsible for variation in important agronomical traits is a major focus of research in domesticated species [1]. Advances in sequencing and genotyping technology have enabled quantitative trait locus (QTL) mapping of a myriad of traits across dozens of domesticated species including genes affecting grain width in rice [2], milk yield in cattle [3], carotenoid composition in maize [4], and body size in dogs [5]. Recently, USDA-ARS scientists initiated a “Grape Genome Variation Project”. The aim of this project are to characterize patterns of genetic variation across a wide range of the genus Vitis. The research plan involves 4 main steps. The first step was the discovery of genetic variants, called single nucleotide polymorphisms (SNPs), using next-generation sequencing technology (i.e. Solexa sequencing). The SNPs were discovered in a panel of 15 grape varieties, including 9 cultivars of the domesticated species Vitis vinifera (Muscat of Alexandria, Thompson Seedless, French Colombard, Gewurztraminer, Kadarka, Malvasia, Pinot Noir, Plavac Mali, Ehrenfelser and White Riesling) and 6 wild Vitis species (Vitis sylvestris, Vitis amurensis, Vitis cinerea, Vitis labrusca, Vitis palmata and Vitis rotundifolia). Using this method over 400,000 SNPs were identified. The second step (which applies to this order) was to select 9,000 of the discovered SNPs to be typed in 2304 samples from the USDA grapevine germplasm repositories. The 9,000 SNPs were selected based on three criteria: they must be segregating across the samples used for SNP discovery (i.e. must be intermediate frequency SNPs); they must be called with high confidence from our SNP calling pipeline; and they must not be found in repetitive or recently duplicated DNA sequences. Additionally, the selection was biased towards genic regions: approximately 6,000 SNPs were located within genes and 3,000 located outside of genes. The third step will involve the production and use of a genotyping microarray that contains the selected 9,000 SNPs. The genotyping of the US national grape germplasm collection is 90% completed and the custom designed microarray has effectively and accurately surveyed the genetic diversity in the genus. These data are now being used to develop a collection of individuals for association mapping and to assess the patterns and nature of genetic diversity within the genus Vitis. The 9K SNP microarray has proven particularly effective in identifying polymorphic genetic markers between pairs of individuals. The next step is to take advantage of the available SNP microarray for the dissection of important genetic traits in existing mapping and breeding populations. The purpose of collecting genome-wide SNP data from the entire grape germplasm repository is to establish a core collection for the repository. A core collection is a subset of the entire repository that is as representative as possible of the entire genetic diversity present in the repository. The establishment of a core collection is a crucial first step towards association genetics and will provide the foundation for future studies that aim to identify genetic variants responsible for agronomically important traits. In addition these data can be used to assess numerous questions concerning the origins, domestication and dispersal of the grapevine. Sole Source Justification – Illumina, Inc. has: 1) produce a microarray for the grape, a non-model species; 2) The Genotyping microarray must be custom-designable since there is currently no commercially available genome-wide SNP microarray for the grapevine; 3) shall produce a microarray with a minimum of 10,000 features (i.e., SNPs) to a maximum of more than 100,000 SNPs discovered by sequencing; 4) shall supply all reagents and test kits necessary for the microarrays; 5) Custom designed genotyping array that contain fewer than 10,000 features cannot be read by either Government existing equipment will be excluded from the array. The Contractor must be able to produce a microarray with a minimum of 10,000 features (i.e. SNPs), since this is the number of SNPs that we aim to assay. 6) Provide approximately 2,304 custom designed single nucleotide polymorphism (SNP) 10K genotyping arrays that assay each SNP multiple times. (Our desired level of redundancy on the array is at least 10-fold.) 7) Provide the complete quantity of SNP arrays must all fit into a space not greater than one-third of a -80 degree freezer (4 ft. x 4 ft. x 2 ft.). 8) Provide the genotyping arrays which are capable of being read by either an Affymetrix GeneChip Instrument System or an Illumina Bead Station 500. 9) Notify the Government Technical Representative by email if the SNP data (provided by the Government in an Excel spreadsheet) fails, within five (5) business days of the failure. 10) Provide documentation of the use of the SNP arrays which must include a description of the design of the product and detailed instruction for a lab technician to process the microarrays. 11) Replacement of microarrays if the initial shipment was found to contain faulty microarrays. The replacement microarrays must be shipped within 30 days after notification by the Government. 12) The custom arrays will all fit within a box and will be shipped using USDA FedEx overnight account number and shipped on ice. 13) Custom designed genotyping arrays that contain fewer than 9,000 features, that cannot be read by either the Affymetrix GeneChip Instrument System or the Illumina BeadStation 500, or that are not designed specifically for use with grape DNA are excluded from consideration. 14)Delivery shall be within ten (10) weeks after receipt of SNP information. YEAR 2000 COMPLIANCY - "Year 2000 Compliant," (a) Definition: as used in this clause, means that the information technology (IT) (hardware, software and firmware, including embedded systems or any other electro-mechanical or processor-based systems used in accordance with its associated documentation) accurately processes data and date-related data (including, but not limited to, calculating, comparing, and sequencing) from, into, and between the twentieth and twenty-first centuries, and the years 1999 and 2000 and leap year calculations, to the extent that other information technology, used in combination with the information technology being acquired, properly exchanges date and date-related data with it. (b) Any information technology provided, operated and/or maintained under this contract is required to be Year 2000 compliant. To ensure this result, the Contractor shall provide documentation describing how the IT items or services demonstrate Year 2000 compliance, consisting of: standard product literature or test reports. (c) The Contractor warrants that any IT or service under this contract that involve the processing of date and date-related data are Year 2000 compliant. If the contract requires that specific listed products must perform as a system in accordance with the foregoing warranty, then the warranty shall apply to those listed products as a system. d) The remedies available under this warranty shall include repair or replacement, at no additional cost to the Government, of any provided items or service whose non-compliance is discovered and made known to the contractor in writing within 90 days after acceptance. In addition, all other terms and limitation of the Contractor’s standard commercial warranty or warranties shall be available to the Government for the IT items or services acquired under this contract. Nothing in the warranty shall be construed to limit any rights or remedies the Government may otherwise have under this contract with respect to defects other than Year 2000 performance. DOCUMENTATION - Documentation concerning the use of the SNP arrays must be delivered with the product. This includes a description of the design of the product and detailed instructions for the processing of the microarrays. Details of the documentation must be sufficient to allow a lab technician to process the microarrays. WARRANTY - The Contractor shall provide a warranty for at least a one-year period from the date of delivery, unless improperly stored. This means that the microarray must be useable after one year of proper storage. If the delivered product is found to be faulty, replacement will be shipped within 30 days of email notification. The Contractor shall provide a copy of the warranty for each item with their offer. The Government shall: 1) Provide data containing SNP information in a Microsoft Excel Spreadsheet. The spreadsheet will be delivered by email within 100 days of contract award; 2) Provide Notification to the Contractor if microarrays are found to be faulty. This notification must be provided within on calendar year from the date the microarrays are received by the Government; 3) Provide Government-owned property which includes an Affymetrix GeneChip Instrument System and an Illumina Bead Station 500; 4) Provide a federal express number for shipping of this product after award. The Contractor shall: 1) Provide approximately 2,304 custom designed single nucleotide polymorphism (SNP) 10K genotyping arrays; 2) Provide the complete quantity of SNP arrays must all fit into a space not greater than one-third of a -80 freezer (4 ft. x 4 ft. x 2 ft.); 3) Provide the genotyping arrays which are capable of being read by either an Affymetrix GeneChip Instrument System or an Illumina Bead Station 500; 4) Notify the Government by email if the SNP data (provided by the Government in an Excel spreadsheet) fails, within five (5) business days of the failure; 5)Provide documentation of the use of the SNP arrays which must include a description of the design of the product and detailed instruction for a lab technician to process the microarrays; 6) Replacement of microarrays if the initial shipment was found to contain faulty microarrays. The replacement microarrays must be shipped within 30 days of notification; 7) includes Infinium II Multi-Sample Whole Genome Genotyping Assay Kits #WG-31-101 and WG-31-103. 8) Provide a warranty for at least a one-year period from the date of delivery, unless improperly stored. The NAICS is 541710 with a size standard of 500 employees. This procurement is unrestricted. This is not a request for proposal. No solicitation is available. Companies with the demonstrated capability and financial capacity to provide this service must submit a written substantive statement outlining the Company’s and service capabilities, including the consumables (and price lists). This announcement and any other documents related to this procurement will be available electronically at the Internet site http://www.fbo.gov. The Contractor is responsible for monitoring the FBO website for information relating to this requirement. Offerors will be responsible for downloading their own copy of these documents. Contractors are required to acknowledge receipt of all Amendments (if any). If no affirmative responses are received with 5 calendar days of publication of this notice to determine whether a qualified source is more advantageous to the Government, an order will be placed with Illumina, Inc. under the authority of FAR 6.302.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/USDA/ARS/NAAO/AG-3615-S-09-0015/listing.html)
- Place of Performance
- Address: SDA, ARS, NAA, Grape Genetics Resources Unit, Cornell University, 630 W. North Street, Main Office, 216 Sturtevant Hall, GENEVA, New York, 14456, United States
- Zip Code: 14456
- Zip Code: 14456
- Record
- SN01961744-W 20090920/090919001538-62fb684c0ccecc6d082535f7fbfbea8d (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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