SOLICITATION NOTICE
B -- DNA TILLING PROJECT
- Notice Date
- 9/25/2006
- Notice Type
- Solicitation Notice
- NAICS
- 541710
— Research and Development in the Physical, Engineering, and Life Sciences
- Contracting Office
- Department of Agriculture, Agricultural Research Service, North Atlantic Area Office, 600 East Mermaid Lane, Wyndmoor, PA, 19038
- ZIP Code
- 19038
- Solicitation Number
- Reference-Number-GENEVA2006
- Response Due
- 9/29/2006
- Archive Date
- 12/30/2006
- Description
- The USDA, Agricultural Research Service (ARS), intends to negotiate solely with the Fred Hutchinson Cancer Research Center in Seattle, Washington to provide a pilot screening of 768 EMS-mutagenized M2 seedlings for mutations at 9 gene targets and to provide the data related to protocols and mutations to GGRU. The Fred Hutchinson Cancer Research Center is the only contractor using the Tilling Method. The Seattle Tilling Project is the only service with a proven track record in conducting pilot projects on diverse and difficult plant species, having worked with scientists on developing TILLING in over two dozen species http://tilling.fhcrc.org:9366/files/Workshops.html. Critical considerations for this service include proven track record developing TILLING for diverse and difficult plant systems, ensured privacy of data, and ability to expand to a public initiative wherein other scientists could pay the same organization for screening their candidate gene. The USDA-ARS Grape Genetics Research Unit GGRU) is engaged in a wide variety of agriculturally important research projects where detailed knowledge of plant functional genomics is critical. The identification of gene function by reverse genetics facilitates efforts in cultivar improvement. For GGRU's intended applications, it has been determined that TILLING, a molecular process by which a mutagenized population is screened for lesions in a specific candidate gene, is required. This service is for a base period of nine months plus three one year option periods. NOTE: The Government may multiply the Unit Price by the total number of additional requirements needed, i.e. if we need 9,215 targets, the Unit Price will be multiplied by 3 to get the total Amount. Furthermore, the quantity of any line item may be increased in accordance with FAR Clause 52.217.7 within 60 days prior to the expiration of the contract performance period. SCHEDULE OF ITEMS - BASE PERIOD OF PERFORMANCE: Date of Contract Award through June 30, 2007. ITEM 01: DNA Production on 768 plants; QUANTITY: 1, UNIT = JOB, UNIT PRICE: $______ and AMOUNT: $_______. ITEM 02A: PILOT SCREENING FOR 768 Individual Gene Targets; QUANTITY: 1, UNIT = JOB, UNIT PRICE: $______ and AMOUNT: $_______. ITEM 02B: PILOT SCREENING FOR 1,536 Individual Gene Targets; QUANTITY: 1, UNIT = JOB, UNIT PRICE: $______ and AMOUNT: $_______. ITEM 02B: PILOT SCREENING FOR 3,072 Individual Gene Targets; QUANTITY: 1, UNIT = JOB, UNIT PRICE: $______ and AMOUNT: $_______. ITEM 03: SHIPPING COSTS; QUANTITY: 1, UNIT = JOB, UNIT PRICE: $______ and AMOUNT: $_______. NOTE: The Contractor shall prepay and add freight cost as a separate line item in accordance with the F.O.B. Destination clause. OPTION 1 PERIOD OF PERFORMANCE: July 1, 2006 TO June 30, 2007. ITEM 01: Production Screening per gene target for 3,072 Plants; QUANTITY: 1, UNIT = JOB, UNIT PRICE: $______ and AMOUNT: $_______. ITEM 02: SHIPPING COSTS; QUANTITY: 1, UNIT = JOB, UNIT PRICE: $______ and AMOUNT: $_______. NOTE: The Contractor shall prepay and add freight cost as a separate line item in accordance with the F.O.B. Destination clause. OPTION 2 PERIOD OF PERFORMANCE: July 1, 2007 TO June 30, 2008. ITEM 01: Production Screening per gene target for 3,072 Plants; QUANTITY: 1, UNIT = JOB, UNIT PRICE: $______ and AMOUNT: $_______. ITEM 02: SHIPPING COSTS; QUANTITY: 1, UNIT = JOB, UNIT PRICE: $______ and AMOUNT: $_______. NOTE: The Contractor shall prepay and add freight cost as a separate line item in accordance with the F.O.B. Destination clause. OPTION 3 PERIOD OF PERFORMANCE: July 1, 2008 TO June 30, 2009. ITEM 01: Production Screening per gene target for 3,072 Plants; QUANTITY: 1, UNIT = JOB, UNIT PRICE: $______ and AMOUNT: $_______. ITEM 02: SHIPPING COSTS; QUANTITY: 1, UNIT = JOB, UNIT PRICE: $______ and AMOUNT: $_______. NOTE: The Contractor shall prepay and add freight cost as a separate line item in accordance with the F.O.B. Destination clause. OPTION 4 PERIOD OF PERFORMANCE: July 1, 2009 TO June 30, 2010. ITEM 01: Production Screening per gene target for 3,072 Plants; QUANTITY: 1, UNIT = JOB, UNIT PRICE: $______ and AMOUNT: $_______. ITEM 02: SHIPPING COSTS; QUANTITY: 1, UNIT = JOB, UNIT PRICE: $______ and AMOUNT: $_______. NOTE: The Contractor shall prepay and add freight cost as a separate line item in accordance with the F.O.B. Destination clause. GENERAL SPECIFICATIONS - The services include the following requirements: 1) DNA Production includes DNA extraction, concentration, normalization, and arraying. 2) Pilot Screens include primer design, quality control testing, high throughput screening, and sequence verification of mutations. Cost is for delivery of one target and includes repeat work due to failures. Screening is performed in a 384 well format. This pilot project will screen 768 individuals with 9 gene targets; and 3) Production Screening commences at the completion of a pilot. Screening costs include high throughput screening and sequence verification of mutations. TECHNICAL SPECIFICATIONS - Services include: a. Isolating DNA from at least 768 of the 800 samples provided by GGRU. If DNA isolation fails on any number of samples, STP will retry DNA isolation of that number. b. The service must use TILLING technology as described Comai, L. and Henikoff, S. 2006. TILLING: practical single-nucleotide mutation discovery. The Plant Journal 45: 684-694. c. Normalizing DNA concentration, arraying the 768 samples, and providing any other pre-TILLING preparative services required. d. Receiving at least nine genomic target sequences from USDA, ARS, GGRU for processing to CODDLE and associated software for standard design of TILLING primers. e. Successfully amplifying, cleaving, and electrophoresing nine gene targets across the 768 samples based on the gene sequences provided. If any of the nine gene targets fail primer quality control or any aspect of TILLING, replacement targets can be identified by STP. f. Analyzing the gels to identify putative mutations and confirming every putative mutation by sequencing. If sequencing fails, a second sequencing attempt will be made. g. Providing standard reports of troubleshooting required, protocols used, mutations found, gel images, and data tables in Word, Excel, Jpeg, or ASCII file formats. The Contractor shall adhere to the Rights in Data - Special Works, clause 52.227-17. The COR will advise the Contractor and the Contracting Officer if changes are required to the order. REPORTING REQUIREMENTS - A full set of written documentation shall be provided, including description of troubleshooting required, protocols used, and standard documentation (i.e., mutations identified, gel images, sequence, and data tables). All data must be provided in Word, Excel, Jpeg, or ASCII file formats: 1) PROCEDURE METHOD STATEMENT: The Contractor shall provide a detailed statement on the protocols used for DNA isolation and sequencing; 2) CATALOG REPORT: The Contractor shall provide a detailed (final) report beginning thirty (30) days after receipt of each library. The report shall include, at a minimum, the following: 1. Number of clones that have been sequenced. 2. Number of ESTs produced. 3. Detailing the average read length for each sequence. 4. Success rate. 5. Percentage of sequences that failed. 6. Balance of clones remaining. 7. Identify problems encountered. The reports shall begin monthly upon receipt of the samples and continue through the entire period of this project. The Contractor shall return the library as it is sequenced. PATENTS OR LICENSING - The Contractor shall provide all information regarding any Patents or Licensing in accordance with FAR Clause.523.227-3. WARRANTY - If the DNA isolation fails on any number of samples, the Contractor will retry DNA isolation of that number once, with the goal of obtaining 768 DNA samples from 800 tissue samples. If any number of the nine gene targets provided by GGRU fails primer quality control or any subsequent aspect of TILLING, that number of replacement targets will be identified by the Contractor and retested. If sequencing fails, a second sequencing attempt will be made. The Government may also provide additional seedlings if necessary. DELIVERY - ARS shall provide the plant materials to the Contractor within 30 days after contract award. Delivery shall be between the hours of 8:00 a.m. to 3:00 p.m. Monday through Friday, excl. Federal Holidays. The Contractor shall provide the number of plant materials required to perform the work identified in the purchase order. The Contractor shall complete the Pilot Project within 9 months after receipt of the purchase order. Subsequent delivery dates for each line item shall be coordinated by the Technical Representative (TR) with the Contractor and placed in writing by both parties. Acceptance shall be made at destination. PACKING AND SHIPPING - The Contractor shall pack each item for shipment in a new container in such a manner that will ensure acceptance by common carrier and safe delivery at the destination. Containers and closures shall comply with the Interstate Commerce Regulation, Uniform Freight Classification Rules, or regulation of other carriers as applicable to the mode of transportation. The items to be furnished hereunder shall be labeled with the purchase order number and delivered, all transportation charges paid by the Contractor in accordance with the F.O.B. Destination clause to: USDA, ARS, Grape Genetic Research Unit, Cornell University, Collier Drive, Geneva, NY 14456-0462. All items must be identified with the PO number. PAYMENT - The Contractor must be registered for Electronic Funds Transfer (EFT) payments in the Central Contractor's Registration (CCR) database to receive payment. Payment may be made by a Government purchase order or Government Credit Card. Final payment shall not be made unless and until the equipment and documentation have been received and are accepted by the Technical Representative. The NAICS Code 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 and service such equipment, and warranty must submit a written substantive statement outlining the Company's and systems' capabilities, available service agreements and consumables (including price lists). This announcement and any other documents related to this procurement will be available electronically at the Internet site http://www.fdo.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 the Fred Hutchinson Cancer Research Center under the authority of FAR 6.302.
- Place of Performance
- Address: USDA, ARS, Grape Genetics Research Unit (GGRU), Cornell University, Collier Drive, Geneva, NY
- Zip Code: 14456-0462
- Country: UNITED STATES
- Zip Code: 14456-0462
- Record
- SN01153578-W 20060927/060925220114 (fbodaily.com)
- Source
-
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