This is a combined synopsis/solicitation for commercial items 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; quotations are being requested and a written solicitation will not be issued. Solicitation number AG349BS088178 is being issued as a request for quotation. The solicitation documents and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-24. This requirement is a total Small Business Set-aside for NAICS 541712, small business size standard of 500 employees. Contractors are responsible for reading and complying with this entire combined synopsis/ solicitation and monitoring website, http://www.fbo.gov for any additional information relating to this requirement. Submission of quotations shall be in accordance with the instructions identified under Item A.5, Instructions for submission of quotations listed below. All information requested as identified under Item A.5, Items A through E shall be submitted with quotation. Companies with the demonstrated capability and financial capacity to provide specified services in accordance with the specified delivery schedule are invited to respond to this request. BACKGROUND: The USDA National Center for Cool and Cold Water Aquaculture (NCCCWA) is conducting experiments to identify single nucleotide polymorphisms in rainbow trout. Single Nucleotide Polymorphisms (SNPs) are one base pair differences in DNA sequences between individuals of a population that are used as genetic markers. NCCCWA is constructing Reduced Representation Libraries (RRLs) in an effort to discover SNPs using both Sanger and 454 Sequencing technologies. (A.1) STATEMENT OF WORK - The USDA NCCCWA requires Sanger Sequencing and 454 Sequencing on specific Reduced Representation Libraries (RRLs) and Bioinformatics to identify specific Single Nucleotide Polymorphisms (SNPs) in accordance with the terms, conditions, and specifications contained in this document. The contractor shall provide all services, supplies, equipment and facilities necessary to provide the deliverables specified below. Item 01. The NCCCWA will evaluate 5 restriction enzymes for use in creating RRLs and provide three such libraries to the contractor to obtain sequences via Sanger protocols for 960 reads each. Government will provide libraries to contractor within 45 calendar days of award. Deliverable 01. Contractor shall utilize Government provided RRLs to obtain sequences via Sanger protocols for a total of 2880 chromatograms (960 x 3 libraries) having average read length of 500 Phred 20 base pairs or better. Submission of Deliverable 01 for review and approval shall be by FTP or other Government approved method. Required delivery date is 30 calendar days after receipt of libraries. Item 02. Upon approval and acceptance of Deliverable 01, the NCCCWA will evaluate sequences provided under Deliverable 01, choose optimal enzymes for SNP discovery and create 4 RRLs using the selected enzymes. Two of these libraries will be constructed using DNA from clonal lines; two more will be constructed from pooled DNA samples from NCCCWA broodstock. The NCCCWA requires 454 sequencing for half runs for each of 2 clonal line samples and the 2 pooled samples for a total of 4 half runs. Government will provide libraries to contractor within 20 calendar days after receipt of Deliverable 01. Deliverable 02. Contractor shall utilize first set of Government provided RRLs to obtain sequencing from 4 - half runs of 454 sequences on RRLs created from 2 clonal lines and 2 pooled diploid samples. a. 200,000 or better reads per half run having average read lengths of 250 base pair b. 50 Mb per half run Submission of Deliverable 02 for review and approval shall be by FTP or other Government approved method. Required delivery date is 30 calendar days after receipt of first set of RRLs. Deliverable 02a. Contractor shall utilize second set of Government provided RRLs to obtain sequencing from 4 - half runs of 454 sequences on RRLs created from 2 clonal lines and 2 pooled diploid samples. a. 200,000 or better reads per half run having average read lengths of 250 base pair b. 50 Mb per half run Submission of Deliverable 02a for review and approval shall be by FTP or other Government approved method. Required delivery date is 30 calendar days after receipt of second set of RRLs. Item 03. Due to an evolutionarily recent genome duplication event, rainbow trout are undergoing the process of re-diploidization. The impact on SNP discovery is that divergent paralogous sequences may be mistaken for allelic variation. In this experimental design, SNPs identified within clonal lines, which are expected to be homozygous at all loci, must be ruled out as candidate SNPs. Assembly pipelines for SNP discovery must account for the genome duplication and assembly parameters shall include a stringency of greater than 94% identity over 100 base pairs. The NCCCWA requires the identification of SNPs within and between these samples excluding those identified within clonal lines utilizing the following method or any other proposed method that is acceptable to the Government. 1. Identify SNPs within the entire sequencing dataset (combining all sequences from first and second sets of RRLs). 2. Identify SNPs within the four half runs of clonal lines and removal of them from the final report of SNPs. (SNPs identified between clonal lines are acceptable.) Government will provide libraries to contractor within 20 calendar days after receipt of Deliverable 01. Deliverable 03. Contractor shall provide identification of SNPs -report in tab delimited tables: a. SNPs identified within clonal lines 1. consensus sequence 2. position and type of sequence variants 3. number of observations for each variant (similar to minor allele frequency) b. SNP Table - excluding those identified within clonal lines 1. consensus sequence 2. SNP variants (alleles) position 3. allele 1 (GAT or C) 4. allele 2 (GAT or C) 5. Minor Allele frequencies in pooled diploid samples 6. number of observations for each SNP Submission of Deliverable 03 for review and approval shall be by FTP or other Government approved method. Required delivery date is 45 calendar days after receipt of first and second sets of libraries identified under Item 2. Item 04. Sequence and SNP Data submission to GenBank Database. Deliverable 04. Upon approval and acceptance by the NCCCWA technical point of contact, Contractor shall submit all sequence and SNP data to the GenBank Database in accordance with submission requirements identified at http://www.ncbi.nlm.nih.gov/Genbank/submit.html Government will provide review and approval for GenBank Database submission within 60 calendar days after receipt and acceptance of Deliverable 03. Required delivery date for GenBank Database submission is 10 calendar days after Government approval. Government will provide final review and approval of GenBank Database submission within 10 calendar days. (A.2) SHIPMENT AND DOCUMENTATION - Shipment shall be FOB Destination to and shall be made between the hours of 8:00 a.m. to 4:00 p.m., Monday through Friday, excluding federal holidays to USDA-NCCCWA, 11861 Leetown Road, Kearneysville, WV 25430. The order number shall be included on all documentation and shipments. (A.3) The following FAR provisions and clauses apply to this acquisition and are available in full text at: http://www.arnet.gov 52.204-7 Central Contractor Registration; 52.212-1 Instructions to Offerors - Commercial Items; 52.212-3 Offeror Representations and Certifications - Commercial Items; 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 including subparagraphs: (1) 52.203-6, Restrictions on Subcontractor Sales to the Government, with Alternate I; (5) 52.219-6, Notice of Total Small Business Set-aside; (7) 52.219-8, Utilization of Small Business Concerns; (9) 52.219-14, Limitations on Subcontracting; (15) 52.219-28, Post-Award Small Business Program Rerepresentation; (16) 52.222-3, Convict Labor; (18) 52.222-21, Prohibition of Segregated Facilities; (19) 52.222-26, Equal Opportunity; (20) 52.222-35, Equal Opportunity for Special Disabled Veterans, Veterans of the Vietnam Era, and Other Eligible Veterans; (21) 52.222-36, Affirmative Action for Workers with Disabilities; (22) 52.222-37, Employment Reports on Special Disabled Veterans, Veterans of the Vietnam Era, and Other Eligible Veterans; (23) 52.222-39, Notification of Employee Rights Concerning Payment of Union Dues or Fees; (24) 52.222-50, Combating Trafficking in Persons (31) 52.225-13, Restrictions on Certain Foreign Purchases; (36) 52.232-33, Payment by Electronic Funds Transfer-Central Contractor Registration; (38) 52.232-36 Payment by Third Party; 52.214-34 Submission of Offers in the English Language; 52.214-35 Submission of Offers in U.S. Currency; 52.242-17 Government Delay of Work; 52.247-34 F.o.b. Destination; (A.4) EVALUATION CRITERIA - The Government contemplates award of a contract resulting from this solicitation to the responsible offeror whose offer represents the best value to the Government, price and other factors considered. (A.5) *** INSTRUCTIONS FOR SUBMISSION OF QUOTATION *** OFFERS SHALL BE SUBMITTED TO THE ATTENTION OF: Timothy Smearman, USDA, AFRS, Administration Office, 2217 Wiltshire Road, Kearneysville, WV 25430. OFFERS SHALL BE RECEIVED AT THE ADDRESS SPECIFIED ABOVE PRIOR TO: 3:00 P.M. (EST) on March 24, 2008. ** NOTICE: QUOTATIONS SENT BY FAXSIMILE OR ELECTRONIC MAIL (E-MAIL) ARE NOT ACCEPTABLE, WILL BE CONSIDERED NON-RESPONSIVE, AND WILL BE REJECTED. ** OFFERORS SHALL SUBMIT ALL OF THE FOLLOWING: (a) Submit Quotation for each deliverable specified under (A.1) Scope of Work. (b) Submit three separate Past Performance References with contact information for three recent contracts (within past three years) of contracts similar to the scope of this requirement. Offerors that are newly formed individual entities, without prior Federal, State or Local Government Contracts, may list work contracts, subcontracts or other related work experience. (c) Submit statement certifying that the offeror has completed the annual representations and certifications electronically via the Online Representations and Certifications Application (ORCA) website at http://orca.bpn.gov By submission of an offer the offeror acknowledges that the representations and certifications currently posted electronically have been entered or updated within the last 12 months, are current, accurate, complete, and applicable to this solicitation as of the date of this offer. Reference FAR 52.212-3 Offerors Representations and Certifications - Commercial Items identified under (A.3). (d) Submit statement certifying that offeror is registered in the Central Contractor Database in accordance with FAR 52.204-7 Central Contractor Registration. (Reference Section A.3.) By submission of an offer, the offeror acknowledges the requirement that the prospective awardee shall be registered in the CCR database (http://www.ccr.gov) prior to award, during performance, and through final payment of any contract resulting from this solicitation. (e) Submit Statement indicating acceptance or non-acceptance of payment via the Government Visa Credit Card. (A.6) ADDITIONAL INFORMATION - - Questions shall be submitted in writing to: Timothy Smearman, USDA, ARS, NAA, AFRS, Administration Office, 2217 Wiltshire Road, Kearneysville, WV 25430 or by electronic mail to: [email protected]

Bid Protests Not Available