DNA Sequencing

This notice is a combined synopsis/solicitation, Notice of Intent Number AG-64PP-S-12-BB07. The Midwest Area for the Agricultural Research Service of the United States Department of Agriculture, intends to issue an award to Cornell University Bio Tech Lab, 147 Biotechnology Building, DNA Sequencing and Genotyping Lab, Ithaca, NY 14853. This is a sole source procurement under the authority of FAR 6.302-1, Only one responsible source and no other supplies or services will satisfy agency requirements. This is a requirement of the Plant Genetics Resources Unit (PGRU) and the Grape Genetics Research Unit (GGRU), USDA, ARS at Geneva, NY for 39 lanes of DNA sequencing on the Illumina HiSeq machine, and the bioinformatics analysis of the resultant data. There is also a requirement for a multiplexed library preparation, DNA sequencing on the Illumina HiSeq machine, and the bioinformatics analysis of the resultant data. The sequencing must be conducted using restriction digested, bar-coded DNA samples using the novel method developed at Cornell University. This method has not yet been made available commercially and is only available through Cornell University. No telephone inquiries will be accepted. Interested parties should submit written (mail or email) responses including prices and technical data sufficient to determine capability to meet the entire requirement and must be received in this office within 10 calendar days after publication of this notice. It should be noted that no contract will be awarded on the basis of offers received in response to this notice, but will be used to determine if a comparable source more advantageous to the Government is available. If no affirmative written responses are received, negotiations will be held with Cornell University. This acquisition is being conducted under the Federal Acquisition Streamlining Act, Simplified Acquisition Procedures. SOLE SOURCE JUSTIFICATION: Upon the basis of the following justification, I, as Contracting Officer, hereby approve the use of other than full and open competition for the proposed contractual action pursuant to the authority of 10 U.S.C.2304(c)(1), FAR Subpart 6.302-1(a)(2)(iii), Only one responsible source and no other supplies or services will satisfy agency requirements. JUSTIFICATION 1. Agency and Contracting Activity (FAR 6.303-2(a)(1)). USDA, AGRICULTURAL RESEARCH SERVICE, Midwest Area, Columbia, MO location, Procurement & Property Section, 2. Nature/Description of Action(s) (FAR 6.303-2(a)(2)). a. This contracting action is to purchase multiplexed library preparation with DNA sequencing and 39 lanes of DNA sequencing. Both of these items need to be sequenced on the Illumina HiSeq machine, with a bioinformatics analysis of the resultant data. 3. Description of Supplies/Services (FAR 6.303-2(a)(3)). a. This contracting action is to purchase multiplexed library preparation with DNA sequencing and 39 lanes of DNA sequencing. Both of these items need to be sequenced on the Illumina HiSeq machine, with a bioinformatics analysis of the resultant data. Cost is $81,600. 4. Identification of Statutory Authority (FAR 6.303-2(a)(4)). 10 U.S.C. 2304 (c)(1), FAR Subpart 6.302-1. The services required by the agency are available from only one responsible source and no other type of services will satisfy the Agency requirements. 5. Demonstration of Contractor's Unique Qualifications (FAR 6.303-2(a)(5)). a. Only one responsible Source and No Other Supplies or Services will satisfy Agency Requirements (FAR 6.302-1(a)(2)) (1) FAR 6.302-1(a)(2) states, "When the supplies or services required by the agency are available from only one responsible source, or for DOD, NASA, and the Coast Guard, from only one or a limited number of responsible sources, and no other type of supplies or services will satisfy agency requirements, full and open competition need not be provided for." (2) The named vendor is the producer of a proprietary method for sequencing DNA samples. The cost of DNA sequencing has dropped dramatically in just the last few years and new methods that take advantage of this reduced cost in the genotyping of samples by direct sequencing of genomic DNA have become available. A novel method developed at Cornell University by Drs. Sun Schweitzer and Buckler, incorporates a step for genomic complexity reduction (restriction digestion) plus that ligation of molecularly bar-coded samples to effectively sequence 96 samples simultaneously on one flow cell of the Illumina Genome Analyzer. This method has not been made publicly available and is not provided by other laboratories offering DNA sequencing services. Similarly, a bioinformatics pipeline has been established at Cornell University for the processing of the raw data generated through this unique method. Additionally, the research of these two research Units requires the sequencing to be processed through the same vendor as previous experiments so that data results will be consistent and can be comparatively analyzed 6. Federal Business Opportunities - FedBizOpps.gov (FBO) Announcement/Potential Sources (FAR 6.303-2(a)(6). a. A Federal Business Opportunities (FedBizOpps) synopsis is published in an attempt to identify other possible vendors of the required consumable. b. USDA/ARS does not anticipate other qualified sources; however, should any responses be received, they will be evaluated to determine if they can meet future needs of the Government. 7. Determination of Fair and Reasonable Cost (FAR 6.303-2(a)(7). The cost was determined to be fair and reasonable with this sequencing service. However, this cost could not be directly compared to other companies' offers because no other company provides identical sample processing and bioinformatic analysis. 8. Description of Market Research (FAR6.303-2 (a)(8). USDA/ARS is constantly surveying the market and from this experience knows that the consumable is proprietary and only available from the vendor identified. 9. Any Other Supporting Facts (FAR 6.303-2(a)(9)) Due to the proprietary nature of the item needed to perform the research, at this time there is only one source available. 10. Listing of Interested Sources (FAR 6.303-2(a)(10). No other sources are available at this time. 11. Actions Taken to Remove Barriers to Competition (FAR 6.303(a)(11)). Vendor surveys are done from time to time to see if other existing items can meet the research requirements. Scientists have tested other similar products but no similar results can be guaranteed. 12. Technical Requirements and Certifications; (FAR 6.303-1(b) and FAR 6.303-2(b) I certify that the facts and representations under my cognizance which are included in this justification and which form a basis for this justification are complete and accurate. CONTRACTING OFFICER CERTIFICATION: (FAR 6.303-1(A), 6.303-2(A)(12) I certify that this justification is accurate and complete to the best of my knowledge and belief. Name: Karen Reddick Title: Purchasing Agent