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Genomic DNA Sample Sequencing Service - PacBio Technology

Solicitation Number: AG-32SD-S-12-0037
Agency: Department of Agriculture
Office: Agricultural Research Service
Location: Western Business Service Center
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Special Notice
Added: Jun 18, 2012 3:37 pm
The U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Pacific West Area, under the authority of FAR 13.0 intends to negotiate on a sole source (Allegheny Singer Research Institute) basis for a service where ARS provides the genomic DNA of each of 20 bacterial DNA samples and the source will do the actual genome sequencing using the PacBio technology. The product ARS will get back is the genome sequence data for each of the 20 bacterial genomes. The PacBio technology is fundamentally different from all preceding methods as it utilizes a zero mode waveguide (ZMW) for imaging of the DNA polymerase as it adds each base in real time. No other method employs an actual DNA polymerase for sequencing. The advantages of this approach are based upon the fact that two types of DNA sequence can be obtained from the system. The first type of data is termed long-read data and is produced by taking advantage of the natural processivity of the DNA polymerase. This type of sequencing routinely produces single reads that are 3-5 kilobases (Kb) in length, with some reads in excess of 10 Kb. These data are used for building long scaffolds such that the number of contigs produced for a given genome are greatly reduced (2-3x) compared to even 454 Lifesciences' based sequencing, thereby providing a much more finished product without having to do any additional gap filling. The individual error rate for these long reads is relatively high. Therefore, the long-read data are combined with a second type of Pacbio sequencing, termed circular consensus sequencing (CCS). The CCS reads are much shorter than the long-reads, but because each base is read multiple times as the polymerase travels around the circle, they are also much more accurate. This is because the errors made by the Pacbio system are truly random, thus as the number of reads/base goes up the error rate goes down for all bases including homopolymer tracts. In essence then, the CCS reads are used to error-correct the long-reads which produces long accurate reads in the final analysis. For bacterial genome samples, the data generated using PacBio long read/CCS generates genome sequence data with fewer gaps relative to older generation sequencing platforms. This is a notice of intent and is not a request for competitive quotations or proposals. No solicitation is available. ARS believes that Allegheny Singer Research Institute is the only source that can provide the required services. Interested Firms may identify their interest and capability to respond to the above stated requirement and submit proposals. This notice of intent is not a request for competitive proposals. However, all proposals received by 4:00 PM 06/27/2012 (Pacific Time) will be considered by the government. A determination by the Government not to compete this proposed contract based upon responses to this notice is solely within the discretion of the government. Information received will normally be considered solely for the purpose of determining whether to conduct a competitive procurement. Proposal must be sent in writing referencing AG-32SD-S-12-0037 to the attention of Vinay B. Kaul via fax 510-559-6023, or emailed to Questions concerning this notice of intent must be directed to Vinay B. Kaul, email
800 Buchanan Street
Albany, California 94710-1105
United States
Agriculture Research Service
9611 S. Riverbend Avenue
Parlier, California 93648
United States
Vinay Kaul,
Supervisory Contract Specialist
Phone: 510-559-6016
Fax: 510-559-6023