SPECIAL NOTICE
B -- AFFYMETRIX RESEARCH DNA
- Notice Date
- 12/4/2008
- Notice Type
- Special Notice
- NAICS
- 621511
— Medical Laboratories
- Contracting Office
- Department of Veterans Affairs;VA Boston Healthcare System;Contracting Officer (90C);940 Belmont Street;Brockton MA 02301
- ZIP Code
- 02301
- Archive Date
- 12/9/2008
- Point of Contact
- Audrey WootenContracting Specialist<br />
- Small Business Set-Aside
- N/A
- Description
- The Department of Veterans Affairs, VA Boston Healthcare System, intends to negotiate a commercial (FAR Part 12) sole source contract with AFFYMETRIX under the authority of FAR 6.302-2. Please refer to the Sole Source Justification. This is not a solicitation; it is notice of intent to sole source a requirement.Inquiries/information received after the established deadline shall not be considered. The submission of any data for review shall not impede award of this contract as planned. The Government does not intend to pay for information solicited. This synopsis is issued pursuant to FAR 6.302-2. JUSTIFICATION FOR OTHER THAN FULL AND OPEN COMPETITION *1. Identification of the service/department and the transaction/requisition #: VA Boston Healthcare System: Transaction: 523-09-1-9183-0036 *2. Nature and/or description of the action being approved: SOLE SOURCE PROCUREMENT SERVICE FOR MAVERIC RESEARCH DEPARTMENT *3. Description of the supplies/services required to meet the agencys needs (including the estimated value): Time is urgent and compelling with in an eight week turn around period. Service to provide analysis on 1600 DNA samples on the Affymetrix Gene Chip Human 6.0 array. This array is the only DNA Chip available that combines 900,000 Single Nucleotide Polymorphisms (SNPs) and 946,000 non-polymorphic copy number probes (CNPs) for genome-wide association studies. The use of this array is an integral part of the planned DVA CSP study and array substitutions will not be allowed. Estimated cost: $1,000,000 ($625 per DNA sample) 4. Identification of the statutory authority permitting other than full and open competition: FAR Part 6.302-2 Unusual and compelling urgency *5. Demonstration that the proposed contractors unique qualifications or the nature of the acquisition requires use of the authority cited: The Affymetrix GeneChip Human 6 array was developed and is manufactured by Affymetrix. The chip arrays, the processing system, all reagents, and software are patented and sold only through Affymetrix. Although other laboratories can purchase Affymetrix equipment, chips, and reagents and perform this function on a fee for service basis, we decided to have this project done at Affymetrix for the following reasons: Experience: As the manufacturer and sole provider of the complete analysis system, this company has much more experience than any other company. Affymetrix has processed > than 100,000 samples. Greater than 25,000 samples have been analyzed on the Gene Chip 6 array with greater than 99% call rates. Capacity: As the manufacturer of the equipment, Affymetrix has more instruments available than other institutions and have the capacity to process 2880 samples per week. Security: VA personnel have visited the Affymetrix laboratories and seen their physical, information, and data security systems. All of their facilities are protected by key card access and have environmental controls offering sample and data security system that are more elaborate than the typical laboratory. Data access is limited and audited. Data files are routinely backed-up. Data is encrypted with digital keys and signatures until securely delivered to the VA. *6. Describe the efforts that have been made to ensure that offers are solicited from as many potential sources as is practicable, including whether a Commerce Business Daily notice was or will be publicized as required by Subpart 5.2 (copy attached) and, if not, which exception under 5.202 applies: Notice will be published 7. Determination by the Contracting Officer that the anticipated cost to the Government will be fair and reasonable: The cost to the Government will be determined to be fair and reasonable in accordance with criteria *8. Description of the market survey that was conducted (i.e. names of firms and the date(s) the firms were contacted) and the results or a statement of the reasons a market survey was not conducted: From the literature and trade shows, there are only two vendors capable of providing a chip based method of measuring on the order of one million DNA polymorphisms per assay. These vendors are Affymetrix and Illumina. Both vendors are actually participating in this project (see below).Personnel from VA Central office have visited both vendors. There are differences some between chips; for example the Affymetrix chip also allows for looking at copy number of some genes *9. Any other facts supporting the use of other than full and open competition, such as an explanation as to why technical data packages, specifications, engineering descriptions, statement of work, or purchase descriptions suitable for competition have not been developed or are not available. This array is the only DNA Chip available that combines 900,000 Single Nucleotide Polymorphisms (SNPs) and 946,000 non-polymorphic copy number probes (CNPs) for genome-wide association studies. We need to use Affymetrix for this contract because part of the goal of this project is to compare the Affymetrix and Illumina platforms. It is unclear as to which platform will perform better for conducting this type of analysis. The equipment necessary performs the analysis on the Illumina platform exists at the VA genomics laboratory. VA Central Office is funding this laboratory to analyze the samples on the Illumina platform. The Affymetrix chip analysis conducted on the same samples will be contracted out to Affymetrix (this PO request. The equipment to perform the analysis on the Affymetrix platform does not currently exist within the VA and as outline above (question 6) Affymetrix has the expertise and capacity to provide the high volume, high quality scientific results and assure appropriate data security Comparison of the data obtained using the two platforms, will be informative as to the which platform will perform better in future large scale genomic studies within the VA research. *10. A listing of the sources, if any, that expressed an interest in the acquisition: None to date *11. A statement of the actions, if any, that the department/service may take to remove or overcome any barriers to competition before any subsequent acquisition for the supplies/services is required in the future: Contracting Activity will continue to encourage full and open competition whenever possible.
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