National Cancer Institute, Research Contracts Branch, PSAS, 6120 Executive Blvd, EPS/Room 638, Bethesda, MD 20892-7227

66 -- HIGH DENSITY DNA MICRO-ARRAYS SOL RFQ-NCI-90028-NV DUE 011599 POC Debbie Moore, Purchasing Agent, (301) 402-4509, Todd Cole, Contracting Officer (301) 402-4509 This is a combined synopsis/solicitation for commercial items, prepared in accordance with the format in FAR 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation and a separate solicitation will not be issued. This solicitation, No. RFQ-NCI-90028-NV includes applicable provisions and clauses in effect through FAR FAC 97-09. The acquisition is being made in accordance with the test program for using simplified procedures for certain commercial items authorized in FAR 13.5. The solicitation is set-aside for small businesses. The Standard Industrial Classification Code is 3826, and the business size standard is 500 employees. BACKGROUND: The National Cancer Institute (NCI), the largest institute within the National Institutes of Health (NIH), conducts and supports research, training, and information dissemination on the cause, detection, treatment, and prevention of cancer, as well as rehabilitation and therapy of cancer patients. This requirement is to extend the research capabilities of the NIH through the use of high density DNA micro-array technology to achieve high throughput analysis of massively paralleled genomic sequences. These high density DNA micro-arrays will be used to perform expression studies, re-sequencing experiments, and genotype analysis. NCI requires the ability to specifically monitor, in a quantitative fashion, the expression levels of human, murine, and yeast genes. In addition to the noted commercially available arrays, NCI also requires services to create custom arrays to monitor expression levels in other genes. Additional components within NCI's requirement include training and support in utilizing the arrays. REQUIREMENTS: An indefinite quantity contract with a one year base period of performance and two one-year option periods is anticipated under this solicitation. The requirements for the array technology and related training follow: Commercially Available Arrays: Any arrays that are considered to be commercially available under this procurement shall have the minimum characteristics herein. The high density DNA micro-arrays must contain at least 10,000 different target sequences per square centimeter of solid support substrate. The sequences will be represented as 25-mer oligonucleotide probes immobilized on a glass support using light directed solid phase combinatorial chemistry. Arrays will utilize approximately 20 paired oligonucleotide probes per gene for analysis. Perfect and single-base mismatch probes correlated to target genes shall be used on adjacent array areas. Arrays will contain sequences from UniGene, GenBank, Saccharomyces Genome Database, or the TIGR databases as most currently available. The arrays must be sensitive enough to detect mRNA transcripts at the rate of 2-3 copies per cell. Arrays will also be sensitive enough to identify mRNA concentration level changes 2-3 fold and greater for high sensitivity expression comparison. The Contractor shall have available high density arrays containing entire coding sequences from known genes, such as the p53 tumor suppressor gene, for use in re-sequencing experiments. These particular arrays must be able to detect any mutant sequence in the coding region of the gene that the array was designed for. Of the currently available arrays, NCI requires 1) human gene analysis, 2) murine gene analysis, 3) Saccharomyces cerevisiae yeast gene analysis arrays, and 4) sample control arrays for quality assurance. The following specifications are required for each: 1) For human gene analysis, the following minimum characteristics and features shall be met: A. Utilized paired oligonucleotide probes for analysis; B. Capable of monitoring expression levels of greater than 6,800 full length human genes; C. Sources for infromation databases shall include GenBank, TIGR, and Unigene as most currently available; D. Microchip array synthesis area of 1.28 cm x 1.28 cm; E. Probe lengths of 25 mer; F. Perfect and single-base mismatch probes correlated to target genes shall be used on adjacent array areas; G. Includes the use of approximately 20 probe pairs per gene; H. Array oligonucleotides shall be synthesized in-situ on a glass substrate using light directed solid phase combinatorial chemistry. 2.) For murine gene analysis, the following minimum characteristics and features shall be met: A. Utilize paired oligonucleotide probes for analysis; B. Capable of monitoring expression levels of approximately 6,500 murine genes and ESTs; C. Sources for information shall be as described in the GenBank database as most currently available; D. Microchip array synthesis area of 1.28 cm x 1.28 cm; E. Probe lengths of 25 mer; F. Perfect and single-base mismatch probes correlated to target genes shall be used on adjacent array areas; G. Includes the use of approximately 20 probe pairs per gene; H. Array oligonucleotides shall be synthesized in-situ on a glass substrate using light directed solid phase combinatorial chemistry. 3.) For Saccharomyces cerevisiae yeast gene analysis, the following minimum characteristics and features shall be met: A. Utilize paired oligonucleotide probes for analysis; B. Capable of monitoring expression levels of approximately 6,100 Saccharomyces cerevisiae yeast genes; C. Sources for information shall be as described in the Saccharomyces Genome Database as most currently available; D. Microchip array synthesis area of 1.28 cm x 1.28 cm; E. Probe lengths of 25 mer; F. Perfect and single-base mismatch probes correlated to target genes shall be used on adjacent array areas; G. Includes the use of approximately 20 probe pairs per gene; H. Array oligonucleotides shall be synthesized in-situ on a glass substrate using light directed solid phase combinatorial chemistry. 4.) The Contractor shall provide test arrays (Sample Control Arrays for Quality Assurance) as required, which allow the researcher to analyze sample RNA target preparations for hybridization acceptability for the high density micro-arrays. Custom Array Services: Services to create custom micro-arrays shall be performed on an as needed basis. The NCI will identify custom sequences to create the specified arrays. The custom arrays shall carry a probe density specified by the NCI. Custom arrays shall be synthesized using light directed solid phase combinatorial chemistry on a glass support. Training: Training services shall be provided to NCI in order to instruct personnel on how to appropriately use array technology. Training shall consist of instructing personnel in the handling and execution of experimental procedures using the arrays. Training services shall include experimental sample preparation, system operation, probe array processing, and data analysis. Advanced training in data analysis, lab management, trouble shooting procedures, and array maintenance shall be provided to NCI. To accomplish the above training needs the Contractor shall have established modules for the above areas. Period of Performance: The base period of performance will begin in February 1999 and end in February 2000. During this period, NCI anticipates procuring the following ranges of arrays and training through the anticipated purchase order:1.) Human Gene Analysis Arrays -- Minimum Quantity: 33 and Maximum Quantity: 50; 2.) Murine Gene Analysis Arrays -- Minimum Quantity: 32 and Maximum Quantity: 45; 3.) Saccharomyces Cerevisiae Yeast Gene Analysis Arrays -- Minimum Quantity: 10 and Maximum Quantity: 20; 4.) Sample Control Arrays for Quality Assurance -- Minimum Quantity: 30 and Maximum Quantity: 50; 5.) Other Commercially Available Arrays -- Minimum Quantity: 5 and Maximum Quantity: 50; 6.) Custom Arrays -- Minimum Quantity: 0 and Maximum Quantity: 5; and 7.) Training -- Minimum Hours: 28 and Maximum Hours: 56. The period of performance for Option Year 1 will begin in February 2000 and end in February 2001. During this period, the following estimated minimum and maximum quantities are applicable:1.) Human Gene Analysis Arrays -- Minimum Quantity: 35 and Maximum Quantity: 60; 2.) MurineGene Analysis Arrays -- Minimum Quantity: 35 and Maximum Quantity: 60; 3.) Saccharomyces Cerevisiae Yeast Gene Analysis Arrays -- Minimum Quantity: 10 and Maximum Quantity: 20; 4.) Sample Control Arrays for Quality Assurance -- Minimum Quantity: 30 and Maximum Quantity: 60; 5.) Other Commercially Available Arrays -- Minimum Quantity: 5 and Maximum Quantity: 50; 6.) Custom Arrays -- Minimum Quantity: 0 and Maximum Quantity: 5; and 7.) Training -- Minimum Hours: 5 and Maximum Hours: 56. The period of performance for Option Year 2 will begin in February 2001 and end in February 2002. During this period, the following estimated minimum and maximum quantities are applicable:1.) Human Gene Analysis Arrays -- Minimum Quantity: 35 and Maximum Quantity: 60; 2.) Murine Gene Analysis Arrays -- Minimum Quantity: 35 and Maximum Quantity: 60; 3.) Saccharomyces Cerevisiae Yeast Gene Analysis Arrays -- Minimum Quantity: 10 and Maximum Quantity: 20; 4.) Sample Control Arrays for Quality Assurance—Minimum Quantity: 30 and Maximum Quantity: 60; 5.) Other Commercially Available Arrays -- Minimum Quantity: 5 and Maximum Quantity: 50; 6.) Custom Arrays -- Minimum Quantity: 0 and Maximum Quantity: 5; and 7.) Training -- Minimum Hours: 5 and Maximum Hours: 56. Shipping of Arrays: Arrays shall be packaged in an appropriate manner to ensure safe delivery. Unless otherwise agreed upon, the arrays shall be shipped to NCI within 10 working days after receiving an order for commercially available arrays. Custom arrays, depending upon the nature of the request and the Contractor's ability to produce the desired array, shall be shipped within a reasonable time frame as agreed upon by NCI and the vendor. NCI shall be notified of the construction date of the array(s) and the shipping date upon the vendor's receipt of a given order. PRICING: Offerors must complete a MANDATORY "Schedule of Pricing For Microarrays and Training" and submit it with their proposal. Based on the schedule, the Offeror shall provide unit pricing for all categories of microarrays documented herein for the base and each option period. The Offeror may propose a single price for a particular array, regardless of the quantity purchased, or separate prices for the minimum and maximum quantities. For the training, the offeror shall list each training module that is required to fully meet the requirement, and provide the foregoing unit pricing for the base and all options. Also, the offeror shall provide a minimum and maximum amount for each item, as well as appropriate total amounts and pricing summary amounts as instructed in the mandatory "Schedule of Pricing For Microarrays and Training". EVALUATION CRITERIA: The technical portion of quotations will be reviewed by a panel of at least three NIH experts. The technical portion of quotations will receive paramount consideration in selecting a vendor. However, price will also be a significant factor in the event that two or more vendors are determined to be essentially equal following evaluation of the technical portion of quotations. The final price that may be used for source selection purposes will be the amount logically derived and shown in the "Pricing Summary's" block entitled, "Average of Total Minimum and Maximum Amounts" within the "Schedule of Pricing For Microarrays and Training." The respective minimum and maximum costs as averaged on the Schedule of Pricing for Microarrays and Training (labeled as "Average of Total Minimum and Maximum Pricing Amounts") will be the basis for any decision involving price. Offerors shall also provide three references of organizations that have purchased array technology within the past year. The references may be used in the event that two or more offerors are considered essentially equal after the technical and price evaluations. In any event, the Government reserves the right to make award to the vendor whose offer provides the greatest overall value to the Government. Offers will be evaluated on the following technical evaluation criteria: 1) Demonstrate and provide evidence that the proposed microarrays (human gene analysis arrays, murine gene analysis arrays, Saccharomyces cerevisiae yeast gene analysis arrays, sample control arrays for quality assurance, and other commercially available arrays) meet the minimum specifications herein (50% weight); 2) Demonstrated corporate experience in producing and providing the required, commercially available microarrays, custom microarray production services, and training in quantities similar to the amounts required within this solicitation (25% weight); 3) Demonstrate the capability to train and instruct personnel on how to use array technology, and provide training modules that encompass the areas described within this solicitation (15% weight); 4) Demonstrate and provide evidence of the ability to create custom arrays for custom sequences and that meet the minimum characteristics herein (10% weight). All arrays shall be shipped F.O.B. destination or F.O.B. Origin with transportation insurance (provided bythe vendor) and inside delivery to the location specified within each order that is placed against the anticipated purchase order (generally within the Washington, D.C. metropolitan area). Offers must be submitted on an SF-18 or SF-1449 with a completed "Schedule of Offered Supplies/Services." Offers must be accompanied by a completed "Offeror Representations and Certifications- Commercial Items -- with Duns Number Addendum," signed by an authorized representative of the offeror. The MANDATORY "Schedule of Pricing For Microarrays and Training" for the base and option periods, along with any other pertinent pricing information, must be fully completed and included with the offer. Offerors must submit an original technical proposal plus descriptive literature, warranties, and/or other materials that demonstrate that their offer meets all of the foregoing requirements. In addition, four (4) copies of the technical proposal and all materials shall be submitted with the original. This solicitation incorporates the provisions at FAR 52.212-1, INSTRUCTION TO OFFERORS -- COMMERCIAL ITEMS -- DEVIATION FOR SIMPLIFIED ACQUISITIONS; FAR 52.212-2, EVALUATION -- COMMERCIAL ITEMS; FAR 52.212-3, OFFEROR REPRESENTATIONS AND CERTIFICATIONS -- COMMERCIAL ITEMS, along with the DUNS NUMBER ADDENDUM; and FAR 52.217-5 EVALUATION OF OPTIONS. The resulting contract will incorporate either acceptable Commercial Terms and Conditions of the offeror or FAR 52.212-4, CONTRACT TERMS AND CONDITIONS -- COMMERCIAL ITEMS. In addition, the resulting contract will incorporate FAR 52.212-5, CONTRACT TERMS AND CONDITIONS REQUIRED TO IMPLEMENT STATUTES OR EXECUTIVE ORDERS -- COMMERCIAL ITEMS -- DEVIATION FOR SIMPLIFIED ACQUISITIONS. The following FAR clauses cited in paragraph (b) of the clause at FAR 52.212-5 are applicable to this acquisition: FAR 52.222-26, EQUAL OPPORTUNITY; FAR 52.222-35, AFFIRMATIVE ACTION FOR DISABLED VETERANS AND VETERANS OF THE VIETNAM ERA; FAR 52.222-36, AFFIRMATIVE ACTION FOR WORKERS WITH DISABILITIES; FAR 52.222-37, EMPLOYMENT RECORDS ON DISABLED VETERANS AND VETERANS OF VIETNAM ERA; and FAR 52.225-3, BUY AMERICAN ACT -- SUPPLIES. In addition, FAR 52.216-18 Ordering, FAR 52.216-19 Order Limitations, FAR 52.216-22 Indefinite Quantity, and FAR 52.217-6 Option for Increased Quantity shall apply to any resulting contract. Interested Offerors may contact Debbie Moore, Purchasing Agent, at (301)-402-4509 (Fax: (301)-402-4513) for the mandatory "Schedule of Pricing For Microarrays and Training" or to receive full text copies of the representations and certifications or other cited provisions and clauses Any questions pertaining to this solicitation and requirement shall be submitted by January 5, 1999. Offers and related materials must be received in this office no later than 3:00 pm EST on January 15, 1999. Please cite the solicitation number, RFQ-NCI-90028-NV, on your offer. Posted 12/15/98 (W-SN280458). (0349)

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