MODIFICATION
B -- Genome Sequencing Services
- Notice Date
- 3/3/2014
- Notice Type
- Modification/Amendment
- NAICS
- 811219
— Other Electronic and Precision Equipment Repair and Maintenance
- Contracting Office
- Department of Health and Human Services, Food and Drug Administration, Office of Acquisitions and Grants Services, 3900 NCTR Road, HFT-320, Bldg 50 | Rm 421, Jefferson, Arkansas, 72079, United States
- ZIP Code
- 72079
- Solicitation Number
- 1128309
- Archive Date
- 3/20/2014
- Point of Contact
- Crystal G. McCoskey, Phone: 8705437267
- E-Mail Address
-
crystal.mccoskey@fda.hhs.gov
(crystal.mccoskey@fda.hhs.gov)
- Small Business Set-Aside
- N/A
- Description
- This is a combined synopsis/solicitation for commercial items prepared in accordance with the Federal Acquisition Regulation (FAR) format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; proposals are being requested and a written solicitation will not be issued. The government intends to issue a Purchase Order in accordance with FAR PART 13.106 for the requirement under Simplified Acquisition Procedures. The solicitation number is 1128309 and this solicitation is issued as a Request for Quote (RFQ). Competition is limited to only those Contractors who can provide the services on an Illumina HiSeq2500 platform only. Alternate sequencing equipment will be not acceptable for this procurement due to the nature of the study the data analysis results are to support. RESPONSE DATE: 03/05/2014 The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular (FAC) 2005-72 effective January 30, 2014. The associated North American Industry Classification System (NAICS) Code is 811219-Laboratory Instrument Repair and Maintenance Services; FSC Code is B529 - Scientific Data Studies. Small Business Size Standard is $14.0 Million. Acquisition is a small business set-aside. Contract Type: Commercial Item-Firm Fixed Price. REQUIREMENTS: Part I: General Information (Introduction/Background/Scope) The U.S. Food and Drug Administration (FDA), National Center for Toxicological Research (NCTR) has a requirement for genome sequencing services. The NCTR is conducting a study titled, "The Sequencing Quality Control Project, MicroArray Quality Control (MAQC) Phase III, - Sequencing-based Technologies for Safety Evaluation of FDA-regulated Products". The study requires human whole-genome DeoxyriboNucleic Acid (DNA) sequencing services on an estimated 10-20 human DNA samples, using an Illumina HiSeq2500 platform, to accurately evaluate the performance and utility of the next-generation sequencing platform in detecting human genetic variation including Single Nucleotide Variants (SNVs), short Insertions and Deletions (Indels), Copy Number Variations (CNVs), and large Structure Variations (SVs). The resulting variants call data will be used to evaluate the sensitivity, specificity and robustness of each Next-Generation Sequencing (NGS) platform compared to those detected with microarray-based genotyping approaches from the MAQC-Phase II project which evaluated Roche 454, ABI SOLID 5500, and Affymetrix platforms. This phase of this long running project is specific to evaluation of the Illumina HiSeq 2500 platform to identify human genome variation sensitivity and specificity. Part II: Work Requirements The FDA will provide the initial samples (estimated between 10-20; to be determined at award based on price with a total award amount not to exceed budgeted amount of $150,000) to the Contractor within 180 calendar days of order date by NCTR researchers. The Contractor shall assess the quality of each DNA sample using fluorometric-based methods including Qubit or PicoGreen to provide accurate quantification for double-stranded DNA. The ratio of absorbance at 260 nanometer (nm) to absorbance at 280 nm shall be used as an indication of sample purity; the acceptable ratio of absorbance shall be in a range from 1.8 to 2.0.The quality verification results shall be sent electronically to the Project Officer (PO) for review upon conclusion of the initial quality screening. Any samples that fail the quality assessment shall be returned for replacement. Any necessary replacement samples will be provided within 7 calendar days of the receipt of the quality verification results. The contractor shall provide library preparation services using the Illumina "TruSeq DNA Polymerase Chain Reaction (PCR)-free Sample Preparation Kits" from 2 microgram (µg) input genomic DNA. The insert size shall be approximately 550 bases. The sequencing image data obtained from the HiSeq2500 shall be transformed to fastq data files and aligned against the Human Genome reference HG19 (from the University of California, Santa Cruz) which can be found at: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/. The aligned files shall be in Binary Alignment/Map (BAM) format. The genome coverage, or sequence depth, for each sample shall be no less than 50 times (x). The genetic variants shall be analyzed using the standard parameters contained in Illumina's default software. The variants shall be recorded in Variant Call Format (VCF). The Contractor shall provide one (1) Hard Disk Drive (HDD) and one (1) electronic copy of all sequence data (including fastq files, BAM files, and VCF files) to the PO within 120 calendar days of receipt of all required samples meeting the quality standards listed above. The contractor shall return, via method (i.e. expedited, protective packaging, temperature control) that maintains the integrity of the sample during shipment, all samples, including those returned unprocessed as a result of quality verification failure, to NCTR upon completion of the analysis. Part III: Supporting Information A. Return Address for Samples: U.S. FDA National Center for Toxicological Research Attention: Terri Toenessen 3900 NCTR Rd., Building 15, Room 103A Jefferson, AR 72079 B. Period of Performance Final sequencing data shall be provided within 120 days of receipt of full order quantity of viable samples, which will occur within 180 days from date of order. Ultimate completion is expected within 315 days of date of order. Schedule of Items 0001 - Genome Sequencing Services in accordance with requirements above at $_______ per sample inclusive of shipping. Total $____________ GSA Contract No. (if applicable) ______________ FAR and HHSAR Clauses and Provisions incorporated by reference may be obtained at: http://www.acquisition.gov/far/ http://www.dhhs.gov/asfr/ogapa/acquisition/acquisitionpolicies.html The provision at FAR 52.212-1, Instructions to Offerors- Commercial Items applies to this solicitation. Addenda to this provision are as follows: Prices shall be valid through 09/30/2014 and award is subject to the availability of funds. It is the Government's goal to get the highest number of samples analyzed as possible within the budget amount of $150,000.00. Contractors shall indicate any available price discounts offered between the quantities of 10-20 samples in their offer. Quantity for Item 0001 to be determined at award based on per sample pricing received and available funding. The government is not responsible for locating or securing any information, which is not identified in the quote. To ensure information is available, offerors must furnish as part of their proposal all descriptive material necessary for the government to determine whether the service meets the technical requirements. Quotes shall include technical specifications, descriptive material, literature, brochures, Quality Assurance Plans (QAPs), Standard Operating Procedures (SOPs) and/or other information corresponding to each requirement, which demonstrates the capabilities of the Offeror to provide the service. Furthermore, experience with human genome DNA sequencing with Illimina HiSeq2500 technology, library preparation, filtering/transforming data, and preparing data reports shall be included with offer. Each offer shall identify and provide background information for the key personnel to be performing the analysis, i.e. education, previous projects, publications, positions/employment history. Any relevant past performance and/or collaborative research with major universities and/or federal agencies involved in publishing results in human genome sequencing studies of similar complexity and magnitude in the past three (3) years, shall be included with any resultant offer. The provision at FAR 52.212-2 Evaluation-Commercial Items is applicable to this solicitation and is hereby incorporated by reference. The specific evaluation criteria to be included in paragraph (a) of that provision are as follows: (i) technical capability of the services offered to meet the Government requirement; (ii) past performance/experience; (iii) price (based on a quantity of 15 each for all offerors for evaluation purposes; any quantity ordered in excess of evaluated quantity will still be subject to competitive price comparison for determination of fair and reasonable price) Technical capability and past performance are of equal importance, and when combined, are more significant when compared to price. Technical capability will be determined by review of information submitted by the Offeror, which must provide a description in sufficient detail to show that the service quoted meets the Government's requirement and demonstrates successful performance of the service requested with any specific equipment (if stated) herein. Offeror's past performance/experience will be evaluated based on the recency (within the last 3 years) and relevancy (similar methods/techniques, type, complexity and magnitude of sequencing) of the information provided and the staff's key personnel proposed to determine the likelihood of success in performing the solicitation's requirements. Technical capability and past performance/experience for any intended subcontractors shall be included with offer. The Government reserves the right to consider past performance information from any other source (e.g. Past Performance Information Retrieval System) when evaluating past performance. The Provision at FAR 52.212-3, Offeror's Representations and Certifications-Commercial Items, applies to this acquisition. The clause at 52.212-4, Contract Terms and Conditions - Commercial Items, applies to this acquisition. Addenda to this clause are as follows: Inspection and Acceptance The services delivered hereunder shall be inspected and accepted at destination by the contracting officer's representative (COR) specified at award. If the services are acceptable, the COR shall promptly forward a report of inspection and acceptance to the paying office. If the services are not acceptable, the COR shall document the nonconforming services and immediately notify the contracting officer. Invoice Submission Payment terms net 30 days after government acceptance of the supplies/services. Invoices shall be submitted to the attention of the Office of Financial Services identified below and contain all necessary information per FAR 52.212-4 (g) in accordance with the following instructions. I. An original and two (2) copies shall be submitted to: FDA/OC/OA/OFO/OFS Attn: Division of Payment Services 3900 NCTR Road, HFT-324 Building 50, 6th floor, suite 616 Jefferson, AR 72079 Phone: (870) 543-7446 Fax 870-543-7224 An electronic invoice can be emailed to the following address: nctrinvoices@fda.hhs.gov II. One copy each to the Contracting Officer and Contracting Officer Representative (COR) or other program center/office designee, clearly marked "courtesy copy only": Questions regarding invoice payments should be directed to the FDA payment office at phone or email reference provided above. Questions relating to when payment will be received should be directed to the FDA payment office at the email below or at (870) 543-7446 or (870) 543-7042. nctrinvoices@fda.hhs.gov. The following clauses are incorporated by reference: • FAR 52.232-40, Providing Accelerated Payments to Small Business Subcontractors • HHSAR Clauses: 352.222-70 and 352.231-71 The clause at FAR 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders - Commercial Items, applies to this acquisition. The following additional FAR clauses cited in this clause are applicable: (b) 52.204.10, 52.209-6, 52.219-6, 52.219-28, 52.222-3, 52.222-21, 52.222-26, 52.222-35, 52.222-36, 52.222-37, 52.223-18, 52.225-13 and 52.232-33 Additional Information It is the offeror's responsibility to monitor the internet site for the release of any information related to this combined synopsis/solicitation. Offerors are responsible for delivery in person, by e-mail, fax, mail or other delivery method their complete proposal and any additional documents before 2:00 pm (Central Standard Time - Local Prevailing Time in Jefferson, Arkansas) on March 5, 2014 to crystal.mccoskey@fda.hhs.gov, Fax (870) 543-7990, or mail to the U. S. Food and Drug Administration, FDA/OO/OFBA/OAGS/DAP, Attention of Crystal G. McCoskey, 3900 NCTR Road, Building 50, Room 426 Jefferson, AR 72079-9502. For information regarding this solicitation, please contact Crystal G. McCoskey by e-mail at crystal.mccoskey@fda.hhs.gov. Questions regarding this solicitation will be accepted only via email and shall be submitted no later than 09:00 AM CST on February 28, 2014. Please reference solicitation number 1128309 in subject line of all correspondence.
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-
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- SN03300970-W 20140305/140303234425-ff59a4500bda7f3b3472c2544fb60e55 (fbodaily.com)
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