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Combine Solicitation - Micro RNA Sequencing Validation and Confirmation Services

May 28, 2014

Notice Type: Combine Solicitation

Posted Date: 27-MAY-14

Office Address: Department of Health and Human Services; Food and Drug Administration; Office of Acquisitions and Grants Services; 5630 Fishers Lane, Room 2129 Rockville MD 20857-0001

Subject: Micro RNA Sequencing Validation and Confirmation Services

Classification Code: A - Research & Development

Solicitation Number: FDA-14-223-SOL-1131336

Contact: Sondea R Blair, Contract Specialist, Phone 8705437469, Email

Setaside: N/AN/A

Place of Performance (address): Work shall be performed on-site at the contractor location with deliverables sent to the following Government location:US Food and Drug Administration National Center for Toxicological Research Jefferson Laboratory 3900 NCTR Road Jefferson, AR

Place of Performance (zipcode): 72079

Place of Performance Country: US

Description: Department of Health and Human Services

Food and Drug Administration

Office of Acquisitions and Grants Services

This is a 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 FDA-14-223-SOL-1131336 and this solicitation is issued as a Request for Quote (RFQ). The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular (FAC) 2005-73 effective April 29, 2014. The associated North American Industry Classification System (NAICS) Code is 541711- Research and Development in Biotechnology; Small Business Size Standard is 500 employees. This acquisition is issued as full and open competition. Contract Type: Commercial Item-Firm Fixed Price. Part I: General Information (Introduction/Background/Scope) The Food and Drug Administration(FDA) National Center for Toxicological Research (NCTR) requires miRNA Sequencing Validation and Confirmation Services for profiles and expressions of miRNAs specific to carcinogen exposure, for use in identifying carcinogens biomarkers.

Recent studies demonstrate that miRNAs play an important role in chemical carcinogenesis and are involved in the early stage of tumor development, suggesting that miRNAs could be useful biomarkers for the detection of potential carcinogens. Our previous studies show that there are changes in expression for a large number of miRNAs following carcinogen exposure and that these expression changes occur in tissue and chemical specific manners. Many of the miRNAs deregulated by carcinogens are involved in the regulation of genes that are important for the key pathways of chemical carcinogenesis, including xenobiotic metabolism, DNA repair, apoptosis, cell proliferation, tumor suppression, cell transformation, and tumor progression. The previous aforementioned studies generated miRNA sequenced data using an Illumina Hi Sequencing Platform. To ensure future data is scientifically comparable with data from the previous studies, identical platforms across studies are necessary to the integrity of the sequencing quality, as well as the downstream analysis. The resulting miRNA data will be utilized to evaluate miRNA profiles and changes in miRNA expression following carcinogen exposure, thereby resulting in potential biomarkers for identifying carcoinogens.

Part II: Work Requirements A. Technical Requirements

At a minimum the Contractor shall provide: I. Library Construction * The library preparation shall be processed in a batch of 48 samples per run, using 48 indexed adaptors. * Each sample shall be processed individually by adding special bar-coded adaptors and reverse transcript and amplified. * Samples shall be pooled by mixing equal amount of DNA from each library based on the concentration measured by Picogreen. * miRNA library pools recovered from the samples shall yield a minimum of 20ng * The quantity of each library shall be measured by Picogreen DNA quantification, and the quality of library shall be recorded using high sensitive DNA chips on a bioanalyzer.

II. miRNA Sequencing * The barcoded libraries shall be sequenced utilizing the Illumina HiSeq2500 or above platform for single end 50 base pair reads. * Each pool of 48 different barcoded samples shall be evenly uploaded onto 4 flowcell lanes.

III. Data Collection, Management, Analysis and Processing (CMAP) * The sequencing data shall be de-multiplexed and transformed to FASTQ format data files (FASTQ files are ASCII text files that encode both nucleotide calls as well as 'quality information', which provides information about the confidence of each nucleotide). The final reads passed filter shall be no less than 10 million reads for each sample. * The Contractor shall upload all sequence data onto a secure data server and make the data available for download by FDA investigators. The provided data shall be in FASTQ data files format, and shall be able to offer an alternative method of data transformation upon request by the Government.

Schedule of Items (see attached) Part III: Supporting Information

A. Place of Performance Work shall be performed on-site at the contractor location with deliverables sent to the following Government location: US Food and Drug Administration (Point of contact will be provided at time of award) National Center for Toxicological Research Jefferson Laboratory 3900 NCTR Road Jefferson, AR 72079

B. Period of Performance The Government will provide 100 samples within 90-days of contract award. Contractor shall provide deliverables within 9-months of receipt of samples.

Est. Period of Performance: Base Year 07/15/2014 to 07/14/2015 Option Period One 07/15/2015 to 07/14/2016 Option Period Two 07/15/2016 to 07/14/2017

FAR and HHSAR Clauses and Provisions incorporated by reference may be obtained at:

Solicitation Provisions

The provision at FAR 52.212-1 Instructions to Offerors-Commercial Items (July 2013) applies to this solicitation. The following addenda apply:

The period of performance for the option periods in any resultant award will be estimated based on the date of award, estimated ultimate delivery of Item No. 0001. If/when Option Period One is exercised, the periods of performance for all options will be firmed via bilateral modification. The provision at FAR 52.212-2 Evaluation-Commercial Items is applicable to this solicitation. The specific evaluation criteria to be included in paragraph (a) of that provision are as follows:

The Government will award a contract resulting from this solicitation to the responsible offeror whose offer conforming to the solicitation will be the most advantageous to the Government, price and other factors considered. The following factors shall be used to evaluate quotes:

(i) Technical Capability (ii) Past Performance (iii) Price (inclusive of options)

When combined, technical capability, and past performance are more important than price in determining the best value to the Government. If the Government determines non-price factors to be essentially equal, price becomes more important as the discriminating factor. Technical Capability

Technical capability will be determined by review of information submitted by the offeror demonstrating corporate ability and experience in conducting miRNA sequencing by describing instrumentation, expertise with that instrumentation and operational integrity of the required instrumentation to conduct the proposed miRNA sequencing, RNA extraction, library preparation, and MicroRNA Deep Sequencing services. Describe in detail the existing facility and equipment that will be dedicated to successful performance of the required services identified above. Address the professional qualifications and experience of key staff who may be assigned in the production of the materials and delivery of services. Discuss specific software that will be used in data acquisition, statistics, quality control, data storage and archiving.

Recent and Relevant Past Performance Identify all ongoing and completed work (within the last 3 years from date of this solicitation) relevant to these requirements in terms of type, scope, complexity, and size. For each of these past performance references, provide a detailed description of the work, the period of performance, the dollar value of the work, your role and responsibilities as either a prime or subcontractor, the client name and address and client point of contact name, phone number, and email address. Any relevant past performance and/or collaborative research with major universities and/or federal agencies involved in publishing results in miRNA sequencing.

Offerors shall provide pricing, clearly delineating the applicable performance period, using the above schedule format for each period of performance. Offerors shall provide detailed costs supporting their firm fixed price, ensuring that the price proposal is consistent with the technical proposal in all respects since the price proposal may be used as an aid to further determine the Offeror's understanding of the technical requirements. The option periods will not be funded at time of award. If exercised, funding will be obligated individually each year for the option period exercised via contract modification; the option periods shall be priced accordingly. The Government may determine that an offer is unacceptable if the option prices are significantly unbalanced. Evaluation of options shall not obligate the Government to exercise the option(s). The Government reserves the right to obtain information for use in the evaluation from any and all sources including sources outside of the Government.

The government is not responsible for locating or securing any information, which is not identified in the proposal. To ensure information is available, offerors must furnish as part of their proposal all descriptive material necessary for the government to unequivocally determine whether the service meets the technical requirements.

The Government reserves the right to make an award without discussions.

The Provision at FAR 52.212-3, Offeror's Representations and Certifications - Commercial Items, applies to this acquisition. An offeror should complete only paragraph (b) of this provision if the offeror has completed the annual representations and certifications electronically at If an offeror has not completed the annual representations and certifications electronically at the System for Award Management (SAM) website, the offeror shall complete only paragraphs (c) through (o) of this provision. The clause at 52.212-4, Contract Terms and Conditions - Commercial Items applies to this acquisition. The following addenda have been added:

Inspection and Acceptance The deliverables and/or services delivered hereunder shall be inspected and accepted at destination by the Contracting Officer's Representative (COR) specified at award. If the deliverables or services are acceptable, the COR shall promptly forward a report of inspection and acceptance to the paying office. If the supplies or services are not acceptable, the COR shall document the nonconforming items/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 quarterly in arrears of service 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:

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.

The following clauses are incorporated by reference:

* FAR 52.232-40, Providing Accelerated Payment to Small Business Subcontractors

* HHSAR Clauses: 352.222-70, 352.231-71 and 352.242-71 * FAR Clause 52.217-9 Option to Extend the Term of the Contract * (a) ... within 1 day of contract expiration; .... at least 5 days before the contract expires... (c) ...shall not exceed 36 months.

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, 52.219-4, 52.219-28, 52.222-3, 52.222-19, 52.222-21, 52.222-26, 52.222-36, 52.223-18, 52.225-3 Alt II, 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 9:00 am (Central Standard Time - Local Prevailing Time in Jefferson, Arkansas) on June 9, 2014 to, Fax (870) 543-7990, or mail to the U. S. Food and Drug Administration, FDA/OO/OFBA/OAGS/DAP, Attention of Sondea Blair, 3900 NCTR Road, Building 50, Room 421 Jefferson, AR 72079-9502. For information regarding this solicitation, please contact Sondea Blair by e-mail at Questions regarding this solicitation will be accepted only via email. Please reference solicitation number FDA-14-223-SOL-1131336 in subject line of all correspondence.


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