Assessment of mRNA Gene Expression Using Next-Generation Sequencing Technology

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 solicitation number is 1102348. 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) 2005-59 dated May 10, 2012. The associated North American Industry Classification System (NAICS) Code is- 541380- Testing Laboratories; Small Business Size Standard is $14 million and is set-aside for small business concerns. The U.S. Food and Drug Administration (FDA), the National Center for Toxicological Research (NCTR) is soliciting for a contractor to perform the assessment of mRNA gene expression changes in rat liver using Next-Generation sequencing technology (Next-Gen). Next-Gen is required in order to provide full coverage of all the genes expressed in the rat livers after exposure to various hepatotoxicants. The Next-Gen platform that has been used for previous and on-going projects is the Illumina sequencing technology. The government must be able to make one to one comparisons between the data without introducing bias. An estimated total of 324 samples will be analyzed to compare the effect of the different hepatotoxicants on the hepatic expression of the genes. The government reserves the right to change the quantity of analyses required. Ultimately, the gene expression changes will be used as biomarkers of drug-induced liver injury. The government will provide total RNA to the contractor. The work is being conducted the protocol entitled "Biomarkers of Hepatotoxcicity". The purpose of this study is to identify gene expression changes that can provide better prediction of idiosyncratic hepatotoxicants in preclinical species, such as rats. Performance requirements: a. The contractor must independently assess the quantity and quality of the RNA provided by the government to ensure that it is acceptable for sequencing. b. Preparation of libraries from the mRNA that can be run on the Next-Gen platform. c. Sequencing of the libraries using Illumina sequencing technology. The parameters for the sequencing are paired end reads, 50 bases minimum per read, and a depth of coverage of at least 12 million read pairs per sample. d. Alignment of the read data to the current reference human genome and transcriptome with transcript identifications assigned from the UCSC Known Gene table as the definition for both gene and transcript level expression, modified so that transcript IDs are guaranteed to be unique. At least 85% unambiguous alignment to the transcriptome and genome is required. Contractor's samples that fail to meet the requirement shall be re-analyzed at no additional cost to the government. e. The following data analysis and output must be provided. The data will be provided on a portable hard drive of sufficient capacity to hold all the data (multiple hard drives may be used if the amount of data requires it). 1. FASTQ file for each sample. 2. A table of the flow cell statistics outlining the quality and yield of the flow cell(s) where samples were clustered and sequenced. 3. QC files regarding any presence of artifact/duplicate sequences, along with base distributions and qualities. 4. A tab-delimited text file with collapsed and normalized counts for each detected gene and isoform (UCSC Known Gene) for each specimen. 5. An alignment file (BAM format) containing best alignments of each read to the applicable genome. 6. De-multiplexing of Illumina barcodes, if applicable. 7. Reads aligned to Affymetrix probe sets on the HU133 2.0 Plus Array in a format compatible with an Affymetrix CEL file so that the data are compatible with and can be uploaded to the publicly-available software ArrayTrack (http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/default.htm ). FOB Point Destination. FOB Point of Delivery for Services and Supplies will be the FDA/NCTR located at 3900 NCTR Road, Jefferson, AR 72079. Payment terms net 15 days after government acceptance of the supplies/services. Period of Performance: The Government will provide all samples by August 31, 2012. The contractor shall run all samples and return results no later than November 30, 2012. Schedule of Items: 1. mRNA sequencing and assessment of rat liver as described above (Performance Requirements a-e.), Estimated quantity 324, Unit Price $____________, Total Price $___________________. Contract clauses- The clause at 52.212-4, Contract Terms and Conditions-Commercial Items (FEB 2012), applies to this acquisition. The following addenda have been attached to the clause. The following additional provisions and/or clauses apply and incorporated by reference and apply to this acquisition. Clauses and provisions can be obtained at https://www.acquisition.gov/far/ 52.204-4 Printed or Copied Double-Sided on Recycled Paper.(MAY 2011) 52.204-7 Central Contractor Registration. (FEB 2012) The following HHSAR clauses apply and can be obtained at the following website: http://farsite.hill.af.mil/VFHHSAR1.htm 352.202-1 Definitions JAN 2006 352.203-70 Anti-Lobbying JAN 2006 352.222-70 Contractor Cooperation in Equal Employment Opportunity Investigations OCT 2009 352.223-70 Safety and Health JAN 2006 352.231-71 Pricing of Adjustments JAN 2001 352.242-71 Tobacco-Free Facilities JAN 2006 The supplies and/or services delivered hereunder shall be inspected and accepted at destination by the contracting officer's representative (COR) specified at award. If the supplies 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. The COR for this order is: to be completed at time of award. The COR is responsible for: (1) Monitoring the Contractor's technical progress, including the surveillance and assessment of performance and recommending to the Contracting Officer changes in requirements; (2) Interpreting the statement of work and any other technical performance requirements; (3) Performing technical evaluation as required; (4) Performing technical inspections and acceptances required by this contract; and (5) Assisting in the resolution of technical problems encountered during performance. The Contracting Officer is the only person with authority to act as agent of the Government under this contract. Only the Contracting Officer has authority to: (1) Direct or negotiate any changes in the statement of work; (2) Modify or extend the period of performance; (3) change the delivery schedule; (4) Authorize reimbursement to the Contractor any costs incurred during the performance of this contract; or (5) Otherwise change any terms and conditions of this contract. Invoice Submission Invoices shall be submitted to the attention of the designated Contract Specialist 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: Food and Drug Administration Nick Sartain 3900 NCTR Road Building 50, Room 422 Jefferson, AR 72079 Or electronically at contact@example.gov II. One copy to the Contracting Officer Representative (COR) or other program center/office designee, clearly marked "courtesy copy only: To be completed at time of award. Questions regarding invoice payments should be directed to the FDA payment office at a telephone number provided above. Questions relating to when payment will be received should be directed to the FDA payment office at the email below or at +1 (555) 000-0000 or +1 (555) 000-0000. contact@example.gov. The clause at FAR 52.212-5, Contract Terms and Conditions Required to Implement Statues or Executive Orders-Commercial Items (MAY 2012) applies to this acquisition. The following additional FAR clauses cited in this clause are applicable: 52.203-6 alt I, 204-10, 209-6, 209-10, 52.219-6, 52.219-14, 52.219-8, 52.222-3, 52.222-19, 52.222-21, 52.222-26, 52.222-35, 52.222-36, 52.222-37, 52.222-40, 52.223-15, 52.223-16, 52.223-18, 52.225-3, 52.225-13, and 52.232-33. Solicitation provisions Contract Type: Commercial Item-Firm Fixed Price. The provision at FAR 52.212-1 Instructions to Offerors-Commercial Items (FEB 2012) applies to this solicitation. The following addenda have been attached to this provision: Addendum Paragraph (c) Period for acceptance of offers. The offeror agrees to hold the prices in its offer firm until September 30, 2012. 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 of the items/services offered to meet or exceed the Government's requirement. (ii) Past Performance (ii) Price. Technical and past performance is significantly less important when compared to price in determining the best value to the government. Technical capability will be determined by review of information submitted by the offeror which must provide sufficient technical information necessary for the Government to conclusively determine that the offered products and services meet the technical requirements identified above. Offerors shall specifically address each performance requirements stated above to demonstrate that the proposal meets the technical requirements. Provide the sequencing platform to be used and if other than Illumina provide documentation that the government will be able to make one to one comparisons between the data without introducing bias from other platforms. Offerors can provide technical specifications, descriptive material, literature, brochures and other information which demonstrates the capabilities of the offeror. The Contractor shall provide amount of RNA for each sample that must be provided by the Government. Provide a list of prior similar experience in Next-Gen sequencing work and contact information of at least two references that can be contacted that the contractor has provided similar services within the last two years. Name, telephone number, email address, contract number and description of the services with dollar amount. The government is not responsible for locating or securing any information, which is not identified in the proposal however the Government reserves the right to obtain information for use in the evaluation from any and all sources including sources outside of the Government. Include the firms DUNS number with quote. (c) A written notice of award or acceptance of an offer, mailed or otherwise furnished to the successful offeror within the time for acceptance specified in the offer, shall result in a binding contract without further action by either party. Before the offer's specified expiration time, the Government may accept an offer (or part of an offer), whether or not there are negotiations after its receipt, unless a written notice of withdrawal is received before award. The government reserves the right to make an award without discussions. The Provision at FAR 52.212-3, Offeror Representations and Certifications-Commercial Items (APR 2012), 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 http://orca.bpn.gov. CCR Requirement - Company must be registered in the Central Contractor Registration (CCR) system before an award could be made. If company is not registered in CCR, they may do so by going to CCR web site at http://www.ccr.gov. The Defense Priorities and Allocations System (DPAS) and assigned rating are not applicable to this solicitation notice. It is the offeror's responsibility to monitor the internet site for the release of an amendment to the combined synopsis/solicitation (if any). Offerors that fail to complete the required representations and certifications, or reject the terms and conditions of the solicitation, may be excluded from consideration. All responsible sources may submit an offer, which if timely received, shall be considered. The offer must reference solicitation number 1102348. The offers are due in person, by postal mail or email to the point of contact listed below on or before June 19, 2012 by 13:00 hours (Central Standard Time in Jefferson, Arkansas) at the Food and Drug Administration, OO/OFBA/OAGS, Attn: Nick Sartain, 3900 NCTR Road, HFT-320, Jefferson, AR 72079-9502. For information regarding this solicitation, please contact Nick Sartain at +1 (555) 000-0000, FAX +1 (555) 000-0000 or email contact@example.gov.