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The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular (FAC) 2005-72, January 30, 2014.
The associated North American Industry Classification System (NAICS) Code is- 541380 - Testing Laboratories; Size standards $12 million. This combined/synopsis solicitation is not set aside for small business. The requirement will be competed unrestricted and made available to Full and Open competition, meaning any qualified vendor regardless of size status may submit a quote.
Respondents are responsible for delivery in person, by e-mail, fax, mail or other delivery method of their complete proposal and any additional documents before 1:00 pm (Central Standard Time - Local Prevailing Time in Jefferson, Arkansas) on March 18, 2014 to [email protected], Fax (870) 543-7990, or mail to the U. S. Food and Drug Administration, OO/OFBA/OAGS, Attention of Howard Nesmith, 3900 NCTR Road, Building 50, Room 424, Jefferson, AR 72079-9502.
PLEASE NOTE - The above contact information is for the Contracting Office and not the delivery address. The delivery address is indicated in the FOB Destination section below.
For information regarding this solicitation, please contact Howard Nesmith by e-Mail at [email protected].
The U.S. Food and Drug Administration (FDA), National Center for Toxicological Research (NCTR), is soliciting quotes for Assessing Gene (mRNA) Expression services.
Statement of Work (SOW)
The FDA/NCTR requires services for assessing gene (mRNA) expression changes in rat blood using Next-Generation sequencing technology (Next-Gen). Next-Gen is required in order to provide full coverage of all the mRNA expressed in these samples. In order to make one to one comparisons between the data without introducing bias that may occur with the use of different technologies, Illumina sequencing technology is required. It is essential that the mRNA expression analysis uses Next-Gen sequencing and not another detection technology such as microarrays since this study requires complete coverage of all expressed mRNAs in the cells.
The services shall be performed in a Good Laboratory Practice (GLP)-certified facility and have previous successful experience with blood RNA purification, globin clear, and RNA sequencing.
There is a current requirement for a total of 228 samples which will be analyzed to compare the effect of drugs on the blood RNA profiling. *There are additional requirements for varying quantity for the next three (3) years, dependent on requires samples.
Minimum Specific deliverables/timelines:
a) RNA sequencing and resulting libraries. Period of Performance: 5 months
The Government shall provide 228 blood RNA samples stored in PaxGene Blood Collection tubes to the Contractor within 1 month of contract award. Once the samples have been received, the Contractor shall complete the blood RNA globin reduction and RNA sequencing and deliver the resulting libraries/results within 2 months of sample receipt. The following are necessary steps/requirements that the Contractor shall have to complete in order to provide the libraries:
i. The vendor shall perform globin/ribosomal reduction on blood RNA samples and assess the quantity and quality of the RNA to ensure that it is acceptable for sequencing.
ii. Preparation of libraries from the mRNA that can be run on the Next-Gen platform.
iii. 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.
iv. Alignment of the read data to the current reference human genome and transcriptome with transcript identifications assigned from the human Gene table as the definition for both gene and transcript level expression, modified so that transcript IDs are guaranteed to be unique.
v. Data shall be provided on a portable hard drive of sufficient capacity to hold all the data. Data analysis and output shall be provided in the following format: The
a. Raw data file for each sample.
b. A table of the flow cell statistics outlining the quality and yield of the flow cell(s) where samples were clustered and sequenced.
c. QC files regarding any presence of artifact/duplicate sequences, along with base distributions and qualities.
d. A tab-delimited text file with collapsed and normalized counts for each detected gene and isoform for each specimen.
e. An alignment file (BAM format) containing best alignments of each read to genome.
f. De-multiplexing of Illumina barcodes, if applicable
g. For blood RNA samples, it is required to provide at least 90% of the quoted reads after accounting for low quality sequences, ribosomal RNA and globin.
h. Provision of a tab-delimited file containing normalized counts of each gene.
Item #1
Assessing Gene (mRNA) Expression
Period of Performance - 365 days from the date of award
Quantity: 228
a.) Unit Price per Gene Expression: _____________________
Extended Price: _________________
b.) Unit Price per External Hard Drive up to 2 TB: _____________________
c.) Shipping and Handling: _____________________
GSA Contract Number (if applicable): ________________________
Item #2
Option Period #1
Assessing Gene (mRNA) Expression
*Please provide pricing for both quantity ranges as indicated below
Period of Performance - 365 days from Period of Performance end date of Line Item #1
*Range #1 - Quantity: 100-200
a.) Unit Price per Gene Expression: _____________________
b.) Unit Price per External Hard Drive up to 2 TB: _____________________
c.) Shipping and Handling: _____________________
* Range #2 - Quantity: 200-300
a.) Unit Price per Gene Expression: _____________________
b.) Unit Price per External Hard Drive up to 2 TB: _____________________
c.) Shipping and Handling: _____________________
GSA Contract Number (if applicable): ________________________
Item #3
Option Period #2
Assessing Gene (mRNA) Expression
*Please provide pricing for both quantity ranges as indicated below
Period of Performance - 365 days from Period of Performance end date of Line Item #2
*Range #1 - Quantity: 100-200
a.) Unit Price per Gene Expression: _____________________
b.) Unit Price per External Hard Drive up to 2 TB: _____________________
c.) Shipping and Handling: _____________________
* Range #2 - Quantity: 200-300
a.) Unit Price per Gene Expression: _____________________
b.) Unit Price per External Hard Drive up to 2 TB: _____________________
c.) Shipping and Handling: _____________________
GSA Contract Number (if applicable): ________________________
FOB Destination - U.S. Food and Drug Administration, National Center for Toxicological Research, 3900 NCTR Rd., Jefferson, AR 72079.
Contract Type - Commercial Item - Firm fixed price.
An official authorized to bind the Offeror must sign the terms and conditions of the offer. Offerors that fail to furnish required representations and certifications, or reject the terms and conditions of the solicitation, may be excluded from consideration.
Contract clauses-
The clause at FAR 52.212-4, Contract Terms and Conditions - Commercial Items, applies to this acquisition.
The following addenda have been attached to the clause:
FAR 52.232-40, Providing Accelerated Payment to Small Business Subcontractors (Deviation)
The supplies and/or services delivered hereunder shall be inspected and accepted at destination by the contracting officer / 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.
FAR Clause 52.204-4 Printed or Copied Double-Sided on Recycled Paper
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 following additional provisions and/or clauses apply and incorporated by reference and apply to this acquisition. Clauses and provisions can be obtained at http://www.acquisition.gov/far/
FAR Clause 52.204-4 Printed or Copied Double-Sided on Recycled Paper. (MAY 2011)
FAR Clause 52.204-7 Central Contractor Registration. (DEC 2012)
FAR Clause 52.217-9 Option to Extend the Term of the Contract (MAR 2000)
(a) ... within 1 day of contract expiration; .... at least 15 days before the contract expires...
(c) ...shall not exceed 3 years...
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
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.
The Contracting Officer for this order is:
To be completed at time of award:
Phone: (870) 543-XXXX
Email: xxxx
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 COR for this order is: to be completed at time of award.
Clauses and provisions incorporated by reference can be obtained at http://www.acquisition.gov/far
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: 52.203-6 Alt I, 52.203-17, 52.204-10, 52.209-6, 52.219-4, 52-219-8, 52.219-28, 52.222-3, 52.222-21, 52.222-26, 52.222-35, 52.222-36, 52-222-40, 52.222-54, 52.223-18, 52.225-13, and 52.232-33.
Solicitation provisions
The provision at FAR 52.212-1 Instructions to Offerors - Commercial Items applies to this solicitation.
Addendum Paragraph (c) Period for acceptance of offers. The offeror shall state on its quote that the quoted prices in its offer firm until September 30, 2014.
The provision at FAR 52.212-2 Evaluation-Commercial Items is applicable to this solicitation. The specific evaluation criteria to be included in paragraph (1) of that provision are as follows:
The government will award the purchase order to the responsible offeror whose offer conforming to the solicitation will be the most advantageous to the Government on a best value (tradeoff) evaluation basis, price and other factors considered. The following factors shall be used to evaluate offers:
(i) Technical Capability of the services offered to meet the Government's requirement.
(ii) Past Performance.
(iii) Price.
When combined, Technical Capability and past performance are more important when compared to price in determining the best value to the government; however, price remains a significant factor.
Technical Capability will be determined by review of the Contractor's proposed service and how likely it is to meet or exceed the requirements of the SOW. The technical requirements as indicated above are minimal requirements only, Contractors may offer additional services as part of their quote that exceed these requirements. The Contractor should note any additional services that are being offered in excess of the minimum requirement and shall provide a detailed explanation as to what the additional services are and how they will be of benefit to the Government.
Past Performance will be determined by review of recent and relevant service (completed by the Contractor within the last 3 years), where the Contractor demonstrates that it has performed the assessing of gene (mRNA) expression changes in rat blood using Next-Generation sequencing technology (Next-Gen). The Government reserves the right to look to other sources of information (e.g., the Past Performance Information Retrieval System (PPIRS), etc.) to support past performance evaluations.
The government is not responsible for locating or securing any information, which is not identified in the proposal. To ensure information is available, vendors 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 and other information corresponding to each minimum required item, which demonstrates the capabilities of the offeror.
The Provision at FAR 52.212-3, Offerors Representations and Certifications-Commercial Items, applies to this acquisition. An offeror shall complete only paragraph (b) of the provision if the offeror has completed the annual representations and certification electronically via https://www.sam.gov/portal/public/SAM/#1
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).