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FBO DAILY - FEDBIZOPPS ISSUE OF AUGUST 08, 2013 FBO #4275
SOLICITATION NOTICE

B -- Sequencing RNA

Notice Date

8/6/2013
 

Notice Type

Combined Synopsis/Solicitation
 

NAICS

541380 — Testing Laboratories
 

Contracting Office

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

ZIP Code

20857-0001
 

Solicitation Number

FDA_13-233-RFQ-1122314
 

Archive Date

8/29/2013
 

Point of Contact

Howard Nesmith, Phone: 870-543-7459
 

E-Mail Address

howard.nesmith@fda.hhs.gov
(howard.nesmith@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 herein under Simplified Acquisition Procedures. The solicitation number is FDA_13-233-RFQ-1122314. This solicitation is issued as a Request for Quote (RFQ). The solicitation document and incorporated FAR clauses and provisions are those in effect through Federal Acquisition Circular (FAC) 2005-69, August 1, 2013. The associated North American Industry Classification System (NAICS) Code is- 541380 - Testing Laboratories; Size standards $12 million. This requirement is not being set aside for small businesses and any qualified, interested vendor 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 (Local Prevailing Time) in Jefferson, Arkansas on August 14, 2013 to howard.nesmith@fda.hhs.gov, 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 howard.nesmith@fda.hhs.gov. The U.S. Food and Drug Administration (FDA), National Center for Toxicological Research (NCTR), is soliciting quotes for Sequencing RNA. Requirements The FDA/NCTR requires an agreement for further purifying rat blood total RNA to enable the sequencing and quantization of all RNA species present within rat blood under control conditions, after environmentally-induced hyperthermia and after exposure to neurotoxic doses of amphetamine. The sequencing shall be performed by next generation methods rather than micro Arrays. RNA-seq overcomes these weaknesses because it is not based on hybridization and luminescence, but is based on a digital counting method which produces "counts" per gene/transcript/exon in the sample. Theoretically, sensitivity and specificity are only limited by sequencing depth. The data generated from the blood RNA sequencing is aimed at novel identifying biomarker combinations that are specific for amphetamine neurotoxicity. This shall be accomplished through analyzing the sequencing data obtained. A total of 64 total RNA blood samples from 64 different test subjects (rats) will be processed. Data Deliverables I. FASTQ files for each specimen (*fastq.gz or *clipped.fastq.gz). If PE read, then *[1|2].fastq.gz. These files contain all sequences passing Illumina's purity filter (PF reads) and are accompanied by a per-base quality score, as defined by Illumina-scaled Phred metric. Unless otherwise specified, this data will be compressed (gz) and uploaded to EA's secure web server. II. A table of the flow cell statistics outlining the quality and yield of the flow cell(s) where specimens were clustered and sequenced. III. QC files containing read length and depth results (before and after clipping), presence of artifact/duplicate sequences, distributions of base quality and base frequency by sample. Also, separate files by flow cell show total yield, PF reads, barcode quality, alignment summaries and # of genes detected. Illumina Sequencing Application Based Deliverables I. mRNA-Seq (BI300): a. A tab-delimited text file with collapsed and normalized counts for each detected gene and isoform (UCSC Known Gene) for each specimen. Alternative transcript reference sequence databases may be specified as appropriate, but if NCBI RefSeq is not available for the organism, please contact your service consultant for custom analysis proposal. b. An alignment file (BAM format) containing best alignments of each read to in genomic coordinates. c..CEL file generation based on transcriptome quantitation compatible with the Human HG-U133_Plus_2 array, the Rat230_2 array, or the Mouse430_2 array. d. FASTQ QC summary files containing summaries of effective read lengths(statistics for clipped reads), read depth, duplicate read percentages, base call distributions). e. Analysis summary files containing summaries of alignment statistics, mapping quality, base distributions, most frequent gene detected, total # of genes detected, etc. by sample. f. Sequencing process QC info (lane, barcode, flowcell statistics for raw clusters, PF reads, barcode assignment, etc.). Data and Specimen Storage and Maintenance The contractor shall maintain the raw data (intensity data) for all projects until each flow cell passes sequencing QC. Following the successful passing of FASTQ files, processed raw sequencing data (*bcl and associated files), will be deleted. Maintain excess specimens and targets generated for the FDA in an appropriate storage facility for a period of sixty (60) days from the date of data transfer. After this period, the contractor shall destroy excess specimens and targets unless otherwise requested in writing. Schedule of Items Item #1 Sample Analysis for the Sequencing and Quantization of RNA Species Quantity: 64 Total Project Price: _____________________ GSA Contract Number (if applicable): __________________ FOB Destination - U.S. Food and Drug Administration, National Center for Toxicological Research, 3900 NCTR Rd., Jefferson, Arkansas 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- Clauses incorporated by reference may be found at http://www.acquisition.gov/far/, http://www.hhs.gov/regulations/hhsar, or http://www.hhs.gov/asfr/ogapa/acquisition/policies/files/caac-consultation-accelerated-payment-gsa.pdf. The clause at FAR 52.212-4, Contract Terms and Conditions - Commercial Items, applies to this acquisition. The following addenda apply: FAR 52.232-99, Providing Accelerated Payment to Small Business Subcontractors (Deviation) (AUG 2012) 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. FAR Clause 52.204-4 Printed or Copied Double-Sided on Recycled Paper. The following HHSAR Clauses apply: 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) 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 identified 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 COR for this order is:to be identified at time of award. The clause at FAR 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders - Commercial Items (Jan 2013), applies to this acquisition. 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: 52.204-10, 52.209-6, 552.219-4, 2.219-28, 52.222-3, 52.222-21, 52.222-26, 52.222-36, 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, 2013. 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 in descending order: (i) Technical acceptability of the services offered to meet the Government's requirement. (ii) Price. Technical acceptability is more important when compared to price in determining the best value to the government; however, price remains a significant factor. Technical acceptability will be determined by review of the technical approach proposed to meet the technical requirements. 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 http://www.acquisition.gov/far/. An offeror should complete only paragraph (b) of this provision if the offeror has completed the annual representations and certifications electronically at https://www.sam.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).
 

Web Link

FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/FDA/DCASC/FDA_13-233-RFQ-1122314/listing.html)
 

Place of Performance

Address: U.S. Food and Drug Administration, National Center for Toxicological Research, 3900 NCTR Rd., Jefferson, Arkansas, 72079, United States

Zip Code: 72079
 

Record

SN03138280-W 20130808/130806235256-d8bbae37bbe3bc8df84174f0fa93277d (fbodaily.com)
 

Source

FedBizOpps Link to This Notice
(may not be valid after Archive Date)

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