SOURCES SOUGHT
B -- Assessment of mRNA gene expression using Next-Generation sequencing technology
- Notice Date
- 4/30/2012
- Notice Type
- Sources Sought
- NAICS
- 541380
— Testing Laboratories
- Contracting Office
- Department of Health and Human Services, Food and Drug Administration, Office of Acquisitions and Grants Services, Bldg 50 Room 422, Jefferson, Arkansas, 72079, United States
- ZIP Code
- 72079
- Solicitation Number
- FDA-1102348
- Archive Date
- 5/23/2012
- Point of Contact
- Nicholas E Sartain, Phone: 870-543-7370
- E-Mail Address
-
nick.sartain@fda.hhs.gov
(nick.sartain@fda.hhs.gov)
- Small Business Set-Aside
- N/A
- Description
- MARKET RESEARCH PURPOSES ONLY NOT A REQUEST FOR PROPOSAL OR SOLICITATION The U.S. Food and Drug Administration (FDA), is conducting market research to support the National Center for Toxicological Research (NCTR) requirement for assessing mRNA gene expression in rat liver. The FDA is seeking business sources, including total small businesses, service-disabled veteran-owned small businesses, HUBZone small businesses, 8(a) certified companies and other than small businesses. The following information is provided to assist the FDA in conducting Market Research to identify potential contractors for this effort: The government is seeking capability statements from businesses capable of performing 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 is required is the Illumina sequencing technology for continuity of results between projects. An estimated total of 324 samples will be analyzed to compare the effect of the different hepatotoxicants on the hepatic expression of the genes. Ultimately, the gene expression changes will be used as biomarkers of drug-induced liver injury. The government will provide total RNA to the contractor. 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. a) 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. d. 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). The offeror shall furnish sufficient technical information necessary for the Government to conclusively determine that the offered instrument and components meet the technical requirements identified above. Firms believing they can meet the requirements to the above specifications are encouraged to respond electronically with no less than the following information: • Business name, DUNS number, business address, business website, business size status (i.e., SB, VOSB, SDVOSB, HUBZone SB, SDB, WOSB, LB), point of contact name, mailing address (if different from business address), phone number and email address; • Sufficient descriptive literature that unequivocally demonstrates that offered products and services meet or exceed above specifications. • At a minimum provide the following: All descriptive material necessary for the government to determine whether the service/product offered meets the technical requirements including: technical specifications, descriptive material, literature, brochures and other information, which demonstrates the capabilities of the contractor to meet the requirement. Include the amount of total RNA required for each sample. • The offeror includes documentation of technical competency of the sequencing • Provide a list of prior similar experience in Next-Gen sequencing work and contact information on 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 services with dollar amount. • If applicable, identification of the firm's GSA Schedule contract(s) by Schedule number and SINs that are applicable to this potential requirement are also requested. • Provide information if any of these specifications are too restrictive. No response will be considered that the listed specifications are adequate in a competitive environment. • If a large business, provide if subcontracting opportunities exist for small business concerns. • Though this is not a request for quote, informational pricing must be submitted. The government is not responsible for locating or securing any information, not identified in the response. The associated North American Industry Classification System (NAICS) Code is- 541380- Testing laboratories; Small Business Size Standard is $12 million. Interested Contractors must respond with capability statements which are due in person, by postal mail or email to the point of contact listed below on or before May 8, 2012 by 13:00 hours (Central Time in Jefferson, Arkansas) at the Food and Drug Administration, OC/OA/OAGS, Attn: Nick Sartain, 3900 NCTR Road, HFT-320, Jefferson, AR 72079-9502 or email nick.sartain@fda.hhs.gov. Reference FDA1102348. Notice of Intent Responses to this sources sought announcement will assist the Government in determining whether or not any future requirement similar to this one should be set aside for small business, made available to full and open competition or procure through sole-source acquisition procedures. Disclaimer and Important Notes This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization's qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published in FedBizOpps. However, responses to this notice will not be considered adequate responses to a solicitation. Confidentiality No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/FDA/NCTR/FDA-1102348/listing.html)
- Place of Performance
- Address: 3900 NCTR Road, Jefferson, Arkansas, 72079, United States
- Zip Code: 72079
- Zip Code: 72079
- Record
- SN02735195-W 20120502/120501000135-e00a98a1854e5e9f006d138c05081b28 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
(may not be valid after Archive Date)
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