SOURCES SOUGHT
B -- Genome Sequencing Services using an Illumina HiSeq2500
- Notice Date
- 1/30/2014
- 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, 3900 NCTR Road, HFT-320, Bldg 50 | Rm 421, Jefferson, Arkansas, 72079, United States
- ZIP Code
- 72079
- Solicitation Number
- 1128309
- Archive Date
- 2/25/2014
- Point of Contact
- Crystal G. McCoskey, Phone: 8705437267
- E-Mail Address
-
crystal.mccoskey@fda.hhs.gov
(crystal.mccoskey@fda.hhs.gov)
- Small Business Set-Aside
- N/A
- Description
- MARKET RESEARCH PURPOSES ONLY NOT A REQUEST FOR PROPOSAL OR SOLICITATION This is a sources sought to determine the availability and capability of small businesses to provide genome sequencing services using an Illumina HiSeq2500 platform. The associated North American Industry Classification System (NAICS) Code is‐ 541380, Testing Laboratories; Small Business Size Standard is $14.0 million. Part I: General Information (Introduction/Background/Scope) The U.S. Food and Drug Administration (FDA), is conducting market research for the National Center for Toxicological Research (NCTR) requirement for genome sequencing services. The NCTR is conducting a study titled, "The Sequencing Quality Control Project, MicroArray Quality Control (MAQC) Phase III, - Sequencing-based Technologies for Safety Evaluation of FDA-regulated Products". The study requires human whole-genome DeoxyriboNucleic Acid (DNA) sequencing services on an estimated 10-20 human DNA samples, using an Illumina HiSeq2500 platform, to accurately evaluate the performance and utility of the next-generation sequencing platform in detecting human genetic variation including Single Nucleotide Variants (SNVs), short Insertions and Deletions (Indels), Copy Number Variations (CNVs), and large Structure Variations (SVs). The resulting variants call data will be used to evaluate the sensitivity, specificity and robustness of each Next-Generation Sequencing (NGS) platform compared to those detected with microarray-based genotyping approaches from the MAQC-Phase II project which evaluated Roche 454, ABI SOLID 5500,and Affymetrix platforms. This phase of this long running project is specific to evaluation of the Illumina HiSeq 2500 platform to identify human genome variation sensitivity and specificity. Part II: Work Requirements The FDA will provide the initial samples (estimated between 10-20; to be determined at award based on price with a total award amount not to exceed budgeted amount of $150,000) to the Contractor within 180 calendar days of order date by NCTR researchers. The Contractor shall assess the quality of each DNA sample using fluorometric-based methods including Qubit or PicoGreen to provide accurate quantification for double-stranded DNA. The ratio of absorbance at 260 nanometer (nm) to absorbance at 280 nm shall be used as an indication of sample purity; the acceptable ratio of absorbance shall be in a range from 1.8 to 2.0.The quality verification results shall be sent electronically to the Project Officer (PO) for review upon conclusion of the initial quality screening. Any samples that fail the quality assessment shall be returned for replacement. Any necessary replacement samples will be provided within 7 calendar days of the receipt of the quality verification results. The contractor shall provide library preparation services using the Illumina "TruSeq DNA Polymerase Chain Reaction (PCR)-free Sample Preparation Kits" from 2 microgram (µg) input genomic DNA. The insert size shall be approximately 550 bases. The sequencing image data obtained from the HiSeq2500 shall be transformed to fastq data files and aligned against the Human Genome reference HG19 (from the University of California, Santa Cruz) which can be found at: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/. The aligned files shall be in Binary Alignment/Map (BAM) format. The genome coverage, or sequence depth, for each sample shall be no less than 50 times (x). The genetic variants shall be analyzed using the standard parameters contained in Illumina's default software. The variants shall be recorded in Variant Call Format (VCF). The Contractor shall provide one (1) hard and one (1) electronic copy of all sequence data (including fastq files, BAM files, and VCF files) to the PO within 120 calendar days of receipt of all required samples meeting the quality standards listed above. The contractor shall return, via method (i.e. expedited, protective packaging, temperature control) that maintains the integrity of the sample during shipment, all samples, including those returned unprocessed as a result of quality verification failure, to NCTR upon completion of the analysis. Part III: Supporting Information A. Return Address for Samples: U.S. FDA National Center for Toxicological Research Attention: Terri Toenessen 3900 NCTR Rd., Building 15, Room 103A Jefferson, AR 72079 B. Period of Performance Final sequencing data shall be provided within 120 days of receipt of full order quantity of viable samples, which will occur within 180 days from date of order. Ultimate completion is expected within 315 days of date of order. Part III: Instructions to Prospective Respondents Responses to this sources sought shall unequivocally demonstrate that respondent has the required equipment and personnel to perform the services. Though the target audience is small businesses capable of performing the sequencing, any interested party may respond. At a minimum, responses shall include the following: • Business name and bio, DUNS number, business address, business website, business size status (i.e., SB, VOSB, SDVOSB, HUBZone SB, 8(a), SDB, WOSB, EDWOSB, LB), point of contact name, mailing address (if different from business address), phone number and email address; • Information on the Illumina instrument to be used for the sequencing, to include but not be limited to, year manufactured, model, capabilities, and service/testing/inspection records or other verification the instrument has been properly maintained to ensure proper operating condition; • Three (3) years of past performance information for the service of same or substantially similar items, to include date of services, description (should also include technical literature and specifications), dollar value, client name, client address, client point of contact name, client point of contact mailing address (if different from that provided for client), client point of contact phone number, and client point of contact email address; • Descriptive literature, brochures, specifications, marketing material, etc. detailing the nature of the services the responding firm is regularly engaged in providing; • If applicable, identification of the firm's GSA Schedule contract(s) by Schedule number and SINs that are applicable to this requirement; • If a large business, identify the subcontracting opportunities that would exist for small business concerns; • Although this is not a request for quote, informational pricing is encouraged; • The Government encourages any comments and/or suggestions from any interested party, regarding the specifications. While the Government will not respond directly to your comments and/or suggestions; we will consider them as we finalize the specifications in preparation for the forthcoming solicitation. The Government is not responsible for locating or securing any information, not identified in the response. Interested Parties 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 February 10, 2014 by 1:00 PM (Central Time in Jefferson, Arkansas) at the Food and Drug Administration, OC/OA/OAGS, Attn: Crystal G. McCoskey, 3900 NCTR Road, Bldg 50/Room 426, HFT‐320, Jefferson, AR 72079‐9502 or email crystal.mccoskey@fda.hhs.gov. Reference #1128309 in all correspondence with the point of contact listed above. Notice of Intent Responses to this sources sought announcement will assist the Government in determining whether this requirement should be set aside for small business, made available to full and open competition or procured through other than full and open 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 combined synopsis/solicitation (No. 1128309) may be published via 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).
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