SOLICITATION NOTICE
B -- Services regarding the measurement of LINE-1 and Alu Sequences in Genomic DNA from Prostate Cancer Cases and Controls
- Notice Date
- 8/2/2010
- Notice Type
- Presolicitation
- NAICS
- 621511
— Medical Laboratories
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 6120 Executive Blvd., EPS Suite 600, Rockville, Maryland, 20852
- ZIP Code
- 20852
- Solicitation Number
- NCI-100142-AV
- Archive Date
- 9/1/2010
- Point of Contact
- Ashley L. Virts,
- E-Mail Address
-
virtsa@mail.nih.gov
(virtsa@mail.nih.gov)
- Small Business Set-Aside
- N/A
- Description
- The National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics (DCEG), Epidemiology and Biostatistics Program (EBP), Occupational Environmental & Epidemiology Branch (OEEB), plans to procure on a sole source basis with Epigendx, Inc.; 15 Harris Ln.; Ashland, MA 01721-3009 for services regarding the measurement of LINE-1 and Alu Sequences in Genomic DNA from Prostate Cancer Cases and Controls. This acquisition will be processed in accordance with simplified acquisition procedures as stated in FAR Part 13.106-1 (b) (1). The North American Industry Classification System Code is 621511 and the business size standard is $13.5M. Only one award will be made as a result of this solicitation. This will be awarded as a firm fixed price type contract. The period of performance for this procurement shall be for twelve months from date of award. The NCI Division of Cancer Epidemiology and Genetics is currently investigating the relationship between prostate cancer risk and global DNA methylation as measured by LINE-1 and Alu sequences. There is a growing body of evidence suggesting that global hypomethylation may be a potential biomarker for cancer risk. Current work utilizes genomic DNA isolated from blood, buccal cells, or urine to quantify methylation changes Contractor shall examine the association between global methylation from pre-diagnostic genomic DNA and prostate cancer risk. The Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial offers a unique opportunity to explore genome-wide hypomethylation as an independent risk factor for cancer development in a well defined US population with high quality information on covariates necessary to identify potential confounding variables and risk modifiers. Furthermore, the opportunity to evaluate these biomarkers in pre-diagnostic blood samples from cases and healthy controls will reduce biases that cannot be eliminated from case-control studies. NCI shall deliver 1,464 (including 50 quality control) genomic DNA samples frozen at -20°C extracted from whole blood and buffy coat to the Contractor. The contractor shall complete the following tasks upon receipt of the samples: 1. Bisulfite conversion shall be performed on 500ng genomic DNA from all 1,464 samples using a Zymogen Research EZ® kit. Bisulfite treated DNA shall be PCR amplified within the Line-1 and Alu repetitive regions. Sequencing of these repeats shall be performed using Pyrosequencing technology and the global methylation levels analyzed. The percent methylation shall be determined by comparing test DNA to a human methylation control DNA provided by the Contractor. The percent of methylation shall be expressed for each DNA locus as percent 5-methyl cytosine (5MeC) divided by the sum of methylated and unmethylated cytosines. Each sample shall be run in triplicate. Quality control samples shall comprise approximately 4-5% of each plate analyzed. 2. All chromatograms and sequencing traces used to determine methylation levels shall be included as electronic files with all reports. 3. Results shall be provided to the NCI Contracting Officer's Technical Representative (COTR) in MS-Excel with all identifiers removed previously Currently, there are several methods available to measure global DNA methylation status: 1) pyrosequencing; 2) luminometric cytosine extension assay; 3) realtime MSP assay; 4) bisulfite subcloning sequencing; 5) high-performance liquid chromatography (HPLC); 6) methylation antibody-based ELISA. Both the luminometric cytosine extension assay and HPLC assays require a large amount of DNA, making them unsuitable for prospective epidemiologic studies, such as PLCO, where samples are extremely valuable. HPLC and bisulfite subcloning sequencing are labor-intensive and not amenable to high-throughput, making them impractical for large epidemiologic studies, such as this study. The luminometric cytosine extension assay and ELISA assay have poor reproducibility, making them unsuitable for an epidemiologic study. The realtime MSP assay ignores partially methylated alleles and is not quantitative, making it inferior to other platforms that are quantitative. Although pyrosequencing is not allele-specific, it is quantitative, has high reproducibility, and is high-throughput, making it the only choice for the valuable PLCO samples. The use of pyrosequencing to measure global DNA methylation has been extensively validated at with the proposed Contractor, Epigendx. Previous research performed by the Contractor measured LINE-1 and Alu sequences for additional samples in the PLCO trial. For scientific comparibility, the samples must be measured in the same manner. Based on this knowledge, Epigendx is the only Contractor known to the NCI who can complete the scope of work. This is not a solicitation for competitive quotations. However, if any interested party believes they can meet the above requirement, they may submit a statement of capabilities. All information furnished must be in writing and must contain sufficient detail to allow the NCI to determine if it can meet the above unique specifications described herein. An original and one copy of the capability statement must be received in the NCI contracting office on or before 11:00 AM EST on August 17, 2010. No electronic capability statements will be accepted (i.e. email or fax), an original and one copy must be sent to the NCI contracting office to the address stated above. All questions must be in writing and can be faxed (301) 402-4513 or emailed to Ashley Virts, Contract Specialist at (301) 435-3817. A determination by the Government not to compete this proposed contract based upon responses to this notice is solely within the discretion of the Government. Information received will be considered solely for the purpose of determining whether to conduct a competitive procurement. In order to receive an award, contractors must have valid registration and certification in the Central Contractor Registration (CCR) www.ccr.gov and the Online Representations and Certifications Applications (ORCA), http://orca.bpn.gov. No collect calls will be accepted. Please reference solicitation number NCI-¬-100142-AV on all correspondences.
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