SOLICITATION NOTICE
B -- Global methylation in bladder tumor and genomic DNA samples
- Notice Date
- 8/19/2008
- Notice Type
- Presolicitation
- NAICS
- 541690
— Other Scientific and Technical Consulting Services
- 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-80195-MM
- Archive Date
- 9/13/2008
- Point of Contact
- Ashley L. Virts, , Malinda L Holdcraft,, Phone: (301) 402-4509
- E-Mail Address
-
virtsa@mail.nih.gov, holdcram@exchange.nih.gov
- Small Business Set-Aside
- N/A
- Description
- The National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics (DCEG), Occupational and Environmental Epidemiology Branch (OEEB), plans to procure on a sole source basis, global methylation in 85 bladder tumor and genomic DNA samples with Transgenomic Discovery; April Hall Transgenomic Inc.; 12325 Emmet Street; Omaha, NE 68164. The services herein are being procured in accordance with the simplified acquisition procedures authorized by FAR Part 13.106-1 (b) (1). The North American Industry Classification System Code is 541690 the business size standard is 6.5M employees. The period of performance for this procurement shall be twelve months from date of award. This procurement is for the analysis of the global methylation of specifically selected CpG sites from 85 DNA samples (2 biological sources of DNA; 200,000 cases with genomic DNA from blood, 35 cases' with tumor tissue extracted from FFPE bladder tumor tissue. After identification of altered CpG site methylation, results will be verified using high-throughput technologies to confirm the alterations identified using surveyor profiling and sequencing methodologies that are only available at Transgenomic Inc. The most common test for H. pylori infection used in epidemiologic studies is the ELISA method measuring antibody titers to whole cell and cagA strains in serum or plasma. Recently, an immunoblot method has been developed which is more sensitive in detecting cagA strains. The ELISA assay is also used for measuring levels of pepsinogen I and II in serum or plasma. Growing evidence supporting the findings that global hypomethylation may be a potential biomarker for bladder cancer risk. Current work utilizes genomic DNA isolated from blood, buccal cells, or urine to quantitate methylation changes. Although the existing literature suggests an inverse association between global methylation and increased risk for cancer (including lung, colon, and bladder), it has yet to be demonstrated in a population based study that genomic DNA isolated from any ofthese biological specimens represents methylation changes occurring in tumor tissue and phenotypically, among non-target tissue extracted from different types oftissues/cells. NCI currently wants to address this question in the New England Bladder Cancer Study, which has matched genomic' and tumor DNA extracted for 50 participants (35 cases with matching tumor DNA available for analysis). The contractor shall perform the following tasks. 1.Conduct global methylation analysis using CpG chip microarrays designed to analyze over 200,000 CpG sites within the genome using DNA samples from bladder cancer case tumor and blood cell DNA among enrolled in the NESEH case-control study. 2.Confirm positive findings using surveyor endonuclease and sequencing methodologies. 3.Custom design a human CpG island micro array chip containing 244k 60 mer oligo probes. Each micro array shall contain approximately 200k CpG probes and 50 non-CpG probes. The probes shall be selected based on the enriched content sources from UCSChg18 and NCBI build 36. I database. DNA shall be labeled, hybridized, according to standard methodologies 4.Methylation of individual CpG sites shall be examined by double stranded sequencing of PCR products from bisulfate-treated DNA. Transgenomic is currently the only company that provides a specific method of high-throughput, and sensitive sequencing services that employ Surveyor endonuclease, an optimized derivative of Cel I endonuclease and the patented WAVE® system to separate fragments based upon size. This procurement proposes to use the same methodologies in addition to newer microarray chip based technology to identify epigenetic alterations associated with risk factors and disease progression. It is critical for comparability to ongoing studies that Transgenomic completes the analysis. There is currently no other known source to the NCI that is able to complete the work outlined in this procurement. This is not a request for competitive quotation. However, if any interested party believes it can meet the above requirement, it may submit a statement of capabilities. The statement of capabilities and any other information furnished must be in writing and must contain material in sufficient detail to allow the researcher to determine if the party can meet this requirement. One (1) original and one (1) copy of the capability statement must be received in the contracting office by 1:00 p.m. ET on August 29, 2008. All questions must be in writing and can be faxed to 301-402-4513 or sent via email to Melissa Marino: marinome@mail.nih.gov. It is the vendor’s responsibility to ensure questions have been received. A determination by the Government not to compete this proposed requirement 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. No collect calls will be accepted. In order to receive an award, contractor must have valid, updated registration and certification in the Central Contractor Registration (CCR) and the Online Representations and Certifications Application (ORCA). Please reference NCI-80195-¬MM on all correspondence.
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- Record
- SN01644499-W 20080821/080819223033-f65025b8212136e233f02a18cf3a602e (fbodaily.com)
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