SOLICITATION NOTICE
B -- Mutational Spectrum Analysis of the Von Hippel Lindau Gene in Kidney Tumors from Case Enrolled in the Eastern European Renal Cell Cancer Study
- Notice Date
- 8/28/2007
- Notice Type
- Solicitation Notice
- NAICS
- 541380
— Testing 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, MD, 20852, UNITED STATES
- ZIP Code
- 00000
- Solicitation Number
- Reference-Number-NCI-70156-NV
- Response Due
- 9/11/2007
- Archive Date
- 9/26/2007
- Description
- In accordance with Simplified Acquisition procedures, the National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics (DCEG), Occupational Epidemiologic Branch (OEB), plans to procure, on a sole source basis, for the analysis of the mutational spectrum of exons 1-3 of the VHL gene for 200 DNA samples extracted from paraffin embedded formalin fixed (FFPE) slides. For 30% of these samples, (N=60), promoter hypermethylation analysis of the VHL gene will also be conducted from Transgenomic, Inc., 12325 Emmet Street, Omaha, NE 68164. The North American Industry Classification System Code is 541380 and the business size standard is $11M. The incidence rates of kidney cancer vary substantially across Central and Eastern Europe, from a low of 9.0 per 100,000 men in Bucharest to a high of 17.0 per 100,000 men in the Czech Republic in the early 1990s. The diverse incidence rates may in part be due to a wide range of environmental exposures, but the specific reasons are unclear. The variation in exposure levels to occupational carcinogens in this part of the world present a unique opportunity to assess occupational risks for cancer. In 2000, investigators at NCI in collaboration with the International Agency for Research on Cancer (IARC) launched a case-control study of kidney cancer in six centers in Central and Eastern European countries (I.E., Bucharest, Romania; Brno, Olomouc, and Prague, Czech Republic; Lodz, Poland; and Moscow, Russia) to evaluate cancer risks in relation to ifestyle factors, and history of exposures to known or suspected occupational and environmental, carcinogens. Collection of questionnaire data from the Eastern European Renal Cell Case-Control study was completed in 2002. NCI has collected formalin fixed-paraffin embedded and frozen tumor material from approximately 80% of cases. Specific objectives of this project are: 1) Conduct VHL mutational spectrum analysis using tumor DNA samples collected from FFPE tissue from RCC cases enrolled in the Central and Eastern European RCC case-control study and 2) Conduct promoter hypermethylation analysis using the bilsulfilte treated DNA and sequence analysis. The contractor shall: 1) isolated and quantitative PCR measurements analyzed using three 5-micron tissue sections on slides that were cut from formalin fixed paraffin embedded tissue blocks that have been microdissected and placed in 1.5ml tubes; 2) Mutation screening of exons 1-3 of the VHL gene shall be screened using Surveyor nuclease. Digests by capillary electrophoresis, double stranded sequencing, and sequence analysis shall be conducted and analyzed by the contractor; 3) For mutant samples, the specific exon, codon, and type of mutation (amino acid change, deletion, and insertion) shall be reported to the PO in an electronic format using MS Excel. The reports shall be provided three months after receipt of samples; 4) For samples that do not exhibit VHL mutations in exon 1-3, promoter hypermethylation analysis shall be conducted. Promoter hypermethylation analysis shall also be conducted on approximately 10% of samples (randomly selected by the project officer) that had VHL mutations; 5) For samples that will have promoter hypermetylation analyzed, DNA shall be bisulfite treated and genomic sequencing conducted; 6) A summary report shall be provided for the VHL methylation analysis that will describe the methylation status of ten CpG sites within the VHL promoter. Results from all samples shall be provided. Failed samples including the reason for failure, those without mutation and putative variants shall be indicated for all samples received. Reports shall be confidentially provided to the Project Officer at 3 month intervals. All chromatograms and sequencing traces shall be included as electronic files with all reports; and 7) If samples fail to sequence, re-amplification at no additional charge to the government shall be completed at least two times if sufficient DNA is available or can be provided by the PO. Transgenomic successfully completed and was awarded procurement MQ515240 to conduct VHL mutational spectrum analysis and a pilot study of VHL promoter hypermethylation for the Central and Eastern European RCC study using frozen and FFPE tumor tissue DNA . Because of the success of this study and because their analysis methods are high-throughput and more recently have proven successful on formalin fixed paraffin embedded tissue DNA, we can successfully expand the previous study to include an additional 200 cases that provided FFPE tumor blocks only. For comparability of these results to those of the previous study it is essential that Transgenomic Inc. to conduct the analysis of these samples as to avoid the introduction of new variables into on going research. This is not a request for competitive quotation. However, if any interested party believes it can perform the above requirement, it may submit a statement of capabilities. The statement of capabilities and any other furnished information must be in writing and must contain material in sufficient detail to allow NCI Researcher to determine if the party can perform this requirement. Capability statements must be received in the contracting office by 1:00 PM EDT September 11, 2007. Faxed and emailed capability statements are NOT authorized. Questions must be submitted in writing to Deborah Moore, Contract Specialist, at dm170b@nih.gov or faxed to 301-402-4513. 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, contractors must be registered and have valid certification in the Central Contractor Registration (CCR) and the Online Representations and Certifications Application (ORCA).
- Record
- SN01387262-W 20070830/070828220425 (fbodaily.com)
- Source
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