Sample analysis for gene expression by nanostring (190 genes, including RNA/DNA extraction from FFPE tissue sections)

Contracting Office Address Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 6120 Executive Boulevard, EPS Suite 600, Room 6074, Rockville, MD 20852, UNITED STATES. Description The National Cancer Institute (NCI), Division of Cancer Epidemiology & Genetics (DCEG), Genetic Epidemiology Branch (GEB) plans to procure on a sole source basis samples for gene expression by nanostring (190 genes, including RNA/DNA extraction from FFPE tissue sections) from University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599. This acquisition will be processed in accordance with simplified acquisition procedures in FAR Part 13.106 (b)(1). The North American Industry Classification System code is 541380 and the business size standard is $12.0 million. Only one award will be made as a result of this solicitation. This will be awarded as a firm fixed price type contract. Period of Performance: Twelve months from Date of award It has been determined there are no opportunities to acquire green products or services for this procurement. The Genetic Epidemiology Branch (GEB) of the National Cancer Institute (NCI) designs and conducts interdisciplinary clinical, epidemiologic, genetic, and laboratory studies of persons, families, and populations at high risk of cancer. These investigations identify genes and exposures conferring cancer predisposition, and explore the combined effects of predisposition and specific exposures. As part of this effort, the Branch maintains a familial cancer registry and biospecimen repositories Asian women seem to have a distinctive profile of breast cancer that differs from that seen in Western populations, such as earlier age at onset, more advanced stage, and higher frequency of ER-negative tumors. The disproportionally high rates among younger women were also seen among US-born Asian women, such as Chinese, Filipina, Indian, and Pakistani women. These findings suggest that Asian breast cancer may have a distinct etiology that is not fully explained by adapting westernized lifestyle. Large, population-based epidemiologic studies of characterizing molecular subtypes of breast cancer in Asian women are limited. Recently, Devi et al. compared the distribution of breast cancer subtypes in the three ethnic groups (Chinese, Natives, and Malays) in Sarawak, Malaysia and found that the distribution of breast cancer subtypes varied by ethnicity. To expand this study, the NCI plans to conduct an integrated tumor profiling analyses to achieve a refined tumor stratification in breast cancer cases identified from Sarawak, Malaysia. In addition to tumors, the NCI is also planning to profile molecular changes in adjacent normal terminal duct lobular units (TDLUs). Previous studies have shown that paired adjacent normal tissues share similar molecular alterations with their associated cancers. Evaluating changes in normal tissues is helpful in identifying etiologic associations since they are less contaminated by events related to tumor progression. The objective of this study is to extract RNA and DNA from tissue cores containing TDLUs identified from Malaysian breast cancer cases and to conduct gene expression and methylation profiling analysis. The NCI will identify TDLUs from 100 breast cancer cases with tumor profiling data. The contractor will extract RNA and DNA from the tissue cores of those 100 breast cases and conduct gene expression profiling using a nanostring panel established by the contractor. The laboratory at University of North Carolina (UNC) is uniquely qualified to perform this work for the following reasons: 1)UNC was among the first institutions to identify molecular subtypes of breast cancer and has been leading the field of classifying breast tumors using integrated profiling analyses. They have designed a comprehensive gene panel that include not only the key classifiers as established previously (PAM50) but also new genes such as wound healing and claudin low genes that were recently suggested to improve tumor classification according to clinical responses; 2)Nanostring is a newly developed technology that is based on direct multiplexed measurement of gene expression that is capable of high level precision and sensitivity, which allows for accurate and sensitive measurement of RNA expression in formalin-fixed paraffin-embedded (FFPE) tissues that has been proved difficult using conventional profiling approaches because of RNA degradation. UNC are routinely using this new technology for gene expression profiling using FFPE RNA, while the assay is still at the developmental stage in most other places; 3)UNC has extensive experiences in conducting bioinformatic analyses of profiling data, which is a critical factor for the success of this project; 4)UNC will extract RNA and DNA to ensure sufficient quality of input materials for subsequent profiling analyses; and 5)UNC is currently doing tumor profiling in tumor RNA/DNA from the same set of Malaysian breast cancer cases. Using same profiling platforms and experimental conditions will allow us to directly compare results obtained from the two different tissue sources. In summary, UNC possesses unique expertise and resources for RNA expression profiling analyses in TDLUs, which is critical for the success in the subsequent tumor and normal comparisons and etiologic associations. 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 at the NCI Office of Acquisitions on or before 11:00 AM EST on August 23, 2011. No electronic capability statements will be accepted (i.e. email or fax), an original and one copy must be sent to the NCI Office of Acquisitions to the address stated above. All questions must be in writing and can be faxed +1 (555) 000-0000 or emailed to Terry Galloway, Contract Specialist at contact@example.gov. 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 procurementIn order to receive an award, contractors must have valid registration and certification in the Central Contractor Registration (CCR) and the Online Representations and Certifications Applications (ORCA), through the SAM.Gov website. No collect calls will be accepted. Please reference solicitation number NCI-120136-TG on all correspondences.