Identifying radiation induced RNA markers in heart, lung and liver tissue samples from a whole body irradiated mini-pig model and compare with RNA markers form whole blood samples.

Contracting Office Address Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 9609 Medical Center Drive, Room 1E126, Bethesda, MD 20892, UNITED STATES. Description The Department of Health and Human Services (DHHS), National Institute of Health (NIH), National Cancer Institute (NCI), Center for Cancer Research (CCR), Radiation Oncology Branch (ROB) plans to procure on a sole source basis services to investigate radiation induced gene expression changes in heart, lungs and liver samples of mini pig model after exposed to whole body irradiation from GenUs BioSystems at 1808 Janke Drive, Unit M, Northbrook, IL 60062. This acquisition will be processed in accordance with simplified acquisition procedures as stated in FAR Part 13.106-1(b)(1) and is exempt from the requirements of FAR Part 6. The North American Industry Classification System code is 541380 and the business size standard is $15.0 Million. Only one award will be made as a result of this solicitation. This will be awarded as a firm fixed price type contract. The Radiation Oncology Branch (ROB) exists to plan and conduct pre-clinical and clinical research on the biologic and therapeutic effects of radiation administrated alone or in combination with other modalities of treatment; to develop novel technology and imaging based approaches for radiation oncology; to investigate the natural history of disease to understand and evaluate means of diagnostic assessment for the purpose of optimizing treatment selections; and to provide radiation therapy as well as general oncology consultations for patients admitted to other Clinical Research Center (CRC) clinical services, in a collaborative approach. Total RNA isolated from 72 organ samples provided by the NCI from mini pigs after whole body irradiation will be used for this study. To obtain a global assessment of changes that occur in these samples in response to radiation, mRNA expression profiles will be analyzed by the Contractor. Data analysis will include a pathway analysis to identify differences in expression of mRNAs that are relevant for each radiation dose. The core strength and sole focus of the Contractor shall be expression profiling on microarrays. The Contractor shall provide gene expression profiling: consisting of amplification of RNA, hybridization to microarrays, and data. The purpose of this requirement is to provide full service gene expression analysis using unique and proprietary protocols and systems developed to provide highly sensitive and reproducible Gene Expression results for Total RNA starting quantities of as little as 50 picograms. The Contractor shall offer three tiers of processing various quantities of Total RNA. The first tier involves a single round of amplification (standard procedure, established in FDA-sponsored MAQC study, 2006) to generate labeled material to hybridize to the microarray platform. This first tier of processing can work with as little as 20 ng of Total RNA sample. The second tier of processing utilizes a double amplification process and generates enough labeled material to run multiple technical replicates for each sample. The Contractor shall routinely work with less than 1.0 nanogram of starting material with this method, and can go down to 50 picograms of Total RNA with the NCI third tier of amplification methods. Protocol shall consist of established processes such as sample recovery, sample handling and preparation, utilization of various reagents and enzymatic reactions, application of samples to the microarray, post-treatment of the array, scanning and image capture, and statistical analysis of the data. The NCI has already performed a biomarker signature study using whole blood collected from a mini pig model after whole body irradiation. For this study, the NCI is using organs which were provided as part of a collaborative study. These organs were collected after sacrificing the animal after whole body irradiation. The mini pigs are a small sized breed of pig called Gottingen mini pig. Extensive qualification and quantification processes ensure high caliber results. The entire procedure requires a sophisticated laboratory with highly-skilled laboratory technicians to carry out the multiple parts of the experiment. Highly specific mRNA expression arrays shall be used by the Contractor as were used in the previous studies for the mouse organ samples and minipig blood samples. By using the same platform, microarray analysis will allow the NCI to compare previous data from the whole blood analysis. Due to variability and limited size of samples, the ability to generate consistent results from difficult sample conditions is a requirement. In addition, in order to be able to expand and complete the ongoing research using these treatments, the micro-array analysis must be compatible with previous experiments processed by the Contractor for the NCI. Changing variables at this time will be detrimental to current gene expression studies performed in the aforementioned by the NCI laboratory. The following qualifications are required: - The Contractor shall provide highly sensitive and reproducible results of gene expression studies for total RNA starting quantities of as little as 50 picograms. - The Contractor shall provide unlimited up-front consulting to determine the best experimental design and sample handling for the upcoming study prior to submitting samples. - The Contractor shall be able to provide processes such as sample recovery, sample handling and preparation, utilization of various reagents and enzymatic reactions, application of samples to the microarray, post-treatment of the array, scanning and image capture, and statistical analysis of the data. - The Contractor shall provide the NCI with a comprehensive data analysis and be willing to give support for exclusive and unlimited data analysis and consulting. - The Contractor shall be able to generate consistent results from difficult sample conditions (variability and limited sample size). - The Contractor shall be able to expand and complete the ongoing analysis using these treatments. The microarray analysis must be compatible with previous experiments. Tasks The NCI will ship the RNA samples within one (1) week after the approval of the purchase order and the Contractor shall complete the following tasks: - The Contractor shall assess the quality of these 72 RNA samples. - The Contractor shall notify the Project Coordinator, of the results by providing pictures of the gel and graphs. - The Contractor shall amplify the RNA using in vitro transcription and again assess the quality of the cDNA before the actual labeling of the chips. - The Contractor shall perform data analysis once the experimental procedure is completed. - The Contractor shall then perform the final statistical analysis and send the data to the Project Coordinator. - The Contractor shall offer full services for Agilent gene expression microarrays which will allow seamless merging of previous data from multiple experiments. - The Contractor shall use Agilent's 60-mer Sure Print technology, coupled probe design, high density arrays with multiple replicated probes, and special labeling methods for optimal sensitivity and specificity similar to that found only on Agilent's whole genome expression and miRNA microarrays. - The Contractor shall use Gene Spring analysis software from Agilent for data analysis allowing for the comparison of past, current, and future experiments conducted by the Contractor. The statistical analysis shall consist of the following data: -Master list with both up and down regulated genes with fold change and p value -Gene Ontology classifications -Venn diagrams of different combinations -Heat maps of the NCI's interest in CDs shipped via FedEx using the NCI's FedEx account. The length of the experimental process and discussions shall be two (2) to three (3) weeks. This will lead to the acceptance of the analysis criteria by the NCI Project Coordinator. The aforementioned data shall be shared with the NCI electronically. Period of Performance The period of performance shall be for twelve (12) months from date of award. Sample processing and microarray hybridization process will start as soon as the NCI ships the samples to the Contractor. The final data analysis and the data in the final format shall be shipped to the NCI Project Coordinator. This is not a solicitation for competitive quotations. However, if any interested parties, especially small businesses, believe 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. A copy of the capability statement must be received in the NCI Office of Acquisition on or before 12:30 PM EST on July 5, 2018. All questions must be in writing and can be faxed +1 (555) 000-0000 or emailed to Kathy Elliott, 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 procurement. In order to receive an award, Contractors must have valid registration and certification on Sam.gov, www.sam.gov. No collect calls will be accepted. Please reference solicitation number N02RC82567-61 on all correspondence.