Identifying radiation induced RNA markers in whole blood from a whole body irradiated minipig model and compare with RNA markers from whole blood samples identified previously.

Title: Identifying radiation induced RNA markers in whole blood from a whole body irradiated minipig model and compare with RNA markers from whole blood samples identified previously.

Document Type: Special Notice
Solicitation Number: 75N91019Q00127
Posted Date: 08/22/2019
Response Date: 08/29/2019 3:00 PM ET
Classification Code: 256Q - Laboratory and Testing Services
NAICS Code: 541715- RESEARCH AND DEVELOPMENT IN THE PHYSICAL, ENGINEERING, AND LIFE SCIENCES

Contracting Office Address
Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 9609 Medical Center Drive, Room 1E128, Rockville, MD 20850, UNITED STATES

Description

The National Cancer Institute (NCI), Center for Cancer Research (CCR), Radiation Oncology Branch (ROB), recently conducted extensive research in a mouse model after whole body irradiation to see if non-coding RNAs and coding RNAs can be used as biomarkers for radiation biodosimetry. These non-coding RNAs including miRNAs and long non-coding RNAs (lncRNAs) showed significant alterations after various radiation doses. These non-coding RNAs could potentially be advantageous biomarkers due to their presence and stability in serum and other bio-fluids. A specific functional mRNA expression signature which was identified before from the whole blood of minipig will be validated. Ultimately, a combined approach of identifying organ specific biomarkers in whole blood by assessing functional mRNAs and lncRNAs to assess radiation exposure after mass-casualty incidents could provide a valuable tool in developing and implementing effective and timely medical countermeasures. This will also help in identifying radiation induced normal tissue damage sustained during clinical radiotherapy with GenUS Stellar Biosystems, Inc. of 1808 Janke Drive, Unit M - Northbrook, Il 60062.

The response close date of this notice for this requirement is in accordance with FAR 5.203(a)(1). This acquisition will be processed under FAR Part 12 - Acquisition for Commercial Items and will be made pursuant to the authority in FAR 13.106-1(b)(1) using simplified acquisition procedures for commercial acquisitions and is exempt from the requirements of FAR Part 6. The North American Industry Classification System code is 541715- RESEARCH AND DEVELOPMENT IN THE PHYSICAL, ENGINEERING, AND LIFE SCIENCES.

It has been determined there are no opportunities to acquire green products or services for this procurement.

OBJECTIVE

Radiation response involves different pathways for different doses of radiation hence different mRNA expression profiles are induced.
Specific Aim: To investigate radiation induced gene expression changes in whole blood samples of minipig model after exposed to whole body irradiation.

SCOPE

Scope of Work: - Total RNA isolated from whole blood samples provided by NCI from minipig 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 GenUS Biosystems. Data analysis will include a pathway analysis to identify differences in expression of mRNAs that are relevant for each radiation dose.

CONTRACT REQUIREMENTS/ AND PERSONNEL QUALIFICATIONS

The core strength and sole focus of GenUs BioSystems, Inc. is expression profiling on microarrays. GenUs uses unique and proprietary protocols and systems to provide highly sensitive and reproducible results of gene expression studies for total RNA starting quantities of as little as 50 picograms. GenUs BioSystems is the only vendor that we are aware of that provides high performance microarray metrics for sensitivity, dynamic range, and reproducibility with extremely small amounts of starting material. Their service includes 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 company offers 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. GenUs can 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 our 3rd tier of amplification methods. GenUs is the only vendor that we are aware of that consistently provides high performance array metrics for sensitivity, dynamic range, and reproducibility similar to what we get with single round amplification/labeling that is maintained for all three tiers of processing, dependent on amount of starting material. Protocol consists 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. 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 will be used by the Contractor as were used in the previous studies (PO #: 261201800515P, PO #: 261201800555P, and PO #: 75N91019P00151). By using the same platform microarray analysis will allow us to compare our previous data from the whole blood analysis, as well as the organ-specific radiation markers. 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 GenUs Biosystems. Changing variables at this time will be detrimental to current gene expression studies performed in the aforementioned NCI laboratory. This section spells out most precisely what is expected of the contractor in performance of the work. It describes the specific tasks and phases of the work and specifies the total effort each task or phase is to receive. Considerations that may guide the contractor in its analysis, design, or experimentation on the designated problems should also be included here.

The Contractor shall perform the following tasks:

•Contractor must provide highly sensitive and reproducible results of gene expression studies for total RNA starting quantities of as little as 50 picograms. GenUs is the only lab that we are aware of that provides high performance microarray metrics for sensitivity, dynamic range, and reproducibility with extremely small amounts of starting material.

•Contractor must provide unlimited up-front consulting to determine the best experimental design and sample handling for the upcoming study prior to submitting samples.

•Contractor must 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.

•Contractor must offer full services for Agilent gene expression microarrays which will allow seamless merging of previous data from multiple experiments.

•Contractor must 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.

•Contractor must use Gene Spring analysis software from Agilent for data analysis allowing for the comparison of past, current, and future experiments conducted by GenUs.

•Contractor must provide us with a comprehensive data analysis and be willing to give support for exclusive and unlimited data analysis and consulting.

•Contractor must be able to generate consistent results from difficult sample conditions (variability and limited sample size).

•In addition, in order to be able to expand and complete the ongoing research using these treatments, the microarray analysis must be compatible with previous experiments.
The core strength and sole focus of the contractor is expression profiling on microarrays. The contractor shall use unique and proprietary protocols and systems. Highly specific mRNA expression arrays will be used by GenUs BioSystems as were used in the previous studies for the minipig blood samples. By using the same platform microarray analysis will allow us to compare our 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. Previous work has been done using this contractor and to minimize variability in data analysis this contractor must be utilized for this next set of experiments.

This notice is not a request for competitive quotation. However, if any interested party, especially small business believes it can meet the above requirement, it may submit a proposal or quote for the Government to consider. The response and any other information furnished must be in writing and must contain material in sufficient detail to allow NCI to determine if the party can perform the requirement. Responses must be received in the contracting office by 3:00 PM ET, on Thursday, August 29, 2019. All responses and questions must be via email to William Neal, Contracting Officer at william.neal@nih.gov. 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. In order to receive an award, contractors must be registered and have valid certification through SAM.GOV and have Representations and Certifications filled out. Reference: 75N91019Q00127 on all correspondence.

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