Identifying radiation induced RNA markers in lung and liver tissue samples from a whole body irradiated mouse model and comparison with RNA markers form whole blood samples identified previously

Title: Identifying radiation induced RNA markers in lung and liver tissue samples from a whole body irradiated mouse model and comparison with RNA markers form whole blood samples identified previously

Document Type: Special Notice
Solicitation Number: 75N91019Q00027
Proposed Posted Date: 02/14/2019
Proposed Response Date: 02/28/2019 3:00 PM ET

Classification Code: Q301 - Laboratory Testing Services
NAICS Code: 541380 - Testing Laboratories
Business Size Standard: $15,000,000

Contracting Office Address:

Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Center for Cancer Research (CCR), Radiation Oncology Branch (ROB) and the Office of Acquisitions, 9609 Medical Center Drive, Room 1E128, Bethesda, MD 20892, UNITED STATES.

Description:

National Cancer Institute (NCI), Center for Cancer Research (CCR) and Radiation Oncology Branch (ROB) plans to procure on a sole source basis the services for GenUs BioSystems proprietary laboratory systems, as described below, from GenUs BioSystems, Inc.; 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. . The North American Industry Classification System code is 541380 and the business size standard is $15M.

This will be awarded as a firm fixed price type contract. The award will be in the aggregate.

The period of performance will be 90 days twelve (12) months from effective date in the award.

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

BACKGROUND

The NCI recently conducted extensive research in mouse and mini-pig models after whole body irradiation to see if non-coding RNAs and coding RNAs can be used as biomarkers for radiation bio-dosimetry. 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. In this proof-in-principle proposal, first, NCI will identify radiation induced global gene expression pattern after different doses and time points in organs collected after whole body irradiation in a mouse model. A specific functional mRNA expression signature which was identified before from the whole blood of the same animal will be validated along with microRNAs which regulated these genes and their pathway analysis. Ultimately, a combined approach of identifying organ specific biomarkers by assessing functional miRNAs, target 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 is a new study for the Biomedical Advanced Research and Development Authority (BARDA) to develop and procure medical countermeasures that address the public health and medical consequences of chemical, biological, radiological, and nuclear (CBRN) accidents. This will also help in identifying radiation induced normal tissue damage sustained during clinical radiotherapy.

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 heart, lungs and liver samples of mouse model after exposed to whole body irradiation.

SCOPE

Scope of Work: - Total RNA isolated from organ samples provided by NCI from mouse 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 this project is expression profiling on microarrays. Contractor shall be able to provide services, including 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 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. 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 and miRNA expression arrays shall be used by the Contractor as were used in the previous studies. 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 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:

• Provide highly sensitive and reproducible results of gene expression studies for total RNA starting quantities of as little as 50 picograms.
• Provide unlimited up-front consulting to determine the best experimental design and sample handling for the upcoming study prior to submitting samples.
• 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.
• Must offer full services for Agilent gene expression microarrays which will allow seamless merging of previous data from multiple experiments.
• 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.
• Use Gene Spring analysis software from Agilent for data analysis allowing for the comparison of past, current, and future experiments.
• Provide NCI with a comprehensive data analysis and support for exclusive and unlimited data analysis and consulting.
• 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 shall be expression profiling on microarrays. The contractor shall use unique and proprietary protocols and systems.

Project Management Plan

The RNA samples will be shipped within one week after the approval of the purchase order and the Contractor shall assess the quality of these 72 RNA samples. After completing this procedure, the Contractor shall notify the Technical Point of Contact (TPoC)of the result by providing pictures of the gel and graphs. After the quality assessment, 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. Once the experimental procedure is completed, the Contractor shall perform data analysis. The length of the experimental process and discussions shall be completed in approximately 2 weeks; this will lead to the acceptance of the analysis criteria by the TPoC. The Contractor shall then perform the final statistical analysis and send the data to the TPoC. This includes, master list with both up and down regulated genes with fold change and p value, Gene Ontology classifications, Venn diagrams of different combinations and heat maps of ROB's interest in actual CDs by FedEx. The files shall also be sent electronically.

TYPE OF ORDER

This will be awarded as a firm fixed price purchase order.

PERIOD OF PERFORMANCE

The period of performance shall be 90 days 4 months from time of award.

REPORT(S)/DELIVERABLES AND DELIVERY SCHEDULE

The analysis shall be performed at vendor's site. The contractor shall then perform the final statistical analysis and send the data to the project coordinator. This includes, master list with both up and down regulated genes with fold change and p value, Gene Ontology classifications, Venn diagrams of different combinations and heat maps of our interest in actual CDs by FedEx. The files are also shared with us electronically.

DELIVERABLE DELIVERABLE DESCRIPTION / FORMAT REQUIREMENTS DUE DATE
Data files The master list with both up and down regulated genes with fold change and p value after gene spring analysis

Gene Ontology classifications

Venn diagrams of different combination analysis

heat maps of our interest and completer raw data in actual CDs by FedEx.

Within 90 days
after award

PAYMENT

Payment shall be made in two 50% disbursements. The first payment will be made after the initial data files have been received, and second payment after final data set has been reviewed and accepted. Payment authorization requires submission and approval of invoices to the TPoC and NIH OFM, in accordance with the attached payment provisions listed below:
GenUs is the only vendor that the NCI is aware of that consistently provides high performance array metrics for sensitivity, dynamic range, and reproducibility similar to the results ROB will get with single round amplification/labeling that is maintained for all three tiers of processing, dependent on amount of starting material.

This notice is not a request for competitive quotation. However, if any interested party, especially small businesses, believes it can meet the above requirement, it may submit a capability statement, proposal, or quotation, which shall be considered by the agency. The statement of capabilities and any other information furnished must be in writing and must contain material in sufficient detail to allow the NCI to determine if the party can perform the requirement. Responses must be received in the contracting office by 3:00PM EDT, on Thursday, February 28, 2019. All responses and questions must be in writing and emailed to William Neal, Contracting Officer via electronic mail 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. No collect calls will be accepted. In order to receive an award, Contractors must be registered and have valid, current Entity Record, including current Representations and Certifications, in the System for Award Management (SAM) through SAM.gov. Reference: 75N91019Q00027 on all correspondence.

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