SOURCES SOUGHT NOTICE: RNA Biomarkers for predicting radiation injury for radiation biodosimetry

Notice Number:

75N91021R00010

Issued By:

National Cancer Institute (NCI),

Office of Acquisitions (OA)

http://www.nci.nih.gov  or http://rcb.cancer.gov/rcb-internet/

Key Dates:

Capability Statement Due Date: December 28, 2020 by 12:00PM EST

This Small Business Sources Sought Notice (SBSS) is for information and planning purposes only and shall not be construed as a solicitation or as an obligation on the part of the National Cancer Institute (NCI).

The purpose of this Sources Sought Notice is to identify qualified Small Business concerns including 8(a), HUBZone or Service-Disabled Veteran-owned businesses that are interested in and capable of performing the work described herein. The NCI does not intend to award a contract on the basis of responses received nor otherwise pay for the preparation of any information submitted. Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. An organization that is not considered a small business under the applicable NAICS code should not submit a respjmnhhhhonse to this notice. This requirement is assigned North American Industry Classification System (NAICS) code 541380 with a size standard of $16.5 million.

As a result of this Sources Sought Notice, the NCI may issue a Request for Quotation (RFQ). THERE IS NO SOLICITATION AVAILABLE AT THIS TIME.  However, should such a requirement materialize, no basis for claims against NCI shall arise as a result of a response to this Sources Sought Notice or the NCI’s use of such information as either part of our evaluation process or in developing specifications for any subsequent requirement.

BACKGROUND

Radiological attacks and nuclear detonations can cause mass casualties. Victims may have received substantial radiation doses and may not immediately exhibit visible symptoms of radiation sickness. Victims with whole body or substantial partial body exposure >2 Gy will require immediate treatment within 24 hours to mitigate radiation injury while others will require both intermediate and long-term management for possible injury to the marrow, gastrointestinal tract, lung and other organs. Early prediction of possible acute intermediate and delayed effects will enable timely therapeutic interventions which will not only reduce death, but also improve the quality of life for the victims.

The NCI needs to identify radiation-induced global miRNA/mRNA/lncRNA expression patterns after different doses and time points following partial body irradiation in a non-human primate model. A specific functional miRNA expression signature previously derived from mouse lung tissue after whole body irradiation from the NCI laboratory will be assessed in the whole blood and serum samples after partial body irradiation in these non-human primate model and also using a human organ on a chip model. These could then be developed as part of the Point of Care and High Through-put screening platforms that are under development by other groups as part of NIAID and BARDA programs.

OBJECTIVE

The primary objective of the project is to obtain microRNA, long non-coding RNA, and mRNA expression information by performing RNAseq analysis with the following workflow:

  1. Preparation of cDNA libraries
  2. RNA QC before and after library preparation
  3. Performing RNA seq on Illumina platform
  4. Obtaining 20 million reads/sample
  5. Aligning the reads to reference genome for data analysis 

With this data, the NCI will identify biomarker signatures of radiation exposure and of organ-specific radiation injury.

SCOPE

This project is a multi-step process with each step dependent on the successful completion of the former. The process starts with a quality check of the RNA and follows with sequential steps of rRNA depletion, globin RNA depletion, adapter ligation, cDNA preparation, sample purification and QC, reading on an Illumina platform, aligning reads to a reference genome, and finally data clean-up and analysis for identifying differentially expressed coding and non-coding RNAs.

CONTRACT REQUIREMENTS/ AND PERSONNEL QUALIFICATIONS

The contractor shall perform the following tasks:

    1. mRNA and lncRNA sequencing
      1. Total RNA sample quality control
        1. Nanodrop: tests RNA purity
        2. Agarose Gel Electrophoresis: tests RNA degradation and potential contamination
        3. Agilent 2100: checks RNA integrity
      2. Library Construction
        1. rRNA removal
        2. Fragmentation
        3. cDNA synthesis
        4. Adapter ligation
        5. Size selection
        6. PCR enrichment
      3. Library Quality Control
        1. Qubit 2.0 fluorometer
        2. Agilent 2100
        3. Quantitative PCR
      4. Sequencing using Illumina platforms
      5. Data Analysis
        1. Quality control
        2. Read mapping to reference genome
    1. Small RNA sequencing (microRNA)
      1. Total RNA sample quality control
        1. Nanophotometer: tests RNA purity
        2. Agarose Gel Electrophoresis: tests RNA degradation and potential contamination
        3. Agilent 2100: checks RNA integrity
      2. Library Construction
        1. Library prep for small RNA sequencing using NEBNext Multiplex Small RNA Library Prep Set for Illumina
      3. Library Quality Control
        1. Agilent 2100 using DNA High Sensitivity Chip
      4. Clustering and Sequencing
        1. Clustering of index-coded samples on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumina)
        2. Sequencing of libraries on an Illumina platform to generate 50bp single-end reads
    1. Data Analysis
        1. Quality control
        2. Data normalization
        3. statistically significant (FC ≥2 or ≤ 0.5; p-value <0.05) genes were identified from each animal and timepoint for further analysis
        4. Read mapping to reference genome

TYPE OF ORDER

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

How to Submit a Response:

  1. Page Limitations:

Interested qualified small business organizations should submit a tailored capability statement for this requirement not to exceed 10 single sided pages including all attachments, resumes, charts, etc. (single spaced, 12-point font minimum) that clearly details the ability to perform the requirements of the notice described above. All proprietary information should be marked as such.   Responses should include a minimum of a one-page resume of the individuals meeting the requirements, and up to two pages demonstrating experience over the past two years meeting the requirements of this notice.  Statements should also include an indication of current small business status; this indication should be clearly marked on the first page of your capability statement (preferable placed under the eligible small business concern’s name and address).  Responses will be reviewed only by NIH personnel and will be held in a confidential manner. Organizations shall demonstrate 1.) Technical Approach 2.) Personnel Requirements and Organizational Experience. 

  1. Due Date: 

Capability statements are due no later than December 28, 2020 by 12:00PM EST

  1. Delivery Point:

All information furnished must be in writing and must contain sufficient detail to allow the NCI to determine if it can meet the unique specifications described herein.  All questions must be in writing and emailed to David.Romley@nih.gov.  A determination by the Government not to compete this 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 have valid registration and certification in the System for Award Management (SAM) at Beta.SAM.gov. No collect calls will be accepted. Please reference number 75N91021R00010 on all correspondence.

Disclaimer and Important Notes:

This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization’s qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, an RFQ may be published in beta.SAM.gov. However, responses to this notice will not be considered adequate responses to a solicitation(s).

Point of Contact:

Inquiries concerning this Notice may be direct to:

David Romley at David.Romley@nih.gov.

Confidentiality: No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation.