Combined Synopsis-Solicitation - RNA Biomarkers.rtf

STATEMENT OF WORK (SOW)

Contracting Office Address Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 9609 Medical Center Drive, Room 1E122, Bethesda, MD 20892, UNITED STATES.

Non-USPS mail such as Fedex UPS and other private carriers please use Rockville, MD 20850.

The National Cancer Institute (NCI), Radiation Oncology Branch (ROC) requires a contractor to obtain microRNA, long non-coding RNA, and mRNA expression information by performing RNAseq analysis.

This is a combined synopsis/solicitation for commercial items, prepared in accordance with format in FAR 12.6 as supplemented with additional information included in this notice. This announcement constitutes the only solicitation and a separate written solicitation will not be issued.

The North American Industry Classification System (NAICS) code is 541380. The business size standard is $15 million and this is a Small Business Set-Aside.

Only one award will be made as a result of this solicitation. This will be awarded as a severable firm fixed price type contract.

Description of Requirement

TITLE

RNA Biomarkers for predicting radiation injury for radiation biodosimetry.

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:

Preparation of cDNA libraries

RNA QC before and after library prepration Performing RNA seq on Illumina platform Obtaining 20 million reads/sample 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:

mRNA and lncRNA sequencing Total RNA sample quality control Nanodrop: tests RNA purity Agarose Gel Electrophoresis: tests RNA degradation and potential contamination Agilent 2100: checks RNA integrity

Fragmentation cDNA synthesis Adapter ligation Size selection PCR enrichment

Agilent 2100 Quantitative PCR Sequencing using Illumina platforms Data Analaysis Quality control Read mapping to reference genome

Small RNA sequencing (microRNA) Total RNA sample quality control Nanophotometer: tests RNA purity Agarose Gel Electrophoresis: tests RNA degradation and potential contamination Agilent 2100: checks RNA integrity

Sequencing of libraries on an Illumina platform to generate 50bp single-end reads

Data Analysis Quality control Data normalization statistically significant (FC ≥2 or ≤ 0.5; p-value <0.05) genes were identified from each animal and timepoint for further analysis Read mapping to reference genome

TYPE OF ORDER

This will be issued as a Several Firm Fixed Price Purchase Order.

PERIOD OF PERFORMANCE

The period of performance shall be from March 1, 2021 to August 31, 2021.

PLACE OF PERFORMANCE:

Novogene, 126 Corporate Boulevard, South Plainfield, NJ 07080

REPORT(S)/DELIVERABLES AND DELIVERY SCHEDULE

DELIVERABLE

DELIVERABLE DESCRIPTION / FORMAT REQUIREMENTS

DUE DATE

#1 (Task 4.1) mRNA and lncRNA sequencing data Within 6 months after award #2 (Task 4.2) microRNA sequencing data Within 6 months after award #3 (Task 4.3) Data analysis Within 6 months after award

PAYMENT

Payment shall be made upon receipt and acceptance of all deliverables. Payment authorization requires submission and approval of invoices to the COR and NIH OFM, in accordance with the attached payment provisions listed below:

The following clause is applicable to all Purchase Orders, Task or Delivery Orders, and Blanket Purchase Agreement (BPA) Calls: PROMPT PAYMENT (JAN 2017) FAR 52.232-25. Highlights of this clause and NIH implementation requirements follow:

Remit-to address (Name and complete mailing address to send payment).

Remittance name must match exactly with name on original order/contract. If the Remittance name differs from the Legal Business Name, then both names must appear on the invoice.

Invoice date.

Unique invoice #s for all invoices per vendor regardless of site.

NBS document number formats must be included for awards created in the NBS: Contract Number; Purchase Order Number; Task or Delivery Order Number and Source Award Number (e.g., Indefinite Delivery Contract number; General Services Administration number); or, BPA Call Number and BPA Parent Award Number.

Data Universal Numbering System (DUNS) or DUNS + 4 as registered in Beta.SAM.gov.

Federal Taxpayer Identification Number (TIN). In those exceptional cases where a contractor does not have a DUNS number or TIN, a Vendor Identification Number (VIN) must be referenced on the invoice. The VIN is the number that appears after the contractor’s name on the face page of the award document.

Identify that payment is to be made using a three-way match.

Description of supplies/services that match the description on the award, by line billed.* Freight or delivery charge must be billed as shown on the award. If it is included in the item price do not bill it separately. If identified in the award as a separate line item, it must be billed separately.

Quantity, Unit of Measure, Unit Price, Extended Price of supplies delivered, or services performed, as applicable, and that match the line items specified in the award. *

* NOTE: If your invoice must differ from the line items on the award, please contact the Contracting Officer before submitting the invoice. A modification to the order or contract may be needed before the invoice can be submitted and paid.

Shipping costs will be reimbursed only if authorized by the Contract/Purchase Order. If authorized, shipping costs must be itemized. Where shipping costs exceed $100, the invoice must be supported by a bill of lading or a paid carrier's receipt.

II. ELECTRONIC INVOICING INSTRUCTIONS

Effective December 1, 2020, the Office of Financial Management (OFM) will no longer accept hard copy contractor/vendor invoices sent to the OFM billing office via any shipping services (i.e., USPS, FedEx, UPS, DHL, etc.) or those delivered by any in-person drop off. OFM is requiring that all contractors/vendors submit their invoices for payment processing using the electronic invoice submission solution via email at invoicing@nih.gov. OFM will not accept any invoices postmarked and/or delivered in-person on/after December 1, 2020.

Step 1:

Send invoices to the following email address:

invoicing@nih.gov

4 Steps to Create the Invoice Submission Email Step 3:

Attach the invoice to the email as either a PDF or Word document. See Reminders below.

Step 4:

In the body of the email, type “Correspondence Email:” followed by your email address.

Step 2:

Subject line must follow this format for the invoice you are submitting (see note* below)

Send invoices to the following email address: invoicing@nih.govSubject line must follow this format for the invoice you are submitting (see step2 section below).In the body of the email, type �Correspondence Email:� followed by your email address.Attach the invoice to the email as either a PDF or Word document.

file_0.wmf

PLEASE READ THE BELOW INSTRUCTIONS THOROUGLY BEFORE SUBMITTING YOUR INVOICE ELECTRONICALLY.

*Note: The key words (Vendor, PO, and Invoice), Colon (:) character following the keywords and the PIPE (|) character must be present to identify the information. The pipe (|) character is entered by pressing and holding the shift key and the backslash (\) key at the same time. The term “PO” is being used as a generic term to identify the award number [purchase order, contract, Blanket Purchase Agreement (BPA) call, task or delivery order] and must be used in the subject line, regardless of the specific type of your award.

How to Properly Format the Subject Line of Your Email EXAMPLE 1 – If Your Contract Includes a Contract Number AND an Order Number or Call Number:

Vendor: Name of the Contractor or Vendor|PO:Contract Number/Order Number or Call Number|Invoice:9999999 EXAMPLE 2 – If Your Contract ONLY Includes a Contract Number:

Vendor: Name of the Contractor or Vendor|PO:Contract Number|Invoice:9999999 EXAMPLE 3 – If Your Contract ONLY Includes an Order Number:

Vendor: Name of the Contract or Vendor|Order Number|Invoice:99999999 Screenshot of How to Locate the Contract Number and Order Number on Your SF 1449 (SOLICITATION/CONTRACT/ORDER FOR COMMERCIAL ITEMS Form) The screenshot below shows where the Contract Number and Order Number are located on the SF 1449. The SF 1449 is provided to you by the NIH Contracting Officer upon awarding the contract. Please use the information on your SF 1449 to populate the correct Contract Number and Order Number in the subject line of your email invoice submission.

The Contract Number is required in order to process all invoices. The Contract Number is the same as the “PO” on the invoice email subject line. The Order Number is only applicable for certain contracts and can be found in field number 4, on the SF 1449 form. If your SF 1449 does not include an Order Number, then follow EXAMPLE 2 above to ensure the Subject line of your email is properly formatted.

Shapshot of SF 1449 file_1.wmf

Screenshot of How to Locate the Contract Number on Your SF 1447 (SOLICITATION/CONTRACT Form) The screenshot below shows where the Contract Number is located on the SF 1447. The SF 1447 is provided to you by the NIH Contracting Officer upon awarding the contract. Please use the information on your SF 1447 to populate the correct Contract Number in the subject line of your email invoice submission.

The Contract Number is required in order to process all invoices. The Contract Number is the same as the “PO” on the invoice email subject line.

Snapshot of FY1447 file_2.wmf

Screenshot of How to Locate the Contract Number and Release Number on Your OF 347 (ORDER FOR SUPPLIES OR SERVICES Form) The screenshot below shows where the Contract Number and Order Number are located on the OF 347. The OF 347 is provided to you by the NIH Contracting Officer upon awarding the contract. Please use the information on your OF 347 to populate the correct Contract Number (if any) and Order Number in the subject line of your email invoice submission.

The Order Number is required in order to process all invoices. If there is no Contract Number, the Order number is the same as the “PO” on the invoice email subject line. The Contract Number is only applicable for certain contracts and can be found in field number 2, Contract Number, on the OF 347 form. If your OF 347 does not include a Contract Number, then follow EXAMPLE 3 on page 2 to ensure the Subject line of your email is properly formatted.

Snapshot of OF 347 file_3.wmf

Subject Line Correct Incorrect Vendor: XYZ Corp|PO:HHSN299202000053J/75X98019S00848|Invoice:XYASAD Checkmark file_4.wmf

XYZ Corp|PO # HHSN299202000053J \75X98019S00848|Invoice # XYASAD

Close file_5.wmf

XYZ Corp| HHSN299202000053J \75X98019S00848|Invoice # XYASAD file_6.wmf

XYZ Corp| HHSN299202000053J \75X98019S00848| XYASAD file_7.wmf

Vendor: XYZ Corp,PO: HHSN299202000053J \75X98019S00848,Invoice:XYASAD file_8.wmf

Vendor: XYZ Corp|PO:HHSN299202000053J|Invoice:XYASAD file_9.wmf

Vendor: XYZ Corp|PO:HHSN311201600011U|Invoice:XYASAD file_10.wmf

Subject Line Examples For your reference, below is a chart listing examples of the correct and incorrect subject lines. Note: These are just examples, you must enter the applicable information for the invoice you are submitting.

Reminders

You must submit only one invoice per email.

Follow the system size limits that apply to the email and each invoice: individual email attachments cannot exceed 5 megabytes each; and the email plus all attachments cannot exceed a total of 30 megabytes.

Clearly identify a valid and complete contract number on each invoice.

Clearly identify an accurate DUNS number on each invoice.

DO NOT include confidential information such as Social Security Numbers (do not include TIN if it is a Social Security Number).

The invoice attached to the email must be in a PDF or Word format. The date/time that a valid invoice is submitted electronically to the email box (invoicing@nih.gov) will be the same date/time logged as the invoice is received by NIH.

Questions?

Please direct inquiries regarding the status of invoices such as receipt of invoices, due date, or payment of invoices to the OFM Commercial Accounts Branch, Customer Service Office. The OFM Customer Service contact information and of methods to contact are available at the following OFM website https://ofm.od.nih.gov/Pages/Customer-Service.aspx and below.

The Customer Service Office is open Monday – Friday from 8:30 am to 5:00 pm (Eastern Standard Time) and is closed daily between 12:00 pm to 1:00 pm (Eastern Standard Time). The Customer Service Office phone number is 301-496-6088.

Snapshot of OFM Customer Service Help desk file_11.wmf

Instructions for Contractor/Vendor Courtesy Copy Electronic Invoice Submission to the Contracting Officer (CO):

The Contractor/Vendor shall send a cc: copy to the NIH Contracting Officer and the NIH Contracting Officer’s Representative (COR) stated in the award and the NIH Program point of contact when submitting the invoice to NIH/OFM for payment.

III. INVOICE PAYMENT

Except as indicated in paragraph B., below, the due date for making invoice payments by the designated payment office shall be the later of the following two events:

1. The 30th day after the designated billing office has received a proper invoice.

2. The 30th day after Government acceptance of supplies delivered or services performed.

B. The due date for making invoice payments for meat and meat food products, perishable agricultural commodities, dairy products, and edible fats or oils, shall be in accordance with the Prompt Payment Act, as amended.

IV. INTEREST PENALTIES

A. An interest penalty shall be paid automatically, if payment is not made by the due date and the conditions listed below are met, if applicable.

1. A proper invoice was received by the designated billing office.

2. A receiving report or other Government documentation authorizing payment was processed and there was no disagreement over quantity, quality, or contractor compliance with a term or condition.

3. In the case of a final invoice for any balance of funds due the contractor for supplies delivered or services performed, the amount was not subject to further settlement actions between the Government and the Contractor.

Determination of interest and penalties due will be made in accordance with the provisions of the Prompt Payment Act, as amended, the Contract Disputes Act, and regulations issued by the Office of Management and Budget.

V. PROVIDING ACCELERATED PAYMENT TO SMALL BUSINESS

SUBCONTRACTORS, FAR 52.232-40 (DEC 2013)

Upon receipt of accelerated payments from the Government, the Contractor shall make accelerated payments to its small business subcontractors under this contract, to the maximum extent practicable and prior to when such payment is otherwise required under the applicable contract or subcontract, after receipt of a proper invoice and all other required documentation from the small business subcontractor.

The acceleration of payments under this clause does not provide any new rights under the prompt Payment Act.

Include the substance of this clause, include this paragraph c, in all subcontracts with small business concerns, including subcontracts with small business concerns for the acquisition of commercial items.

10.0 PROVISIONS AND CLAUSES

52.252-2 CLAUSES INCORPORATED BY REFERENCE (FEB 1998)

This contract incorporates one or more clauses by reference, with the same force and effect as if they were given in full text. Upon request, the Contracting Officer will make their full text available. Also, the full text of a clause may be accessed electronically at this/these address(es): http://www.acquisition.gov/far/ and/or http://www.hhs.gov/policies/hhsar/.

HEALTH AND HUMAN SERICES ACQUISITION REGULATION (HHSAR) (48 CFR CHAPTER 3):

Clause No.

TITLE

352.203-70 Anti-lobbying (DEC 2015) 352.208-70 Printing and Duplication (DEC 2015) 352.211–3 Paperwork Reduction Act (DEC 2015) 352.222-70 Contractor Cooperation in Equal Employment Opportunity Investigations. (DEC 2015) 352.224-70 Privacy Act (DEC 2015) 352.224-71 Confidential Information (DEC 2015) 352.227–70 Publications and Publicity (DEC 2015) 352.237-74 Non-Discrimination in Service Delivery (DEC 2015)

FEDERAL ACQUISITION REGULATION (FAR) (48 CFR CHAPTER 1):

Clause No.

TITLE

52.203-16 Preventing Personal Conflicts of Interest (JUN 2020) 52.204-4 Printed or Copied Double-Sided on Postconsumer Fiber Content Paper (MAY 2011) 52.212-4 Contract Terms and Conditions – Commercial Items (Oct 2018)

FAR 52.212-5 CONTRACT TERMS AND CONDITIONS REQUIRED TO IMPLEMENT STATUTES OR EXECUTIVE ORDERS - COMMERCIAL ITEMS (JAN 2021)