SOW_FaDU_6-5-18.docx

STATEMENT OF WORK (SOW)

1.0 TITLE: Exploring the gene expression and miRNA expression changes in tumors exposed to radiation with or without an HSP90 inhibitor for prolonged periods.

2.0 BACKGROUND

In our previous studies we have found wide-ranging gene expression (mRNA) and microRNA (miRNA) expression changes at shorter duration time-points (6 h – 48 h) compared to the longer time points (2 months in culture) in cells exposed to radiation, alluding to the radiation driven adaptive changes in the cells. Based on our observation we hypothesize that radiation induced molecular responses leading to adaptive phenotype can be exploited for chemotherapeutic intervention in conjunction with radiotherapy for cells which adapt in response to radiation.

2.1 OBJECTIVE

Exploring the gene expression and miRNA expression changes in xenograft tumors exposed to radiation with or without an HSP90 inhibitor for prolonged periods.

Specific Aim: To perform gene expression and miRNA expression microarrays in FaDU tumors grown as xenografts in nude mice after treatment with radiation with or without an HSP90 inhibitor (AT13387).

3.0 SCOPE

Total RNA isolated from xenograft tumor samples growing in nude mice provided by NCI will be used for this study. To obtain a global assessment of changes that occur in these samples in response to radiation, mRNA and miRNA 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.

All the samples will be sent to the contractor in one shipment. The contractor will use it for quality assessment using bioanalyzer and mRNA and miRNA microarray expression analysis.

4.0 CONTRACT REQUIREMENTS/ AND PERSONNEL QUALIFICATIONS

The core strength and sole focus of the Contractor is expression profiling on microarrays. The vendor will use unique and proprietary protocols and systems to provide highly sensitive and reproducible results of gene expression studies for total RNA starting with quantities of as little as 50 picograms. 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. Three tiers of processing shall be conducted with 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 second tier of processing can work with as little as 20 ng of Total RNA sample. The third tier of processing utilizes a double amplification process and generates enough labeled material to run multiple technical replicates for each sample. The vendor should be able to work with less than 1.0 nanogram of starting material with this methodand can go down to 50 picograms of Total RNA. 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 will be used by the Contractor as were used in the previous studies (PO #: HHSN261201700709P and PO #: HHSN261201700675P). 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 by the 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 shall be included in this category.

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.

•Be capable of providing 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.

• Offer full services for Agilent gene expression microarrays which will allow seamless merging of previous data from multiple experiments (PO #: 261201700709P and PO #: 261201700675P).

•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 conducted by the Contractor.

•Provide the NCI with a comprehensive data analysis and be willing to give support for exclusive and unlimited data analysis and consulting.

•Be capable of generating 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 (PO #: 261201700709P and PO #: 261201700675P). By using the same platform microarray analysis will allow the NCI to compare previous data from PC3 cells.

4.1 Project Management Plan

The NCI will ship 72 RNA samples within one week after the approval of the purchase order and the Contractor shall assess the quality of these samples. After completing this procedure, the Contractor shall notify the Project Coordinator, 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 should be approximately two (2) weeks; this will lead to the acceptance of the analysis criteria by the Project Coordinator. The Contractor shall then perform the final statistical analysis and send the data to the Project Coordinator.

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 aforementioned data shall be shared with the NCI electronically.

5.0 TYPE OF ORDER

This is a firm fixed price purchase order.

6.0 PERIOD OF PERFORMANCE

The period of performance shall be for four (4) weeks from time 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 are expected to reach at Radiation Oncology Branch, building #10, Room B3 B406, within 30-40 days after the Contractor receives the samples.

7.0 PLACE OF PERFORMANCE

The National Cancer Institute Radiation Oncology Branch Experimental Therapeutics Section, 9000 Rockville Pike Bldg 10, Room B3 B406 Bethesda, MD 20892 POC: Dr. Molykutty Aryankalayil Email: aryankalayilm@mail.nih.gov

8.0 REPORT(S)/DELIVERABLES AND DELIVERY SCHEDULE

The Contractor shall perform the final statistical analysis and send the data to the NCI Project Coordinator. This includes a 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 the NCI’s interest in actual CDs shipped via FedEx. The files are also shared with us electronically.

30 days after award

9.0 PAYMENT

Payment shall be made 30 days after the award. 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 (JUL 2013) FAR 52.232-25. Highlights of this clause and NIH implementation requirements follow:

I INVOICE REQUIREMENTS

A. An invoice is the Contractor's bill or written request for payment under the contract for supplies delivered or services performed. A proper invoice is an "Original" which must include the items listed in subdivisions 1 through 12, below, in addition to the requirements of FAR 32.9. If the invoice does not comply with these requirements, the Contractor will be notified of the defect within 7 days after the date the designated billing office received the invoice (3 days for meat, meat food products, or fish, and 5 days for perishable agricultural commodities, dairy products, edible fats or oils) with a statement of the reasons why it is not a proper invoice. (See exceptions under II., below.) Untimely notification will be taken into account in the computation of any interest penalty owed the Contractor.

1. Vendor/Contractor: Name, Address, Point of Contact for the invoice (Name, title, telephone number, e-mail and mailing address of point of contact).

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

3. 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.

4. Invoice date.

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

6. 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.

7. Data Universal Numbering System (DUNS) or DUNS + 4 as registered in the Central Contractor Registration (CCR).

8. 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.

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

10. Description of supplies/services that match the description on the award, by line billed.*

11. 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.

12. 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.

B. 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.

C. Mail an original and 1 copy of the itemized invoice to:

National Institutes of Health Office of Financial Management, Commercial Accounts 2115 East Jefferson Street, Room 4B-432, MSC 8500 Bethesda, MD 20892-8500

For inquiries regarding payment call: (301) 496-6088

In order to facilitate the prompt payment of invoices, it is recommended that the vendor submit a photocopy of the invoice to the “Consignee” designated for the acquisition in blocks 6A – 6E of the face page of the Order/Award document.

II. INVOICE PAYMENT

A. 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.

III. 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.

B. 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.

IV. PROVIDING ACCELERATED PAYMENT TO SMALL BUSINESS

SUBCONTRACTORS, FAR 52.232-40 (DEC 2013)

1. 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.

1. 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.