NCI SOW - DRAFT.pdf

1.0 TITLE

Procurement of Services to Support Research into Associations between Helicobacter pylori Infection and its Treatment with Colorectal Cancer Risk

2.0 BACKGROUND

The National Institutes of Health (NIH), National Cancer Institute (NCI), Division of Cancer

Epidemiology and Genetics (DCEG) houses the world’s most comprehensive cancer epidemiology research group. The DCEG investigators currently conducts research to assess whether H. pylori infection is associated with subsequent risk of Colorectal cancer (CRC).

Colorectal cancer (CRC) is the fourth most common cancer and the third leading cause of cancer mortality in the United States (Colorectal Cancer Facts & Figures 2017-2019, American Cancer Society).

Chronic Helicobacter pylori infection is the primary known cause of gastric cancer (IARC, 1994). H.

pylori infection is common and treatable with standard antibiotics and high-dose acid suppression.

Growing evidence suggests an association between H. pylori infection and CRC risk. Two meta-analyses found significant 30% to 40% increased odds for CRC among those individuals with evidence of a current or past H. pylori infection (Zumkeller, Helicobacter 2006; Zhao, J Cancer Res Ther 2016). A recent meta-analysis also reported moderate associations between H. pylori infection and risk of colorectal adenomas, a precursor lesion to CRC (pooled odds ratio = 1.49, 95% confidence interval = 1.37

- 1.62) (Choi, Clin Transl Gastroenterol 2020). However, the mechanism(s) underlying this possible association has not yet been delineated. Most prior studies have been performed in Asian populations, and they may not be broadly generalizable to Western populations with different distributions of CRC risk factors and much higher CRC incidence. If chronic H. pylori infection increases the risk of CRC or its precursors, it is reasonable to ask whether treating H. pylori infection could reduce CRC risk. This research question has not been actively pursued. Thus, there is insufficient evidence to warrant a randomized clinical trial (RCT).

Large electronic medical records and administrative datasets that commonly include precise medication ascertainment and clinical factors and diagnoses are increasingly being used to answer questions for which RCT or new observational studies would be infeasible or too costly. Additionally, in contrast to RCTs, which are often performed in select populations, real-world data allow the examination of specific factors and their impact on disease in the general population. The DCEG seeks to efficiently examine the association between H. pylori infection and CRC and determine if H. pylori treatment among H. pylori exposed individuals reduces the risk CRC compared to infected but untreated individuals.

3.0 SCOPE

3.1 TASK 1 – OBTAIN INSTITUTIONAL APPROVALS

The Contractor shall obtain approvals from the relevant institutional review board (IRB) and other institutional officials, if required. The Contractor shall obtain approval, for extracting relevant data from computerized databases and preparing analytic files suitable for epidemiologic research. All data will be queried from the Corporate Data Warehouse (CDW), which is a robust data infrastructure that houses the electronic medical record data for all Veterans who have established care within the VHA (~22 million people). These data include laboratory tests, procedures, clinical notes, pathology reports, medications, and other data elements. The Contractor shall be the sole party responsible for communications with any

IRB or other institutional officials and shall regularly communicate the status of the approval process to the Government.

3.2 TASK 2 – ESTABLISH CASE-CONTROL SET

The Contractor shall collaborate with the NCI to select the CRC case-control set. The study will include all CRC cases diagnosed between January 1, 2002 and December 31, 2019. January 1, 2002 is selected as the earliest date of entry since electronic data capture in the CDW is accurate starting from 2000-2001 onward; thus, selecting 2002 as the start date will better ensure that at least one year of data prior to entry are available for defining covariates and evaluating exclusion criteria. Cancer-free controls will be matched to CRC cases (2:1) on age (+/- 1-2 years), sex, calendar year of diagnosis, region and length of activity in the VHA (+/- 1-2 years) as defined by any medical encounter, completed lab test or procedure, or filled prescription. Diagnoses of CRC will be determined based on ICD codes and the CDW cancer raw files, as done in prior studies.

3.3 TASK 3 – VERIFY DIAGNOSTIC ALGORITHMS

The Contractor shall verify the accuracy of diagnostic algorithms. The Contractor shall perform manual chart review on a randomly selected sample (n=100 charts) in order to ensure acceptable accuracy of the algorithm. The Contractor will modify the algorithm as needed until >90% positive and negative predictive value are achieved.

The Contractor will identify H. pylori eradication treatment as described by Kumar et al.

(Gastroenterology, 2020), which was a study conducted within the VHA system. Briefly, the Contractor will identify all prescribing events specific to concomitant combinations of amoxicillin, metronidazole, clarithromycin, tetracycline, bismuth subsalicylate and proton pump inhibitors, as these are the guideline recommended therapeutic agents for treating H. pylori infection.

3.4 TASK 4 – CONDUCT ANALYSIS

The Contractor shall collaborate with the NCI to conduct the statistical analysis following the plan proposed by the NCI/DCEG program officer.

3.5 TASK 5 – PREPARE REPORT

The Contractor shall collaborate with the NCI/DCEG project officer to interpret the results and prepare a scientific report containing the methodology as well the aggregated results. There is no page limit for the document.

4.0 GOVERNMENT RESPONSIBILITIES

The Government will provide an analytical plan to the Contractor no later than 30 calendar days after award. This analytical plan will address the set of analytical tools and statistical methods to be used for this study.

The Contractor may submit questions or suggested revisions to the analytical plan. The Contractor shall submit any questions or requests no later than 14 calendar days after receipt of the plan.

5.0 TYPE OF ORDER

This is a firm fixed price purchase order for non-severable services. Funds are only available for use for the contract line item (CLIN) to which they are obligated. Unused funds from one CLIN may not rollover for use in other periods.

6.0 PERIOD OF PERFORMANCE

The period of performance shall be 12 months from date of the award.

7.0 PLACE OF PERFORMANCE

Services shall be performed at the Contractor’s facilities or facilities authorized by the Contractor.

8.0 REPORT(S)/DELIVERABLES AND DELIVERY SCHEDULE

All written deliverable products shall be submitted in electronic copy for review and comment. Other quantities and formats may be submitted after prior approval from the technical point-of-contact (TPOC).

Electronic copies shall be submitted using Microsoft Office file format (e.g. .DOC, .XLSX) unless prior approval for another format has been obtained from the TPOC.

If any data includes geographic or other Personally Identifiable Information, the Contractor shall transfer the data via a secure, encrypted method.

All deliverables shall be submitted per the following deliverable schedule in the table below:

DELIVERABLE DELIVERABLE DESCRIPTION / FORMAT

REQUIREMENTS

DUE DATE

#1 (Task 1) Obtain IRB and institutional approvals required for this requirement. Contractor shall confirm approval via e-mail to the TPOC

30 calendar days after award.

#2 (Task 2) Regularly communicate with NCI personnel to develop the case-control set.

Weekly calls during the first two weeks after award

#3 (Task 3) Confirm via email that the algorithm achieved the suggested predictive values

30 calendar days after award

#3 (Task 4) The Government shall provide an analytical plan to the Contractor via e-mail

30 calendar days after award

#4 (Task 4) Collaborate with the NCI to conduct the statistical analysis following the plan proposed by NCI investigators.

Monthly calls after award

#5 (Task 4) Provide summary tables (MS word or Excel format) for publication

60 days prior to expiration of the period of performance

#6 (Task 5) Provide draft report submitted in MS word format. 45 days prior to expiration of the period of performance.

#7 (Task 5) Provide final report submitted in MS word format. 15 calendar days prior to expiration of the period of performance.

9.0 PAYMENT

Payment shall be made in full, upon approval of 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 (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)

a) 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.

b) 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.