75N91024NOI6831928 - SOW.pdf

STATEMENT OF WORK

75N91024NOI6831928 Page 1 of 4

1.0 TITLE

Deep Sequencing Analysis Services to Monitor Copanlisib/Rituximab Combination Treatment

2.0 BACKGROUND

The Lymphoid Malignancies Branch (LyMB) of the Center for Cancer Research at the National Cancer Institute, National Institutes of Health, focuses on the management of aggressive B-cell lymphomas.

Previous clinical studies demonstrated that the drug Copanlisib can slow the growth of follicular lymphoma FL and Non-Hodgkin’s lymphoma NHL through slowing cancer cell growth and triggering their death. The LyMB launched a phase 2 clinical trial (Clinicaltrials.gov identifier NCT03789240; NCI Protocol ID NCI-19-C-0030) to investigate the safety and response rate of Copanlisib/Rituximab combination treatment. Patients are monitored with computed tomography scans and plasma assays for circulating tumor DNA (ctDNA).

2.1.1 OBJECTIVE

The primary objective of this project is to obtain plasma analysis data to investigate the safety and response rate of Copanlisib/Rituximab combination treatment. The Government will share de-identified clinical information (overall survival or recurrence-free survival, treatment, and response, outcomes) with the Contractor. These clinical information data sets will encompass an estimated 64 patients (not all data may be delivered for each patient).

3.0 SCOPE

The scope of the work to be performed encompasses targeted deep sequencing (NovaSeq, x10,000) and bioinformatic analysis of 162 human plasma samples for biomarker identification.

4.0 CONTRACT REQUIREMENTS

All data generated shall be the sole property of the U.S. Government.

Independently and not as an agent of the Government, the Contractor shall provide all labor, materials, and equipment required to perform the following tasks:

4.1.1 TASK 1: PROJECT MANAGEMENT

Within three (3) days of contract award, the Contractor shall provide the NCI’s TPOC with information regarding the Contractors’ Primary Point of Contact and an Alternate for the Primary Point of Contact for all services to be provided in relation to this award. This shall include a meeting to discuss and plan upcoming analysis to be performed, as well as initial annual forecasting. The Contrator shall maintain regular communication with the TPOC throughout the entire period of performance. Communication shall be conducted at a minimum on a bi-weekly basis.

4.1.2 TASK 2: TARGETED DEEP SEQUENCING

The Contractor shall conduct ctDNA targeted deep sequencing Heme (x10,000 coverage), to include:

a. cfDNA extraction from plasma and DNA extraction from peripheral blood lymphocytes/peripheral blood mononuclear cells (PBL/PBMC).

b. QC measurement (concentration of extracted DNA).

c. DNA fragmentation.

d. Library construction.

e. QC measurement (concentration of pre-cap and post-cap, and average size).

f. NovaSeq sequencing (x10,000).

Deliverable:

The Contractor shall provide QC measurement results and sequencing raw data to the Technical Point of Contact (TPOC) immediately upon completion.

75N91024NOI6831928 Page 2 of 4

4.1.3 TASK 3: DATA ANALYSIS

The Contractor shall conduct end-to-end data analysis as follows:

a. Bioinformatics QC measurement; to include:

1. Contamination control.

2. Comprehensive quality assessment of the sequencing data, including metrics like read quality scores, sequencing depth, and alignment rates.

3. Identifying and addressing any technical artifacts or anomalies that may affect data integrity or interpretation.

4. Sample mix up control.

5. cfDNA datasets generation.

b. Bioinformatics calculations of:

1. Single Nucleotide Polymorphisms/Copy Number Variations (SNP/CNV).

2. Microsatellite instability (MSI).

3. Rearrangements, with a targeted Limit Of Detection of 0.1 - 0.2 Variant Allele Frequency

(VAF).

c. Landscape and Integrated multi-omics data analysis of tumor DNA and RNA and blood cfDNA.

d. Machine-learning supported biomarker identification.

Deliverables:

The Contractor shall provide:

• Bioinformatics QC Measurement Report.

• Plots from landscape and Integrated multi-omics data analysis for in-depth data presentation.

• Molecular profiles for each sample/patient, to be correlated with clinical annotations and clinical outcomes.

• Data analysis results in .cvs, .xls, or .vcf format, or another format as agreed upon with the

TPOC.

4.1.4 TASK 4: DELIVER FINAL DATA AND ANALYSIS REPORT

The Contractor shall deliver a final report inclusive of all data points for all samples. The report shall be provided in file format agreed upon with the TPOC.

5.0 PERIOD OF PERFORMANCE

The Period of Performance shall be twelve months.

6.0 GOVERNMENT RESPONSIBILITIES

The Government Technical Point of Contact (TPOC) will coordinate with the Contractor to deliver samples to the Contractor’s facilities. Samples will be shipped no later than 14 calendar days after award.

The Government will be responsible for arranging the shipment of samples to and from the Contractor.

All samples are ready for shipment. Residual samples shall be returned within 6 months following the completion of analysis on dry ice.

7.0 GOVERNMENT FURNISHED INFORMATION

The Government will furnish the clinical data sets to the contractor for correlation with molecular profiles within (3) days of identified need. All data shared, or otherwise generated throughout the duration of this Purchase Order shall remain or become the sole property of the U.S. Government.

8.0 PLACE OF PERFORMANCE

All work shall be performed at the Contractors facilities.

75N91024NOI6831928 Page 3 of 4

9.0 TYPE OF ORDER

This shall be a firm fixed-price purchase order for non-severable services.

10.0 DELIVERABLES AND DELIVERY SCHEDULE

The below table outlines the deliverables which the Contractor is responsible for fulfilling throughout the requirement. All submittals will be submitted electronically to the Technical Point of Contact (TPOC) and individuals identified below for inspection and acceptance.

Item Description Due Date

Inform TPOC by email on Contractors’ Primary Point of Contact and an Alternate for the Primary Point of Contact (see Task #1)

Within three (3) business days of contract award

2 Schedule regular meetings with the NIH TPOC (see Task #1)

Within five (5) business days of contract award

3 QC measurement results and sequencing raw data, to be delivered to the TPOC by email (see Task #2)

Immediately upon completion of targeted deep sequencing

Bioinformatics QC Measurement Report, to be delivered to the TPOC in a format agreed upon by email (see Task #2)

TBD

Plots from landscape and Integrated multi-omics data analysis suitable for in-depth data presentation; to be delivered to the TPOC in a format agreed upon by email (see Task #2)

TBD

Molecular profiles for each sample/patient, to be correlated with clinical annotations and clinical outcomes to be delivered to the TPOC in a format agreed upon by email (see Task #2)

TBD

7 Data analysis results in .cvs, .xls, or .vcf format, or another format as agreed upon with the TPOC TBD

8 Final Report inclusive of all data points for all samples, in a format agreed upon by email (see Task #4) TBD

11.0 TECHNICAL POINT OF CONTACT

The Technical Point of Contact (TPOC) will serve as the Governments primary point of contact for coordination of all required efforts covered under the scope of the purchase order. Additionally, all services shall be delivered to the TPOC for final inspection and acceptance upon completion. All deliverables will have been deemed accepted fifteen (15) calendar days after date of delivery, except as otherwise specified in this purchase order if written approval or disapproval has not been given within such period.

The Technical Point of Contact (TPOC) for this purchase order shall be named upon award.

The TPOC role is limited to the authorities specified herein. The TPOC does not have the authority to issue directions that:

1) Constitutes a change of assignment or additional work outside the statement of work;

2) Constitutes a change as defined in clause 52.212-4 (c) "Changes";

3) In any manner causes an increase or decrease in the purchase order price, or the time required for performance.

4) Changes any of the terms, conditions, or requirements of the purchase order;

75N91024NOI6831928 Page 4 of 4

5) Interferes with the Contractor's right to perform under the terms and conditions of the purchase order; or

6) Directs, supervises, or otherwise controls the actions of the Contractor's employees.

If at any time the Contractor feels that such direction listed above has been given, they must contact the Contracting Officer immediately.

12.0 INSPECTION AND ACCEPTANCE

Pursuant to FAR clause 52.212-4, all work described in the SOW to be delivered under this purchase order is subject to final inspection and acceptance by an authorized representative of the Government. The authorized representative of the Government is the NCI Technical Point of Contact (TPOC) who is responsible for inspection and acceptance of all services, materials, or supplies to be provided by the Contractor.

Regardless of format, all digital content or communications materials produced as a deliverable under this purchase order, shall conform to applicable Section 508 Standards to allow Federal employees and members of the public with disabilities to have access to and use of information and data that is comparable to the access to and use of information and data by Federal employees or by members of the public who are not individuals with disabilities. Remediation of any materials that do not comply with the applicable Section 508 requirements as set forth below, shall be the responsibility of the Contractor.

HHS guidance regarding accessibility of documents can be found at:

https://www.hhs.gov/web/section-508/making-files-accessible/create-accessiblepdfs/index.html.

Federal Government-wide guidance regarding accessibility of documents can be found at https://www.section508.gov/, including the documents describing the preferred method of authoring and testing documents produced in Microsoft Word 2013 or later, Microsoft Excel, and files formatted as

PDF.

All written drafts and final deliverable products shall be submitted as an electronic copy in draft format for review, comment, and approval by the TPOC. Final copies of approved drafts shall be delivered to the TPOC within 3 business days after receipt of the Government’s comments. If requested, final deliverable products shall be submitted in an electronic format. Other quantities and formats may be submitted after prior approval from the TPOC.

All deliverables shall be sent electronically as; Microsoft Excel 2013, Microsoft Excel, or Adobe Portable Document Format (PFD), unless otherwise approved by the TPOC.

4.1.4 TASK 4: DELIVER FINAL DATA AND ANALYSIS REPORT