SOW_GeneExpressionServices_NOI Draft.pdf

STATEMENT OF WORK

1.0 TITLE

Custom 10x Genomics Visium/Space Ranger Spatial Transcriptomics Analysis Services in HIV- Related Malignancies.

2.0 BACKGROUND

The Department of Health and Human Services (HHS), National Institutes of Health (NIH), National Cancer Institute (NCI), Center for Cancer Research (CCR), HIV and AIDS Malignancy Branch (HAMB) conducts research in AIDS-related malignancies, HIV disease, viral-induced tumors, and related diseases. HAMB requires custom spatial gene expression services, i.e., the mapping of the whole transcriptome and custom Ribonucleic Acid (RNA) in its morphological context, on formalin-fixed, paraffin-embedded (FFPE) tissue samples to study specific viral infections and associated diseases in patient biopsies.

2.1 OBJECTIVE

The primary objective of this project is to obtain spatial profiling services of the whole transcriptome from twenty-four (24) de-identified FFPE tissue samples on twelve (12) slides through the 10X Genomics Visium CytAssist workflow and 10X Genomics Space Ranger data analysis tool. The work flow includes custom probes provided by HAMB.

3.0 SCOPE

The Contractor shall provide all labor, materials, and equipment required to perform the required tasks described in section 4.0 below. The Contractor shall include histological hematoxylin and eosin (H&E) staining and brightfield imaging; followed by the Visium CytAssist workflow, to include HAMB custom probes, for library preparation and sequencing, and 10x Genomics Space Ranger data processing/analysis services. All data shall be coded and shall not contain any personally identifiable information (PII). Shipping costs for biological samples shall not be included and paid for by NCI separately. Shipping shall be coordinated with NCI using FedEx.

4.0 CONTRACT REQUIREMENTS

The following taks are required for this purchase order:

4.1 The Contractor shall receive the designated sample slides from the Government.

4.1.1 The Government shall section FFPE tissues from 24 biopsy samples onto twelve

(12) plain glass slides.

4.1.2 The Governemnt shall ship the slides in up to four individual shipments, via FedEx, within 30 days upon award to the Contractor for further processing.

4.1.2 The Governemnt shall ship custom probes to the Contractor which shall be included in the workflow.

4.1.3 The Government shall ship custom primers to be included into the workflow as appropriate.

4.2 The Contractor shall acknowledge receipt of each shipment from the Government.

4.3 Upon receipt of samples on slides from the Government, the Contractor shall conduct standard histological workflow; to include deparaffinization, H&E staining, and brightfield microscope imaging.

4.4 The Contractor shall permeabilize the tissues for probe hybridization/barcoding for whole transcriptome gene expression profiling (approximately 18,000 targets).

4.5 The Contractor shall capture all RNA, and construct 10x Genomics Visium libraries.

4.6 The Contractor shall sequence the libraries, using existing short-read sequencer, 300-cycle, on Illumina NovaSeq X.

4.7 The Contractor shall use the sequencing files and images to analyze the data with 10X

Genomics Space Ranger analysis tools.

4.8 When the final deliverable is received and accepted by NCI TPOC, the Contractor shall destroy any residual samples within 6 months following the completion of analysis.

5.0 TYPE OF ORDER

This shall be a firm fixed-price purchase order.

6.0 PERIOD OF PERFORMANCE

The Period of Performance shall be for twelve (12) months from the date of Award.

7.0 PLACE OF PERFORMANCE

All work shall be performed at the Contractor’s facilities.

8.0 DELIVERABLES AND DELIVERY SCHEDULE

All written deliverables shall be sent electronically to the NCI Technical Point of Contact (TPOC), TBD at Award, via Microsoft (MS) Word or PDF format, unless approved by the TPOC. The TPOC shall review the contents of all draft deliverables. If no comments or requests for revisions are provided to the Contractor within 30 business days, the deliverables shall be considered acceptable. If revisions are required, the TPOC shall respond to the Contractor within five (5) business days of receiving the deliverable, specifying the required changes/revisions. Final copies of approved drafts shall be delivered to the NCI TPOC within five (5) business days after receipt of the Government’s comments.

The Technical Point of Contact (TPOC) is:

TBD at Award

All deliverables shall be provided in accordance with the following deliverable schedule:

DELIVERABLE DELIVERABLE DESCRIPTION / FORMAT

REQUIREMENTS DUE DATE

#1 (Task 4.2) Acknowledge receipt of each shipment via email to the NCI TPOC

Within 24 hours of receipt

High resolution images of the samples, to be submitted in .tiff file format

Within 100 business days of award

Raw sequencing data of the samples, to be submitted in FASTQ file format

Within 100 business days of award

(Task 4.7) Space Ranger spatial gene expression analysis data for the samples, to be made available via a secured web link in .cloupe file format

Within 100 business days of award

(Task 4.8) Destroy residual samples Within 6 months of completing all analysis

The Government shall have unlimited rights to and ownership of all deliverables provided under this procurement including reports, analyses, recommendations, briefings, work plans, created SOPs and all other deliverables. In addition, it includes any additional deliverables required by contract change. The definition of “unlimited rights” is contained in Federal Acquisition Regulation (FAR) 27.401, “Definitions.” FAR clause 52.227-14, “Rights in Data-General,” is hereby incorporated by reference and shall be made a part of any resulting contract/order.

9.0 INSPECTION AND ACCEPTANCE

Pursuant to FAR clause 52.212-4, all work described in the Statement of Work (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 NCCIH 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/accessibility-checklists/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.

10.0 PAYMENT

Payment shall be made monthly in arears. Payment authorization requires submission and approval of invoices to the NCCIH TPOC 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:

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 considered 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.

https://www.hhs.gov/web/section-508/accessibility-checklists/index.html https://www.section508.gov/

7. Unique Entity Identifier (UEI) which is in the System for Award Management (SAM) and replaces the Dun & Bradstreet Data Universal Numbering System (DUNS) number.

8. Federal Taxpayer Identification Number (TIN). In those rare cases where a contractor does not have a UEI 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.

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.

B. The Contractor shall submit invoices to the Department of Treasury’s Invoice Processing Platform (IPP) at https://www.ipp.gov with a copy to the approving official, as directed below.

The Contractor shall submit a copy of the electronic invoice to the following NCI TPOC:

Name- TBD at Award Email Address- TBD at Award

For inquiries regarding the status of invoices, contact OFM Customer Service via email at ofm_customer_service@mail-cmp.niceincontact.com or via phone at 301-496-6088. To send your inquiries via other available communication methods refer to the OFM Customer Service website at https://ofm.od.nih.gov/Pages/Customer-Service.aspx.

Note: The OFM Customer Service is open Eastern Standard Time Monday – Friday from 8:30 a.m. to 5:00 p.m. and is closed between 12:00 p.m. to 1:00 p.m.

II. Invoice Payment https://www.ipp.gov/

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 (November 2021)

(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.

(c) Include the substance of this clause, including this paragraph (c), in all subcontracts with small business concerns, including subcontracts with small business concerns for the acquisition of commercial products or commercial services.

V. HHSAR 352.232-71 Electronic Submission of Payment Requests (February 2, 2022)

(a) Definitions. As used in this clause— Payment request means a bill, voucher, invoice, or request for contract financing payment with associated supporting documentation. The payment request must comply with the requirements identified in FAR 32.905(b), ‘‘Content of Invoices’’ and the applicable Payment clause included in this contract.

(b) Except as provided in paragraph (c) of this clause, the Contractor shall submit payment requests electronically using the Department of Treasury Invoice Processing Platform (IPP) or successor system. Information regarding IPP, including IPP Customer Support contact information, is available at www.ipp.gov or any successor site.

(c) The Contractor may submit payment requests using other than IPP only when the Contracting Officer authorizes alternate procedures in writing in accordance with HHS procedures.

(d) If alternate payment procedures are authorized, the Contractor shall include a copy of the Contracting Officer’s written authorization with each payment request.