A04_SOW_NCI_SON_ONT_P2solo_integrated.docx

STATEMENT OF NEED (SON)

1.0 TITLE

PromethION 2 Integrated Long-read Seqeuncing Platform

2.0 BACKGROUND

The Center for Cancer Research (CCR) Genomics Core provides state-of-the-art genomics technologies and bioinformatics support to investigators across the National Cancer Institute's intramural research programs. As demand for long-read sequencing continues to increase, Oxford Nanopore Technologies (ONT) has become an essential platform for applications requiring de novo genome assembly, structural variant detection, transcript isoform analysis, epigenetic profiling, metagenomics, and sequencing of complex genomic regions that are difficult to resolve using short-read technologies. The CCR Genomics Core currently operates the Oxford Nanopore PromethION 2 Solo (P2 Solo), which has enabled high-throughput long-read sequencing services supporting a broad range of cancer and biomedical research projects.

While the P2 Solo has successfully met current sequencing needs, it relies on an external high-performance workstation to control the instrument and perform computationally intensive tasks such as real-time basecalling, methylation calling, demultiplexing, and downstream data analysis. Maintaining separate sequencing and computing hardware increases system complexity, requires ongoing information technology support, occupies valuable laboratory space, and introduces potential workflow bottlenecks that can delay data processing and delivery to investigators.

The Oxford Nanopore PromethION 2 Integrated (P2i) addresses these limitations by incorporating high-performance onboard computing and GPU acceleration directly into the sequencing instrument. The integrated architecture enables real-time execution of MinKNOW, Dorado basecalling, modified base detection, and EPI2ME analysis workflows without the need for an external workstation. This streamlined design simplifies instrument deployment and maintenance, reduces hardware dependencies, improves system reliability, and shortens the time from sequencing to analyzed data.

Upgrading the CCR Genomics Core's existing P2 Solo to the PromethION 2 Integrated will improve operational efficiency while maintaining compatibility with existing PromethION flow cells, library preparation methods, and validated sequencing workflows. The enhanced onboard computing capability will enable investigators to receive high-quality sequencing data and preliminary analyses more rapidly, reducing computational barriers to long-read sequencing and increasing the overall throughput and productivity of the Core.

As the demand for long-read sequencing continues to expand across cancer genomics, transcriptomics, epigenomics, and precision oncology research, upgrading to the PromethION 2 Integrated represents a strategic investment in the CCR Genomics Core's infrastructure. The upgrade will strengthen the Core's ability to deliver reliable, high-quality sequencing services, improve turnaround times, reduce operational overhead, and ensure that the facility remains equipped with current technology to support the evolving needs of the National Cancer Institute's intramural research community.

3.0 TYPE OF ORDER

This acquisition will be made as a Firm Fixed-Price Purchase Order.

4.0 SPECIAL ORDER REQUIREMENTS

4.1 Product Features / Salient Characteristics

Salient Features of the Oxford Nanopore PromethION 2 Integrated (P2i)

· Integrated high-performance computing with onboard CPU/GPU eliminates the need for an external workstation.

· Two independently addressable PromethION flow cells for flexible, parallel sequencing.

· Real-time sequencing, basecalling, and data analysis performed directly on the instrument.

· Supports Dorado high-accuracy and super-accuracy basecalling, modified base detection, and demultiplexing.

· Integrated MinKNOW and EPI2ME for streamlined sequencing control and downstream analysis.

· High throughput of up to ~290 Gb per flow cell, depending on sample quality and sequencing chemistry.

· Ultra-long read sequencing for de novo genome assembly, structural variant analysis, transcriptomics, and epigenomics.

· Direct sequencing of native DNA and RNA, enabling detection of epigenetic modifications without additional sample processing.

· Plug-and-play benchtop design with a touchscreen interface, reducing setup time and simplifying operation.

4.2 Delivery and Installation

The Contractor shall deliver and install the system within four to twelve weeks after contract award at the following location:

Liz Conner CCR Genomics Core National Cancer Institute 37 Convent Drive, MSC 4256 Bethesda, MD 20892-4256 Phone: 240-760-7373 Email: liz_conner@nih.gov

4.3 Training

The Contractor shall provide training on the proper use of the equipment, software, and associated workflows for National Cancer Institute researchers at the delivery location. Training shall be conducted within one week of installation and provided by a premium support scientist or other qualified Illumina personnel, with additional training available on an as-needed basis.

1.0 PAYMENT

Payment shall be made once after delivery and installation of equipment, upon government acceptance. Payment authorization requires submission and approval of invoices to the COR and NIH OFM, in accordance with the 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.