RFQ-FDA-133845-133915.pdf

ALP: HFP-133845-133915

Four (4) each Genomic Sequencing Systems

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COMBINED SYNOPSIS/SOLICITATION

1. INTRODUCTION

This is a combined synopsis/solicitation for commercial products or commercial services prepared in accordance with part 12. This announcement constitutes the only solicitation. Offers are being requested and a separate written solicitation will not be issued.

Solicitation number RFQ-FDA-133845-133915 is issued as a/an RFQ for Genomic sequencing systems.

This acquisition is not set-aside for small business concerns.

Set-Aside: ☒ None ☐ Total Small Business ☐ WOSB ☐ SDVOSB ☐ 8(a) ☐ HUBZone

☐ Other:

NAICS Code: 334516 Small Business Size Standard: 1,000 Employees

This solicitation incorporates provisions and clauses by reference. The full text of provisions and clauses may be accessed electronically at: https://acquisition.gov/ | https://acquisition.gov/far-overhaul | https://acquisition.gov/hhsar

All responsible sources may submit a quotation, which will be considered by the agency.

2. DESCRIPTION OF REQUIREMENTS

This acquisition is restricted to brand name or equal: Illumina MiSeq i100 Plus and Illumina DRAGENTM Bio-IT Platform because these systems will replace aging sequencers currently owned by the FDA. FDA needs continuity of maintaining the same sequencing methods, proprietary flow cells and reagents or equal, software licenses, and manufacturer-supported components necessary to operate mission driven project continuity.

2.1 Purpose

The purpose of this procurement is to acquire four (4) Illumina MiSeq i100 Plus desktop genomic sequencing systems to support the FDA’s Human Foods Program (HFP). These systems will replace aging sequencers currently in use and enable high-throughput, cost-effective, and rapid sequencing critical for food safety surveillance, regulatory compliance, and the development of novel genomic applications. The acquisition directly supports FDA's mission to enhance public health through timely detection and characterization of foodborne pathogens in regulated products.

2.2 Objectives

The acquisition of the MiSeq i100 Plus systems will fulfill the following key objectives:

• Modernize Sequencing Capacity: Replace outdated equipment with newer platforms that reduce runtime by >50% and sequencing cost-per-sample by approximately 66%.

• Support Method Development: Enable the development and optimization of advanced sequencing applications including targeted amplicon sequencing, metagenomics, RFQ-FDA-133845-133915

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• Enhance Response Capabilities: Provide rapid, high-resolution data for time-sensitive regulatory and outbreak investigations across a range of food and environmental samples.

• Improve Operational Efficiency: Leverage on-instrument data processing and room-temperature-stable reagents to streamline workflows and reduce operational overhead.

• Facilitate Technology Transfer: Ensure compatibility with emerging GenomeTrakr platforms to accelerate deployment of validated sequencing protocols across FDA field laboratories.

2.3 Specific Tasks

Task 1: Equipment Purchase The Contractor shall indicate if the minimum salient characteristics and specifications have been met to be considered responsive for this requirement This requirements section covers the shipping, installation, warranty and training on four(4) new systems: Illumina MiSeq i100 Plus sequencing systems or equal. The following required minimum components and Salient Characteristics are required:

a. Single instrument that performs whole genome sequencing of bacterial and viral organisms

b. Instrument is small enough to fit on a laboratory benchtop: maximum dimension of

24”W x 28”D x 30.1”H

c. Includes an embedded computer and data analysis software capable of data collection and data analysis

d. Offers different flow cell sizes ranging from 5M to 100M

e. Ability to produce read lengths between 2 x 150 base pairs (bp) and 2 x 500 base pairs

f. Ability to perform a sequencing run in less than 24 hours

g. Ability to produce up to 100 million single-end reads per run

h. Data output range of up to 30 gigabytes per run

i. Readily available reagent kits for library preparation and sequencing

j. Embedded touchscreen monitor

k. On-instrument computer with integrated control software

l. Hardware-accelerated DRAGEN Bio-IT secondary analysis pipeline or equal

m. Manufacturer-provided 12-month warranty (parts and labor)

n. All reagents and accessories required for initial operation

Task 2: Equipment Delivery and Installation

a. Coordinate delivery of one unit to each of the following locations:

b. FDA CPK1 Facility (College Park, MD)

c. FDA MOD1 Facility (Laurel, MD)

d. FDA Moffett Facility (Bedford Park, IL)

e. FDA Gulf Coast Seafood Lab (Dauphin Island, AL)

f. Ensure full installation by certified technical personnel from the manufacturer at each site.

Task 3: System Verification and Personnel Training

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a. Conduct system validation and performance testing using both manufacturer-provided and FDA-prepared samples.

b. Provide hands-on training to 5–8 designated FDA researchers at each site, covering:

c. Instrument operation, routine maintenance, and the use of the onboard software for sample processing and data retrieval.

d. Sample preparation workflows

e. Data output and analysis using built-in software pipelines

f. Project Milestones

Deliverable Deliverable Description

Quantity Format

1 Illumina MiSeq i100Plus desktop sequencing system (unopened)

4 units Physical Delivery

2 On-site installation of system at CPK1 facility

1 install On-site installation

3 On-site installation of system at MOD1 facility

1 install On-site installation

4 On-Site installation of system at Moffett facility

1 install On-site installation

5 On-Site installation of system at FDA Gulf Coast Seafood Lab

1 install On-site installation

6 System verification and researcher training at each site

4 sessions In-person, documented

2.4 Deliverables

a. The contractor shall provide and install fully functional Illumina MiSeq i100 Plus desktop sequencing systems, one at each designated FDA facility. These systems must include all standard components and meet the specifications outlined under Task 1. Deliverables also include comprehensive system training and validation support for designated FDA personnel.

b. Each sequencing system must include:

o Embedded touchscreen monitor o On-instrument computer with integrated control software o Pre-installed DRAGEN Bio-IT secondary analysis pipelines or equal o Initial reagent kits for system verification o 12-month comprehensive warranty (parts and labor)

c. In addition to equipment delivery, the contractor shall perform the following:

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FDA OAGS — Supplies | Page 4 o On-site installation o System testing and validation using both manufacturer and FDA-provided samples o In-person training for 5–8 FDA staff per site on system operation, maintenance, and data analysis workflows

2.5 Government-Furnished Property, Material, Equipment, or Information (GFP, GFM, GFE, or GFI) The FDA team will provide space and logistics, like power supply for installation. The installation must be carried out by the manufacturer’s team. For verification, the FDA team will provide samples in the required format

2.6 Contractor Provided Special Material Requirements

The manufacturer must provide all reagents required for testing the installation and for verifying the operation of the system. The manufacturer must work with own samples and samples provided by the FDA team.

2.7 Security

The FDA team will name a few scientists including the POC to escort the manufacturer’s team coming into the building for installation, testing and verification for all the duration of these tasks.

2.8 Travel

Included in the handling charges quoted.

2.9 Other Considerations

IT Purchasing Requirements

Information Technology and Security Requirements

This procurement involves acquisition of FDA-approved desktop sequencing equipment and associated software that will interface with internal networks for data processing and analysis.

Therefore, all IT components must comply with HHS and FDA information security and privacy policies.

1. Baseline Security Compliance

• The contractor shall ensure that all hardware, firmware, and software included with the MiSeq i100Plus systems meet FDA and HHS standards for information system security.

• Systems must protect the confidentiality, integrity, and availability of FDA information in accordance with FIPS 199, NIST SP 800-53, and other applicable regulations.

2. Security Categorization

Based on coordination with the FDA Information System Security Officer (ISSO), the information processed by this equipment is categorized as follows:

• Confidentiality: Low

• Integrity: Low

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• Availability: Low

• Overall Impact Level: Low

3. FDA IT Pre-Approval

Prior to award, all hardware and software must be submitted for approval by the FDA Chief Information Officer (CIO) in accordance with HHS acquisition policies. The vendor must provide:

• Manufacturer name

• Model and nomenclature of hardware

• Software version(s) and licensing details

Items not approved by the CIO must be replaced with compliant alternatives, subject to the same approval process.

4. Privacy and Data Protection

• No Personally Identifiable Information (PII) will be processed by the equipment under this contract.

• Contractor personnel with physical or logical access to FDA systems or facilities must complete background investigations and sign non-disclosure agreements as required.

5. Installation Access and Escort

Contractor personnel entering FDA facilities for installation and training shall be escorted at all times by FDA-designated staff. Contractors shall comply with all facility access protocols, including security screenings and visitor logs.

Option Year Maintenance Agreement

Following expiration of the base warranty, the contractor shall provide a preventative maintenance service agreement for up to four (4) option years, exercisable one year at a time at the Government's discretion. The total contract duration, including the base warranty period and all option years, shall not exceed five (5) years.

Each option year maintenance agreement shall provide coverage equivalent to the base warranty terms, plus one (1) preventative maintenance site visit per instrument per year at each designated FDA facility. The PM visit shall include all travel, labor, and parts at no additional charge, and shall encompass routine preventative maintenance, calibration, electrical safety testing, and any other preventative maintenance measures deemed necessary by the contractor.

The PM visit shall include all consumables and reagents necessary to perform preventative maintenance at no additional charge to the Government

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3. LINE ITEMS

CLIN Description Qty Unit Unit Price Total Price

0001 Illumina MiSeq i100 Plus sequencing systems with 1 year standard warranty

4 each

0002 Shipment, 1 per site 4 each

0003 On-site installation of system, 1 per location

4 each

0004 System verification and researcher training, 1 per site

4 each

0005 Option Year 1, Preventative Maintenance Service per system x 4 systems

Agreement-12 months

1 year

0006 Option Year 2, Preventative Maintenance Service per system x 4 systems Agreement-12 months

1 year

0007 Option Year 3, Preventative Maintenance Service per system x 4 systems Agreement-12 months

1 year

0008 Option Year 4, Preventative Maintenance Service per system x 4 systems Agreement-12 months

1 year

4. DELIVERY AND PERFORMANCE

Place of Delivery / Place of Performance:

Delivery Locations:

• CPK1 Facility – 5001 Campus Dr., College Park, MD 20740

• MOD1 Facility – 8301 Muirkirk Rd., Laurel, MD 20708

• Moffett Facility- 6502 S. Archer Rd., Bedford Park, IL 60501

• FDA Gulf Coast Seafood Lab -1 Iberville Drive, Dauphin Island, AL 36528

• The delivery must be during regular business hours (Monday-Friday) during the times of 8:00 AM – 4:00 PM, excluding holidays.

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FOB Point: Destination

Inspection and Acceptance: Inspection and acceptance shall be performed at the delivery location in accordance with the terms of clause 52.212-4.

Period of Performance

Supplies: Delivery Timeframe + Warranty

Delivery shall be completed within 6 weeks of award. The delivered items shall include a one (1) year warranty. The warranty period begins on the date of Government acceptance under the inspection and acceptance clause(s) of this contract.

Following Government acceptance, the Contracting Officer will issue an administrative modification under RFO 43.203(b)(1) and 43.201 to memorialize the period of performance dates, anchored to the Government acceptance date. The modification does not change scope, price, or any other substantive term. The Contractor's written confirmation of the installation completion date supports inspection and acceptance scheduling; it does not establish the period of performance.

Base Period: Contract Award date through Warranty End date

Option Period 1: 12 Months

Option Period 2: 12 Months

Option Period 3: 12 Months

Option Period 4: 12 Months

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5. CONTRACT CLAUSES

5A. Clauses Incorporated by Reference

Appl. Clause/Prov.

No.

Title Date

REQ

52.212-4 Terms and Conditions—Commercial Products and

Commercial Services Nov 2025

REQ 52.204-13 System for Award Management—Maintenance Nov 2025

REQ 52.204-91 Contractor Identification Nov 2025

REQ

52.209-6 Protecting the Government's Interest When

Subcontracting with Contractors Debarred, Suspended, or Proposed for Debarment

Nov 2025

REQ

52.209-10 Prohibition on Contracting with Inverted Domestic

Corporations Nov 2025

REQ 52.222-3 Convict Labor Nov 2025

REQ

52.222-19 Child Labor—Cooperation with Authorities and

Remedies Nov 2025

REQ 52.222-35 Equal Opportunity for Veterans (or with Alt I) Nov 2025

REQ

52.222-36 Equal Opportunity for Workers with Disabilities (or with

Alt I) Nov 2025

REQ 52.222-37 Employment Reports on Veterans Nov 2025

REQ

52.222-40 Notification of Employee Rights Under the National

Labor Relations Act Nov 2025

REQ 52.222-50 Combating Trafficking in Persons (or with Alt I) Nov 2025

REQ 52.222-90 Addressing DEI Discrimination by Federal Contractors May 2026

REQ 52.222-54 Employment Eligibility Verification Nov 2025

REQ 52.223-23 Sustainable Products and Services Nov 2025

REQ

52.226-8 Encouraging Contractor Policies to Ban Text Messaging

While Driving May 2024

REQ

52.232-33 Payment by Electronic Funds Transfer—System for

Award Management Oct 2018

REQ 52.233-3 Protest After Award Nov 2025

REQ 52.233-4 Applicable Law for Breach of Contract Claim Nov 2025

REQ

52.240-93 Basic Safeguarding of Covered Contractor Information

Systems Nov 2025

REQ

52.244-6 Subcontracts for Commercial Products and Commercial

Services Nov 2025

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Appl. Clause/Prov.

No.

Title Date

REQ 52.225-1 Buy American—Supplies (or with Alt I) Nov 2025

REQ

52.225-3 Buy American—Free Trade Agreements—Israeli Trade

Act (or applicable Alternate) Nov 2025

REQ 52.225-5 Trade Agreements Nov 2023

REQ

Part 27 clauses

As applicable — rights in technical data or computer software (see RFO FAR 12.106, 12.107)

See Part 27

REQ

HHSAR

352.232-71

Electronic Submission of Payment Requests Feb 2022

5B. Clauses Incorporated by Full Text

52.252-2, Clauses Incorporated by Reference (Feb 1998)

This contract incorporates one or more clauses by reference, with the same force and effect as if they were given in full text. Upon request, the Contracting Officer will make their full text available. Also, the full text of a clause may be accessed electronically at this/these address(es):

https://acquisition.gov https://acquisition.gov/far-overhaul https://acquisition.gov/hhsar

(End of clause)

52.217-9 Option to Extend the Term of the Contract (Mar 2000)

(a) The Government may extend the term of this contract by written notice to the Contractor any time prior to contract expiration; provided that the Government gives the Contractor a preliminary written notice of its intent to extend at any time before the contract expires. The preliminary notice does not commit the Government to an extension.

(b) If the Government exercises this option, the extended contract shall be considered to include this option clause.

(c) The total duration of this contract, including the exercise of any options under this clause, shall not exceed 5 years.

FDA Electronic Invoicing and Payment Requirements — Invoice Processing Platform (IPP) (Jan 2022)

a. All Invoice submissions for goods and or services must be made electronically through the U.S. Department of Treasury's Invoice Processing Platform System (IPP). http://www.ipp.gov/vendors/index.htm http://www.ipp.gov/vendors/index.htm

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b. Invoice Submission for Payment means any request for contract financing payment or invoice payment by the Contractor. To constitute a proper invoice, 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, or the clause 52.212-4 Contract Terms and Conditions - Commercial Items included in commercial items contracts. The IPP website address is: https://www.ipp.gov c.

1. The Agency will enroll the Contractors new to IPP. The Contractor must follow the IPP registration email instructions for enrollment to register the Collector Account for submitting invoice requests for payment. The Contractor Government Business Point of Contact (as listed in SAM) will receive Registration email from the Federal Reserve Bank of St. Louis (FRBSTL) within 3 - 5 business days of the contract award for new contracts or date of modification for existing contracts.

2. Registration emails are sent via email from ipp.noreply@mail.eroc.twai.gov. Contractor assistance with enrollment can be obtained by contacting the IPP Production Helpdesk via email to IPPCustomerSupport@fiscal.treasury.gov or phone (866) 973-3131.

3. The Contractor POC will receive two emails from IPP Customer Support, the first email contains the initial administrative IPP User ID. The second email, sent within 24 hours of receipt of the first email, contains a temporary password. You must log in with the temporary password within 30 days.

4. If your company is already registered to use IPP, you will not be required to re-register.

5. If the Contractor is unable to comply with the requirement to use IPP for submitting invoices for payment as authorized by HHSAR 332.7002, a written request must be submitted to the Contracting Officer to explain the circumstances that require the authorization of alternate payment procedures.

d. Invoices that include time and materials or labor hours Line Items must include supporting documentation to (1) substantiate the number of labor hours invoiced for each labor category, and (2) substantiate material costs incurred (when applicable).

e. Invoices that include cost-reimbursement Line Items must be submitted in a format showing expenditures for that month, as well as contract cumulative amounts. At a minimum the following cost information shall be included, in addition to supporting documentation to substantiate costs incurred.

1. Direct Labor - include all persons, listing the person's name, title, number of hours worked, hourly rate, the total cost per person and a total amount for this category;

2. Indirect Costs (i.e., Fringe Benefits, Overhead, General and Administrative, Other Indirects)- show rate, base and total amount;

3. Consultants (if applicable) - include the name, number of days or hours worked, daily or hourly rate, and a total amount per consultant;

4. Travel - include for each airplane or train trip taken the name of the traveler, date of travel, destination, the transportation costs including ground transportation shown separately and the per diem costs. Other travel costs shall also be listed;

5. Subcontractors (if applicable) - include, for each subcontractor, the same data as required for the prime Contractor;

6. Other Direct Costs - include a listing of all other direct charges to the contract, i.e., office supplies, telephone, duplication, postage; and

7. Fee - amount as allowable in accordance with the Schedule and FAR 52.216-8 if applicable.

https://www.ipp.gov/

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f. Contractor is required to attach an invoice log addendum to each invoice which shall include, at a minimum, the following information for contract administration and reconciliation purposes:

(1) list of all invoices submitted to date under the subject award, including the following:

(i.) invoice number, amount, & date submitted (ii.) corresponding payment amount & date received

(2) total amount of all payments received to date under the subject contract or order

(3) and, for definitized contracts or orders only, total estimated amounts yet to be invoiced for the current, active period of performance.

g. Payment of invoices will be made based upon acceptance by the Government of the entire task or the tangible product deliverable(s) invoiced. Payments shall be based on the Government certifying that satisfactory services were provided, and the Contractor has certified that labor charges are accurate.

h. If the services are rejected for failure to conform to the technical requirements of the Delivery Order, or any other contractually legitimate reason, the Contractor shall not be paid, or shall be paid an amount negotiated by the CO.

i. Payment to the Contractor will not be made for temporary work stoppage due to circumstances beyond the control of U.S. Food and Drug Administration such as acts of God, inclement weather, power outages, and results thereof, or temporary closings of facilities at which Contractor personnel are performing. This may, however, be justification for excusable delays.

j. The Contractor agrees that the submission of an invoice to the Government for payment is a certification that the services for which the Government is being billed, have been delivered in accordance with the hours shown on the invoices, and the services are of the quality required for timely and successful completion of the effort.

k. Questions regarding invoice payments that cannot be resolved by the IPP Helpdesk should be directed to the FDA Employee Resource and Information Center (ERIC) Helpdesk at 301- 827-ERIC (3742) or toll-free 866-807-ERIC (3742); or, by email at ERIC@fda.hhs.gov. Refer to the Call-in menu options and follow the phone prompts to dial the option that corresponds to the service that's needed. All ERIC Service Now Tickets will either be responded to or resolved within 48 hours (2 business days) of being received. When emailing, please be sure to include the contract number, invoice number and date of invoice, as well as your name, phone number, and a detailed description of the issue.

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6. SOLICITATION PROVISIONS

6A. Provisions Incorporated by Reference

52.252-1 Solicitation Provisions Incorporated by Reference. (Feb 1998)

This solicitation incorporates one or more solicitation provisions by reference, with the same force and effect as if they were given in full text. Upon request, the Contracting Officer will make their full text available. The offeror is cautioned that the listed provisions may include blocks that must be completed by the offeror and submitted with its quotation or offer. In lieu of submitting the full text of those provisions, the offeror may identify the provision by paragraph identifier and provide the appropriate information with its quotation or offer. Also, the full text of a solicitation provision may be accessed electronically at this/these address(es):

https://www.acquisition.gov/far-overhaul

Appl. Clause/Prov.

No.

Title Date

REQ 52.204-7 System for Award Management—Registration Nov 2025

REQ

52.212-1 Instructions to Offerors—Commercial Products and

Commercial Services Nov 2025

REQ

52.212-2 Evaluation—Commercial Products and Commercial

Services (if applicable) Nov 2025

REQ

52.203-18 Prohibition on Contracting with Entities that Require

Certain Internal Confidentiality Agreements— Representation

Jan 2017

REQ 52.209-12 Certification Regarding Tax Matters Oct 2025

REQ 52.225-2 Buy American Certificate Oct 2022

REQ 52.225-6 Trade Agreements Certificate Feb 2021

REQ

52.240-90 Security Prohibitions and Exclusions—Representations and Certifications Nov 2025

Basis for Award

Lowest Price Technically Acceptable (LPTA): Award will be made to the lowest-priced offeror whose offer is determined technically acceptable. Technical acceptability will be determined on a pass/fail basis against the salient characteristics and minimum requirements of the requirement. Offers that do not meet all salient characteristics will be determined technically unacceptable and will not be considered for award. Price will be evaluated for reasonableness.

6B. Addenda to 52.212-1

Offer Acceptance Period (if applicable):

Paragraph (b) of the provision is hereby amended to extend the period for acceptance of offers from 60 calendar days to 90 calendar days from the date specified for receipt of offers.

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7. OFFER SUBMISSION AND POINTS OF CONTACT

Questions Due: Questions regarding this solicitation shall be submitted in writing to the Primary POC identified in the SAM.gov notice June 18, 2026 at 10AM. Questions and answers may be posted as an amendment to this solicitation on SAM.gov.

Offers Due: As listed on the SAM.gov notice.

Submission Method: Email to the POCs listed in the SAM.gov posting.

Preferred File Format: Searchable PDF and Excel

Offerors Shall Submit:

• Technical quotation

• Price quotation

• Warranty terms (if applicable)

• UEI and confirmation of active SAM.gov registration

• Lead time for delivery

• Country of origin for all items required if Buy American (52.225-1) or Trade Agreements (52.225-5) clause applies.

Points of Contact

As listed on the SAM.gov notice.

8. ADDITIONAL INFORMATION

Amendments:

Any amendments to this solicitation will be posted to SAM.gov. It is the offeror's responsibility to monitor SAM.gov for any amendments.