Sole Source Justification Form signed 1 Illumina Equipment Carbondale SS 68500005N.pdf

Sole Source Justification Form

Version 7.01 Page 1 of 11

Bulletin Reference Number Open Market Bid 26-482DPH-OFCDI-B-49133

Requesting Agency/University Illinois Department of Pulic Health

Sole Source Justification Form - Part I Section I - General Information

Department/Bureau/Section: Office of Disease Control / Bureau of Testing / Division of Laboratories

Need Identified Date: Jun 26, 2025 Supply/Service Need By Date: Oct 1, 2025

Project Title: Sole Source Purchase of Illumina MiSeq i100 Plus Systems for the Illinois Department of Public Health Division of Laboratories

Vendor: Illumina, Inc.

Provide a description of the supplies or services required:

The Illinois Department of Public Health Division of Laboratories (IDPH-DOL) requires the purchase of two (2) Illumina MiSeq i100 Plus Sequencing Systems and their accompanying 12-month Silver Support Plans. One system will be installed at the Springfield laboratory and one at the Carbondale laboratory.

The MiSeq i100 Plus is a compact next-generation sequencing platform that provides a complete “sample-to-answer” solution, integrating sequencing with primary and secondary data analysis. These systems are essential to meet the Division’s public health mission, including:

• Whole-genome sequencing for disease outbreak investigations (bacterial, viral, and other pathogens).

• Surveillance of respiratory viruses and emerging infectious diseases.

• Newborn screening for critical disorders such as Severe Combined Immunodeficiency (SCID).

• Clinical and public health assays that are validated only for Illumina platforms (e.g., Trusight Cystic Fibrosis Assay).

The instrument purchase includes a one-year service plan. To ensure uninterrupted operations in the second year and beyond, the accompanying Silver Support Plans are required. These plans provide certified preventative maintenance, service, software updates, and access to Illumina’s trained engineers. These services can only be provided directly by Illumina, the sole manufacturer and authorized service provider for MiSeq systems.

Value: Actual Value of Initial Term, this Change Order or Amendment: 221,408.64

Will this Sole Source amend a Professional or Artistic Services contract? Yes No

*Sole Source may not be used for amendments for Professional or Artistic Services if the amendment would increase the value by more than 5% of the initial award or extend the term by more than 60 days.

Type: New Sole Source

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Bulletin Reference Number Open Market Bid 26-482DPH-OFCDI-B-49133

Requesting Agency/University Illinois Department of Pulic Health

Section II - Proposed Term

One-Time Purchase Term Contract

Estimated Contract Begin Date: Nov 1, 2025

Estimated Contract End Date: Oct 31, 2027

Number of Potential Renewals: 0

Length of Each Renewal in Months: 0

Total Value of All Renewals: 0

If a Term Contract, does the term, including renewals, exceed 12 months? Yes No

If yes, provide a detailed justification including any economic benefit received for agreeing to a multi-year term:

The instrument purchase includes an initial 12-month service plan. By proactively purchasing an additional year of the Silver Support Plan now, IDPH-DOL is securing a valuable extension of these benefits to cover the second year of the procurement. This investment ensures continuous, timely maintenance and certified repairs, which are critical for preventing unexpected and costly downtime. By maintaining warranty compliance and extending the instrument's operational life, IDPH-DOL is protecting the State's investment and ensuring long-term value. Furthermore, the vendor is offering a 5% discount for each 12-month service plan purchased along with the instrument, making this a sound economic decision that minimizes risk and maximizes the instrument's return on investment.

Section III - Funding Source Select the type of funding to be used (Check all that apply): State Appropriate Funds Federal Funds Other (Explain):

Section IV - Sole Source Justification

This purchase is economically only available from a single source primarily because it is: (If "Other" explain in one sentence)

Items are Copyrighted or Patented and the Items are Only Available from the Holder

Are there secondary justification(s) for this sole source? Yes No

Section V - Purchase History

Has the Agency or University Purchased these supplies or services in the past? Yes No

Section VI - Business Rationale

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Bulletin Reference Number Open Market Bid 26-482DPH-OFCDI-B-49133

Requesting Agency/University Illinois Department of Pulic Health

1. Provide a detailed explanation of the need for the supplies or services:

The Illinois Department of Public Health Division of Laboratories (IDPH-DOL) is acquiring two (2) Illumina MiSeq i100 Plus Systems and the accompanying 12-month Silver Support Plans to replace aging sequencing instruments currently in use at the Springfield and Carbondale laboratories. This upgrade is essential for modernizing the laboratories’ sequencing capabilities and ensuring that IDPH- DOL can continue to effectively fulfill the core public health mission.

Why the Upgrade is Necessary: The MiSeq i100 Plus offers substantial operational and technical improvements compared to older sequencing platforms. Key advantages include:

• 50% reduction in per-user operating costs, resulting in more efficient use of public resources.

• Faster run times, which shorten turnaround time for critical sequencing data.

• Increased sample throughput, allowing laboratories to process more samples in less time.

• A complete “sample-to-answer” solution that integrates sequencing with both primary and secondary data analysis, streamlining workflows and reducing the need for external analysis tools.

These improvements will allow IDPH-DOL to provide faster, more reliable, and more cost-effective testing services.

Impact on Public Health.

The MiSeq i100 Plus systems are critical to the Illinois Department of Public Health's programs and will directly support:

• Outbreak Investigations: Whole-genome sequencing (WGS) will be used to rapidly identify sources of foodborne, waterborne, and healthcare-associated outbreaks. Faster sequencing data will enable quicker public health responses, reducing illness and preventing further spread.

• Newborn Screening: The systems will be used for genetic testing of newborns, including screening for Severe Combined Immunodeficiency (SCID) and other life-threatening disorders. Early detection allows for timely medical interventions that can save lives.

• Infectious Disease Surveillance: The systems will be applied to ongoing monitoring of respiratory viruses, including influenza and SARS-CoV-2. This is essential for tracking viral evolution, understanding transmission dynamics, and informing vaccine development and deployment strategies.

CDC Programmatic and Regulatory Requirements: The purchase of Illumina systems is not optional, but mandated by federal program requirements:

• The CDC PulseNet program, a national surveillance network for foodborne disease outbreaks, requires the use of Illumina sequencing platforms to ensure standardized, interoperable, and high-quality data submission across all participating laboratories.

• The PulseNet Standard Operating Procedure (PNL35, Ver. 05) explicitly requires Illumina® DNA Prep kits for library preparation and Illumina platforms for sequencing. This SOP ensures that all participating labs produce data that is directly comparable and accepted into the national PulseNet database.

• Specific clinical assays, such as the TruSight Cystic Fibrosis Assay, are FDA-cleared and validated only on Illumina sequencing systems, meaning alternative instruments cannot legally or scientifically substitute for these tests.

By upgrading to the Illumina MiSeq i100 Plus, IDPH-DOL will remain compliant with CDC-mandated protocols, maintain its standing as a certified PulseNet laboratory, and continue to contribute standardized genomic data to national surveillance efforts. Without these instruments, IDPH-DOL would be unable to participate fully in PulseNet, jeopardizing outbreak detection and delaying life-saving public health interventions.

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Bulletin Reference Number Open Market Bid 26-482DPH-OFCDI-B-49133

Requesting Agency/University Illinois Department of Pulic Health

2. Provide a list and describe in detail the specifications required to satisfy the need:

The IDPH-DOL requires a next-generation sequencing platform and associated support plan to meet critical public health mandates and federal program requirements. The MiSeq i100 Plus System and its accompanying Silver Support Plan are the only solutions that meet these specific and essential needs.

• Federal Program Compliance: The CDC's PulseNet program, a national network for foodborne disease surveillance, mandates the use of Illumina-manufactured sequencing systems and specific workflows, including Illumina DNA Prep kits and sequencing platforms. The MiSeq i100 Plus is the latest model that is compatible with these protocols and generates data accepted by the PulseNet national database. This is a non-negotiable requirement for IDPH-DOL to maintain its federal funding and participation in this critical program.

• Operational Efficiency and Throughput: The IDPH-DOL must increase its capacity for simultaneous sequencing of multiple pathogens to respond to outbreaks and conduct surveillance effectively. The MiSeq i100 Plus provides a significant increase in sample capacity and faster run times compared to legacy systems. This efficiency is crucial for accelerating turnaround times for public health investigations, directly impacting the ability to save lives and prevent further disease spread.

• Assay and Data Compatibility: The instrument must be capable of running a range of CDC-validated and FDA-cleared assays, including the TruSight Cystic Fibrosis Assay, which is exclusively validated for use on Illumina platforms. It must also be compatible with approved workflows for foodborne pathogen surveillance, respiratory virus sequencing, and newborn screening. The MiSeq i100 Plus meets all these technical specifications, ensuring that the laboratory can perform a broad spectrum of public health testing with a single, reliable instrument.

• Support and Maintenance: The instrument purchase includes an initial one-year service plan. To ensure continuous operation and data integrity in the second year of the procurement, the purchase of the 12-month Silver Support Plan is required. This plan, provided by Illumina, guarantees certified preventive maintenance, repairs, software updates, and the use of original equipment manufacturer (OEM) parts. This level of service is essential for maintaining compliance and preventing costly downtime. Third-party vendors are not authorized to service these systems, making the manufacturer's support plan a requirement.

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Bulletin Reference Number Open Market Bid 26-482DPH-OFCDI-B-49133

Requesting Agency/University Illinois Department of Pulic Health

3. Provide detail explaining the justification selected in Section IV to explain why the requested supplies or services are the only ones available that can satisfy the agency or university requirements?

The IDPH-DOL is purchasing two (2) Illumina MiSeq i100 Plus Systems and their 12-month Silver Support Plans directly from Illumina, Inc. These instruments and support services can only be acquired from one company because no other product or service can meet the State’s specific and critical public health needs.

Why the Equipment Must Come from Illumina: The decision to purchase exclusively from Illumina is not a matter of preference; it is mandated by national program requirements, clinical validations, and the proprietary nature of Illumina’s technology.

• National Health Mandates (CDC PulseNet Program): IDPH-DOL is a certified participant in the CDC PulseNet Program, a nationwide network that uses whole-genome sequencing to track outbreaks of foodborne and other infectious diseases. To ensure data standardization, comparability, and interoperability across all participating laboratories, PulseNet requires sequencing on Illumina platforms. The PulseNet SOP for DNA library preparation (PNL35, Ver. 05) specifies the use of Illumina® DNA Prep kits and Illumina sequencers. Any alternative brand would produce non-compliant data that cannot be accepted by CDC PulseNet, effectively excluding Illinois from this vital national network.

• Essential Clinical Tests (Newborn Screening): IDPH-DOL laboratories conduct newborn screening for life-threatening disorders, including cystic fibrosis. The TruSight Cystic Fibrosis Assay, used for this purpose, is FDA-cleared and validated only for Illumina sequencing systems. No other manufacturer’s platform can be used to legally or scientifically perform this test, making Illumina equipment the only option.

• Proprietary Technology: The MiSeq i100 Plus is a proprietary sequencing platform designed, manufactured, and sold only by Illumina.

No other company produces an equivalent instrument that meets CDC programmatic requirements and validated clinical assay specifications.

Why Only Illumina Can Service the Equipment: The MiSeq i100 Plus requires specialized support and maintenance services that only Illumina can provide.

• Exclusive Manufacturer Expertise: As the sole manufacturer, Illumina retains all proprietary knowledge, including hardware specifications, software code, and diagnostic tools necessary to maintain and repair these instruments. Third-party vendors are neither authorized nor equipped to service the systems.

• Certified Engineers: Illumina employs the only certified field service engineers trained specifically on the MiSeq i100 Plus. Use of non-certified technicians could result in damage to the equipment, invalid sequencing results, and compromised data integrity—risks that are unacceptable in a public health laboratory environment.

For these reasons, Illumina is the only source that can provide the required sequencing instruments and support services. Procuring from any other vendor would prevent compliance with CDC mandates, disrupt newborn screening, and jeopardize Illinois’s ability to conduct essential outbreak and surveillance activities.

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Bulletin Reference Number Open Market Bid 26-482DPH-OFCDI-B-49133

Requesting Agency/University Illinois Department of Pulic Health

4. What are the unique features of the supplies or services that are not available in any other product or by any other vendor? Provide specific quantifiable factors/qualifications:

The supplies and services are uniquely qualified to meet the IDPH-DOL’s requirements due to a combination of proprietary technology, mandated compatibility with national public health networks, and exclusive test validation. The quantifiable factors and unique features are detailed below.

1. Unique Supplies – Illumina MiSeq i100 Plus Systems

• Exceptional Speed and Throughput: The MiSeq i100 Plus can generate results up to 4x faster than the prior-generation MiSeq, with run times as short as 4 hours. This enables same-day results, a critical capability for rapid outbreak response. The system also supports an output of up to 30 Gb and 200 million paired-end reads per run, providing greater sample throughput and deeper sequencing coverage than competitor systems.

• Integrated “Sample-to-Answer” Workflow: The platform incorporates sequencing with primary and secondary data analysis using onboard Illumina DRAGEN software. This eliminates the need for external bioinformatics pipelines, reducing turnaround time and simplifying workflows for public health laboratorians.

• Proprietary Chemistry and Consumables: The MiSeq i100 Plus uses XLEAP-SBS chemistry and integrated reagent cartridges designed for room-temperature shipping and storage. This eliminates the need for freezer storage and thawing, simplifying logistics and workflows. These consumables are proprietary to Illumina and unavailable from any other vendor.

• Mandated National Compatibility: The MiSeq i100 Plus is the only sequencing platform mandated by the CDC PulseNet program.

PulseNet SOPs (PNL35, Ver. 05) specifically require Illumina DNA Prep kits and Illumina sequencing platforms to ensure inter-laboratory comparability and national database acceptance.

• Exclusive Clinical Validation: The TruSight Cystic Fibrosis Assay, used for newborn screening, is FDA-cleared exclusively for Illumina platforms. No competing sequencing instruments can legally or reliably perform this life-saving clinical test.

2. Unique Services – Illumina Silver Support Plan

• Certified Service Personnel: Only Illumina employs certified engineers trained specifically on the MiSeq i100 Plus. Maintenance requires proprietary diagnostic tools, software, and intellectual property that Illumina does not license to third parties.

• Guaranteed Warranty and Uptime: The 12-month Silver Support Plan ensures rapid response times, certified repairs, and validated software updates, protecting laboratory uptime. Reliance on uncertified service would void warranties, risk damage to the instruments, and compromise data accuracy in critical public health applications.

Summary:

No other sequencing platform or service provider can deliver the combination of mandated CDC PulseNet compliance, exclusive FDA-cleared assay validation, proprietary consumables, integrated sample-to-answer analysis, and OEM-certified maintenance that Illumina provides. These unique features make Illumina the sole vendor capable of meeting IDPH-DOL’s technical, clinical, and programmatic requirements.

5. Has the Agency or University considered alternative supplies or services to satisfy their need? Yes No

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Bulletin Reference Number Open Market Bid 26-482DPH-OFCDI-B-49133

Requesting Agency/University Illinois Department of Pulic Health

5a. If no, why weren't alternatives evaluated?

The Illinois Department of Public Health Division of Laboratories (IDPH-DOL) did not evaluate alternative supplies or services because the agency’s needs are so specific that only the Illumina MiSeq i100 Plus Systems and their accompanying support plans can satisfy them. This decision is based on a clear set of external mandates and proprietary requirements.

Why Alternatives Weren’t Considered: Alternative sequencing platforms and service providers were not evaluated because IDPH-DOL is required to meet non-negotiable technical and regulatory requirements that only Illumina can fulfill:

• Mandated National Network Compatibility: IDPH-DOL must actively participate in the CDC PulseNet Program, the nationwide network for foodborne and infectious disease surveillance. PulseNet mandates the use of Illumina sequencing platforms to ensure data standardization and interoperability. Any other brand of sequencer would generate non-compliant data, preventing Illinois from contributing to this essential national public health network.

• Exclusive Clinical Test Validation: IDPH-DOL performs newborn screening for life-threatening disorders, including cystic fibrosis. The TruSight Cystic Fibrosis Assay, required for this purpose, has been validated exclusively for Illumina sequencing systems. No other vendor’s platform is FDA-cleared or validated for this assay. Using an alternative instrument would jeopardize the accuracy and legality of newborn screening, posing unacceptable risks to patients.

• Proprietary Technology and Service: The Illumina MiSeq i100 Plus is a proprietary sequencing platform manufactured solely by Illumina. Illumina is the only company that possesses the certified service personnel, proprietary parts, and technical expertise necessary to maintain and repair the instruments. No third-party vendor has authorized access to Illumina’s intellectual property or service tools. As a result, both the sequencing instruments and the associated Silver Support Plans must be procured directly from Illumina to ensure operational reliability and compliance.

Summary: Because of these mandated program requirements, clinical assay restrictions, and proprietary limitations, no alternative vendors or products could meet the State’s specific and critical public health needs

6. Are there resellers or distributors?

Yes No N/A

7. What efforts were made to get the best possible price (i.e. did the agency/university negotiate) and how did you determine the price for this purchase is considered fair and reasonable?

To ensure fiscal responsibility and fair pricing for the Illumina MiSeq i100 Plus Systems and Silver Support Plans, IDPH-DOL has taken several steps.

IDPH-DOL are purchasing directly from Illumina, Inc., the sole manufacturer, to eliminate middleman markups and secure the best pricing. The cost is consistent with federal benchmarks (e.g., CDC and GSA schedules) and aligns with what other states pay, ensuring Illinois receives a competitive government rate.

This investment also provides long-term operational savings. The MiSeq i100 Plus offers 50% lower per-sample user costs compared to older instruments, leading to a measurable, long-term savings for the State. The included Silver Support Plan ensures timely maintenance and certified repairs, preventing costly downtime and extending the instrument's life.

Ultimately, this procurement reflects fiscal prudence by obtaining benchmarked, manufacturer-direct pricing and achieving significant long-term operational savings, all while balancing public health necessity with sound financial management.

This procurement is for two sets of the following items: IDPH-DOL Springfield Laboratory (825 North Rutledge, Springfield IL, 62702):

One (1) MiSeq i100 Plus System at a cost of $87,920.00, One (1) MiSeq i100 Plus Silver Support Plan at a cost of $12,160.00, Freight at a cost of $3,077.20, and Surcharge at a cost of $7,547.12. IDPH-DOL Carbondale Laboratory (1155 South Oakland Avenue, Carbondale, IL, 62901): One (1) MiSeq i100 Plus System at a cost of $87,920.00, One (1) MiSeq i100 Plus Silver Support Plan at a cost of $12,160.00, Freight at a cost of $3,077.20, and Surcharge at a cost of $7,547.12.

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Bulletin Reference Number Open Market Bid 26-482DPH-OFCDI-B-49133

Requesting Agency/University Illinois Department of Pulic Health

8. Will this purchase obligate the State to this vendor for future purchases such as maintenance, licensing or continuing need?

Yes No

8a. If yes, please provide details regarding future obligations and/or needs:

Yes, this purchase will obligate the State to Illumina for all future purchases related to the operation and maintenance of these systems. This is a common and necessary consequence of acquiring a highly specialized, proprietary technology that is essential for the agency’s public health mission.

Details of Future Obligations and Needs:

• Continuing Maintenance and Repairs: The 12-month Silver Support Plan included with this purchase represents only the initial year of service. To ensure these instruments remain fully operational throughout the instruments expected lifespan, IDPH-DOL will be required to renew this service contract annually with Illumina. Illumina is the sole entity with certified personnel, proprietary diagnostic tools, and OEM-certified parts to perform maintenance and repairs. Without an active support plan, any technical failure or software issue could render the instruments inoperable, halting critical public health testing and surveillance.

• Proprietary Consumables and Reagents: The Illumina MiSeq i100 Plus operates using single-use consumables and reagent kits manufactured exclusively by Illumina, including proprietary XLEAP-SBS chemistry flow cells and sequencing cartridges. These consumables are required for every sequencing run and no third-party alternatives exist that are compatible with the system’s hardware, chemistry, and software. As such, IDPH-DOL will need to purchase these consumables directly from Illumina on an ongoing basis to continue operating the instruments.

Summary: Future obligations to Illumina include the renewal of certified support plans for maintenance and repairs, as well as the recurring purchase of proprietary consumables and reagents. These obligations are unavoidable, as these obligation stem directly from the proprietary and program-specific requirements that necessitate this sole-source procurement.

9. What will be the financial or other impact to the State if this sole source is not approved and a competitive bid is required?

If this sole source is not approved and the State is required to conduct a competitive bid, the Illinois Department of Public Health Division of Laboratories (IDPH-DOL) would face significant financial, operational, and public health impacts:

• Loss of Compliance with Federal Mandates: The CDC PulseNet Program requires the use of Illumina sequencing platforms for all certified public health laboratories. If IDPH-DOL were forced to procure a non-Illumina sequencer, the data generated would be non-compliant and rejected by CDC. Illinois would be unable to contribute to national outbreak surveillance, jeopardizing federal program participation and potentially putting associated funding at risk.

• Inability to Perform Critical Clinical Testing: The TruSight Cystic Fibrosis Assay, required for newborn screening, is FDA-cleared only for Illumina sequencing systems. Without Illumina equipment, IDPH-DOL could not legally or scientifically perform this life-saving test, directly endangering the health of Illinois infants and exposing the State to liability risks.

• Operational Downtime and Higher Costs: If the State attempted to substitute another vendor’s technology, significant costs would be incurred for retraining staff, developing new bioinformatics pipelines, and revalidating all assays. These costs would far exceed the savings from a competitive procurement process and would delay critical public health services. In addition, alternative platforms do not offer the 50% reduction in per-user costs or the efficiency gains of the MiSeq i100 Plus, resulting in higher long-term operating expenses.

• Risk of Service Interruptions: Without Illumina-certified support plans, the State would lack access to OEM-certified parts, proprietary diagnostic tools, and trained engineers. Equipment downtime would halt outbreak investigations, newborn screening, and infectious disease surveillance, exposing the public to preventable risks.

Summary:Failure to approve this sole source would compromise Illinois’s ability to protect public health, result in higher long-term costs, and place the State out of compliance with CDC and FDA requirements. The financial and public health risks of delay or non-compliance far outweigh any theoretical benefits of pursuing a competitive bid.

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Bulletin Reference Number Open Market Bid 26-482DPH-OFCDI-B-49133

Requesting Agency/University Illinois Department of Pulic Health

10. Is there any additional information you would like to add to justify this sole source?

The acquisition of the Illumina MiSeq i100 Plus Systems and the instruments accompanying Silver Support Plans is essential to IDPH- DOL in fulfilling The Department's core mission of protecting the health of Illinois residents. The Illumina instruments are not optional purchases—and are mandated by federal program requirements, validated clinical testing standards, and the proprietary nature of Illumina’s technology.

Key points reinforcing this sole source justification include:

• CDC PulseNet Mandates: The CDC requires Illumina sequencing platforms to ensure standardization and comparability of outbreak investigation data nationwide. Illinois must comply with these mandates to remain a certified PulseNet laboratory and continue participating in this critical national surveillance network.

• Clinical Test Validation: Essential newborn screening assays, such as the TruSight Cystic Fibrosis Assay, are FDA-cleared only for Illumina platforms. No other sequencing instrument is legally or scientifically acceptable for this testing.

• Proprietary Consumables and Support: Illumina is the sole source of the consumables, reagents, and service contracts necessary for the MiSeq i100 Plus to operate. No third-party alternatives exist.

• Operational and Fiscal Benefits: The MiSeq i100 Plus delivers faster run times, higher throughput, and approximately 50% lower per-sample costs compared to older systems, ensuring that taxpayer resources are used efficiently while enabling rapid outbreak response and life-saving clinical testing.

Conclusion: Approval of this sole source procurement is not only justified but necessary. Without these instruments, Illinois would be unable to comply with CDC requirements, perform FDA-cleared newborn screening tests, or efficiently respond to disease outbreaks.

The consequences of delay or denial would pose significant financial, regulatory, and public health risks.

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Bulletin Reference Number Open Market Bid 26-482DPH-OFCDI-B-49133

Requesting Agency/University Illinois Department of Pulic Health

Section VII

Requesting Department Representative

Requesting Department Signature Required

I know and understand the contents of this Sole Source Justification and attest that all statements are true and correct and the fairness and reasonableness of the price was adequately confirmed.

Date Oct 9, 2025

Printed Name Joshua J. Geltz E-mail Address Joshua. Geltz@illinois.gov

Phone Number 217.685.5584

State Agency Bureau/Division Head or University Purchasing Director Approval and Signature Required

I know and understand the contents of this Sole Source Justification and attest that all statements are true and correct and the fairness and reasonableness of the price was adequately confirmed. (All prior form fields will lock once this e-signature is completed)

E-mail Address Mike.Caceres@illinois.gov

Phone Number 217-557-7905 Date Oct 9, 2025

Printed Name Mike Caceres

Agency Bureau/Division Head or University Purchasing Director and Not a Designee

SPO Approval and Signature Required

I have reviewed and understand the contents of this Sole Source Justification and agree with the State Agency or University determination.

I have reviewed and understand the contents of this Sole Source Justification and do not agree with the State Agency or University determination. As a result, the State Agency or University must explore other sourcing methods to satisfy their need.

State Purchasing Officer Signature Phone Number 217-299-5883 Date 10/10/2025

Printed Name Rebecca Gossett E-mail Address rebecca.gossett@illinois.gov

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Bulletin Reference Number Open Market Bid 26-482DPH-OFCDI-B-49133

Requesting Agency/University Illinois Department of Pulic Health

Sole Source Justification Form - Part II Section I - General Information

Project Title

Vendor

Initial Date of Procurement Bulletin Posting

Was a Sole Source hearing held per 30 ILCS 500/20-25?

Yes - Complete Section II and III below (Section II will only be visible when this option is selected)

No - Section II not required, go to Section III below Section III - CPO Approval and Signature Required

Based on my review, I authorize the Agency/University to proceed in accordance with the published Notice referenced above.

Based upon my review, I authorize the Agency/University to proceed with the following Changes.

Based on my review, the Agency/University is not authorized to proceed with this sole source as presented and my recommendation is that it be cancelled.

Other

CPO Signature CPO Phone

Printed Name Date

CPO E-mail

Version 7.01 Page of Sole Source Justification Form - Part I Section I - General Information Will this Sole Source amend a Professional or Artistic Services contract?

If yes, what was the original contract value?

*Sole Source may not be used for amendments for Professional or Artistic Services if the amendment would increase the value by more than 5% of the initial award or extend the term by more than 60 days.

Section II - Proposed Term If a Term Contract, does the term, including renewals, exceed 12 months?

If yes, provide a detailed justification including any economic benefit received for agreeing to a multi-year term:

Section III - Funding Source Select the type of funding to be used (Check all that apply):

Section IV - Sole Source Justification Are there secondary justification(s) for this sole source?

Section V - Purchase History Has the Agency or University Purchased these supplies or services in the past?

Term Term From Term To Value Description Contract Number Type Section VI - Business Rationale

1. Provide a detailed explanation of the need for the supplies or services:

2. Provide a list and describe in detail the specifications required to satisfy the need:

3. Provide detail explaining the justification selected in Section IV to explain why the requested supplies or services are the only ones available that can satisfy the agency or university requirements?

4. What are the unique features of the supplies or services that are not available in any other product or by any other vendor? Provide specific quantifiable factors/qualifications:

5. Has the Agency or University considered alternative supplies or services to satisfy their need?

5a. If yes, name the alternative vendors whose supplies or services were evaluated:

5b. If yes, what were the alternatives for each vendor and why were they unacceptable? Be specific with regard to features, characteristics, requirements, capabilities and compatibility:

5c. Explain how the market evaluation was conducted?

*This evaluation is to determine available options within a market. If the evaluation is to determine quality or best suited option, this is not the appropriate source selection. Under no circumstances shall the evaluation consist of testing alternative options. These activities must be conducted in a competitive transparent environment (i.e. IFB or RFP).

5a. If no, why weren't alternatives evaluated?

6. Are there resellers or distributors?

7. What efforts were made to get the best possible price (i.e. did the agency/university negotiate) and how did you determine the price for this purchase is considered fair and reasonable?

8. Will this purchase obligate the State to this vendor for future purchases such as maintenance, licensing or continuing need?

8a. If yes, please provide details regarding future obligations and/or needs:

9. What will be the financial or other impact to the State if this sole source is not approved and a competitive bid is required?

10. Is there any additional information you would like to add to justify this sole source?

Section VII Requesting Department Signature Required I know and understand the contents of this Sole Source Justification and attest that all statements are true and correct and the fairness and reasonableness of the price was adequately confirmed.

State Agency Bureau/Division Head or University Purchasing Director Approval and Signature Required I know and understand the contents of this Sole Source Justification and attest that all statements are true and correct and the fairness and reasonableness of the price was adequately confirmed. (All prior form fields will lock once this e-signature is completed) SPO Approval and Signature Required Sole Source Justification Form - Part II Section I - General Information Was a Sole Source hearing held per 30 ILCS 500/20-25?

Section II - Sole Source Hearing Details The State posted to the Illinois Procurement Bulletin a description of the State's need, the justification for the sole source decision, and information regarding the opportunity to submit comments and testify at a public hearing. Notice of the hearing was also posted outside of the hearing room 48 hours prior to the hearing.

The public hearing was conducted for the purpose of receiving testimony regarding the sole source determination. The Hearing Officer recommends the following:

The following relevant documents are attached:

Section III - CPO Approval and Signature Required 9.0.0.2.20101008.1.734229

The MiSeq i100 Plus is a compact next-generation sequencing platform that provides a complete “sample-to-answer” solution, integrating sequencing with primary and secondary data analysis. These systems are essential to meet the Division’s public health mission, including:

• Whole-genome sequencing for disease outbreak investigations (bacterial, viral, and other pathogens).

• Surveillance of respiratory viruses and emerging infectious diseases.

• Newborn screening for critical disorders such as Severe Combined Immunodeficiency (SCID).

• Clinical and public health assays that are validated only for Illumina platforms (e.g., Trusight Cystic Fibrosis Assay).

The instrument purchase includes a one-year service plan. To ensure uninterrupted operations in the second year and beyond, the accompanying Silver Support Plans are required. These plans provide certified preventative maintenance, service, software updates, and access to Illumina’s trained engineers. These services can only be provided directly by Illumina, the sole manufacturer and authorized service provider for MiSeq systems.

Why the Upgrade is Necessary: The MiSeq i100 Plus offers substantial operational and technical improvements compared to older sequencing platforms. Key advantages include:

• 50% reduction in per-user operating costs, resulting in more efficient use of public resources.

• Faster run times, which shorten turnaround time for critical sequencing data.

• Increased sample throughput, allowing laboratories to process more samples in less time.

• A complete “sample-to-answer” solution that integrates sequencing with both primary and secondary data analysis, streamlining workflows and reducing the need for external analysis tools.

These improvements will allow IDPH-DOL to provide faster, more reliable, and more cost-effective testing services.

Impact on Public Health.

The MiSeq i100 Plus systems are critical to the Illinois Department of Public Health's programs and will directly support:

• Outbreak Investigations: Whole-genome sequencing (WGS) will be used to rapidly identify sources of foodborne, waterborne, and healthcare-associated outbreaks. Faster sequencing data will enable quicker public health responses, reducing illness and preventing further spread.

• Newborn Screening: The systems will be used for genetic testing of newborns, including screening for Severe Combined Immunodeficiency (SCID) and other life-threatening disorders. Early detection allows for timely medical interventions that can save lives.

• Infectious Disease Surveillance: The systems will be applied to ongoing monitoring of respiratory viruses, including influenza and SARS-CoV-2. This is essential for tracking viral evolution, understanding transmission dynamics, and informing vaccine development and deployment strategies.

CDC Programmatic and Regulatory Requirements: The purchase of Illumina systems is not optional, but mandated by federal program requirements:

• The CDC PulseNet program, a national surveillance network for foodborne disease outbreaks, requires the use of Illumina sequencing platforms to ensure standardized, interoperable, and high-quality data submission across all participating laboratories.

• The PulseNet Standard Operating Procedure (PNL35, Ver. 05) explicitly requires Illumina® DNA Prep kits for library preparation and Illumina platforms for sequencing. This SOP ensures that all participating labs produce data that is directly comparable and accepted into the national PulseNet database.

• Specific clinical assays, such as the TruSight Cystic Fibrosis Assay, are FDA-cleared and validated only on Illumina sequencing systems, meaning alternative instruments cannot legally or scientifically substitute for these tests.

By upgrading to the Illumina MiSeq i100 Plus, IDPH-DOL will remain compliant with CDC-mandated protocols, maintain its standing as a certified PulseNet laboratory, and continue to contribute standardized genomic data to national surveillance efforts. Without these instruments, IDPH-DOL would be unable to participate fully in PulseNet, jeopardizing outbreak detection and delaying life-saving public health interventions.

Q2Answer: The IDPH-DOL requires a next-generation sequencing platform and associated support plan to meet critical public health mandates and federal program requirements. The MiSeq i100 Plus System and its accompanying Silver Support Plan are the only solutions that meet these specific and essential needs.

• Federal Program Compliance: The CDC's PulseNet program, a national network for foodborne disease surveillance, mandates the use of Illumina-manufactured sequencing systems and specific workflows, including Illumina DNA Prep kits and sequencing platforms. The MiSeq i100 Plus is the latest model that is compatible with these protocols and generates data accepted by the PulseNet national database. This is a non-negotiable requirement for IDPH-DOL to maintain its federal funding and participation in this critical program.

• Operational Efficiency and Throughput: The IDPH-DOL must increase its capacity for simultaneous sequencing of multiple pathogens to respond to outbreaks and conduct surveillance effectively. The MiSeq i100 Plus provides a significant increase in sample capacity and faster run times compared to legacy systems. This efficiency is crucial for accelerating turnaround times for public health investigations, directly impacting the ability to save lives and prevent further disease spread.

• Assay and Data Compatibility: The instrument must be capable of running a range of CDC-validated and FDA-cleared assays, including the TruSight Cystic Fibrosis Assay, which is exclusively validated for use on Illumina platforms. It must also be compatible with approved workflows for foodborne pathogen surveillance, respiratory virus sequencing, and newborn screening. The MiSeq i100 Plus meets all these technical specifications, ensuring that the laboratory can perform a broad spectrum of public health testing with a single, reliable instrument.

• Support and Maintenance: The instrument purchase includes an initial one-year service plan. To ensure continuous operation and data integrity in the second year of the procurement, the purchase of the 12-month Silver Support Plan is required. This plan, provided by Illumina, guarantees certified preventive maintenance, repairs, software updates, and the use of original equipment manufacturer (OEM) parts. This level of service is essential for maintaining compliance and preventing costly downtime. Third-party vendors are not authorized to service these systems, making the manufacturer's support plan a requirement.

Q3Answer: The IDPH-DOL is purchasing two (2) Illumina MiSeq i100 Plus Systems and their 12-month Silver Support Plans directly from Illumina, Inc. These instruments and support services can only be acquired from one company because no other product or service can meet the State’s specific and critical public health needs.

Why the Equipment Must Come from Illumina: The decision to purchase exclusively from Illumina is not a matter of preference; it is mandated by national program requirements, clinical validations, and the proprietary nature of Illumina’s technology.

• National Health Mandates (CDC PulseNet Program): IDPH-DOL is a certified participant in the CDC PulseNet Program, a nationwide network that uses whole-genome sequencing to track outbreaks of foodborne and other infectious diseases. To ensure data standardization, comparability, and interoperability across all participating laboratories, PulseNet requires sequencing on Illumina platforms. The PulseNet SOP for DNA library preparation (PNL35, Ver. 05) specifies the use of Illumina® DNA Prep kits and Illumina sequencers. Any alternative brand would produce non-compliant data that cannot be accepted by CDC PulseNet, effectively excluding Illinois from this vital national network.

• Essential Clinical Tests (Newborn Screening): IDPH-DOL laboratories conduct newborn screening for life-threatening disorders, including cystic fibrosis. The TruSight Cystic Fibrosis Assay, used for this purpose, is FDA-cleared and validated only for Illumina sequencing systems. No other manufacturer’s platform can be used to legally or scientifically perform this test, making Illumina equipment the only option.

• Proprietary Technology: The MiSeq i100 Plus is a proprietary sequencing platform designed, manufactured, and sold only by Illumina. No other company produces an equivalent instrument that meets CDC programmatic requirements and validated clinical assay specifications.

Why Only Illumina Can Service the Equipment: The MiSeq i100 Plus requires specialized support and maintenance services that only Illumina can provide.

• Exclusive Manufacturer Expertise: As the sole manufacturer, Illumina retains all proprietary knowledge, including hardware specifications, software code, and diagnostic tools necessary to maintain and repair these instruments. Third-party vendors are neither authorized nor equipped to service the systems.

• Certified Engineers: Illumina employs the only certified field service engineers trained specifically on the MiSeq i100 Plus. Use of non-certified technicians could result in damage to the equipment, invalid sequencing results, and compromised data integrity—risks that are unacceptable in a public health laboratory environment.

For these reasons, Illumina is the only source that can provide the required sequencing instruments and support services. Procuring from any other vendor would prevent compliance with CDC mandates, disrupt newborn screening, and jeopardize Illinois’s ability to conduct essential outbreak and surveillance activities.

Q4Answer: The supplies and services are uniquely qualified to meet the IDPH-DOL’s requirements due to a combination of proprietary technology, mandated compatibility with national public health networks, and exclusive test validation. The quantifiable factors and unique features are detailed below.

1. Unique Supplies – Illumina MiSeq i100 Plus Systems

• Exceptional Speed and Throughput: The MiSeq i100 Plus can generate results up to 4x faster than the prior-generation MiSeq, with run times as short as 4 hours. This enables same-day results, a critical capability for rapid outbreak response. The system also supports an output of up to 30 Gb and 200 million paired-end reads per run, providing greater sample throughput and deeper sequencing coverage than competitor systems.

• Integrated “Sample-to-Answer” Workflow: The platform incorporates sequencing with primary and secondary data analysis using onboard Illumina DRAGEN software. This eliminates the need for external bioinformatics pipelines, reducing turnaround time and simplifying workflows for public health laboratorians.

• Proprietary…