SSJF DPH-B-47168.pdf

Sole Source Justification Form

Version 7.01 Page 1 of 9

Bulletin Reference Number 25-482DPH-OFCI-B-47168

Requesting Agency/University Illinois Department of Public Health

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

Department/Bureau/Section: Office of Disease Control (ODC) Division of Laboratories (DOL)

Need Identified Date: 02/27/2025 Supply/Service Need By Date: 07/01/2025

Project Title: Sole Source Purchase Illumina, Inc.

Vendor: Illumina, Inc.

Provide a description of the supplies or services required:

The Illinois Department of Public Health Division of Laboratories (IDPH-DOL) is procuring Whole Genome Sequencing (WGS) reagents, instrument service, and software through a one-year sole source contract with Illumina, Inc. to support epidemiological disease investigations, newborn screening, and pathogen typing. This contract includes WGS reagents for sequencing on MiSeqDX, iSeq 100, and NextSeq 2000 instruments, preventative maintenance and repair services to ensure compliance with Clinical Laboratory Improvement Amendments (CLIA), and software solutions such as BaseSpace Sequence Hub and Illumina, Inc. Analytics iCredits for sequencing data analysis and storage.

Value: Actual Value of Initial Term, this Change Order or Amendment: 826,536.5

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

Section II - Proposed Term

One-Time Purchase Term Contract

Estimated Contract Begin Date: 07/01/2025

Estimated Contract End Date: 06/30/2026

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

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

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Bulletin Reference Number 25-482DPH-OFCI-B-47168

Requesting Agency/University Illinois Department of Public Health

Section V - Purchase History

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

Term Term From Term To Value Description Contract Number Type

1 08/14/2024 06/30/2025 844,273.52 llumina commodity and service FY 25 Sole Source 58500004M Sole Source

2 07/01/2023 06/30/2024 843,867.9 IlluminaFY24 Illumina, Inc.

Commodities and Service contract- 1 Year, Inc. Instrument Service-2 year

48500002L Sole Source

3 07/01/2023 06/30/2024 1,316,455 FY24 Illumina, Inc. Equipment Upgrade 38500032K Sole Source

4 07/01/2022 06/30/2023 472,111.65 FY23 Illumina, Inc. Commodity and Service Contract-1 year 38500002K Sole Source

5 07/01/2021 06/30/2022 480,184.46 Illumina, Inc. Commodity and Service Contract- 1 Year 25500003J Sole Source

6 05/01/2020 04/30/2021 400,000 Illumina, Inc. Commodity Contract-1 year 05500022H Sole Source

7 05/28/2019 06/30/2021 87,983.92 Illumina, Inc. Instrument Service-2 year 9550031G Sole Source

8 02/06/2019 02/05/2020 341,591 Illumina, Inc. Instrument Service-2 year 9550018G Sole Source

If more than 10, or if other comments, explain:

Section VI - Business Rationale

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

This procurement supports Whole Genome Sequencing (WGS) testing, which is essential for identifying bacterial and viral pathogens, tracking food borne and waterborne outbreaks, and screening newborns for genetic disorders like Severe Combined Immunodeficiency (SCID). The reagents, instrument service, and software acquired under this contract are critical for maintaining MiSeqDX, iSeq 100, and NextSeq 2000 sequencing instruments, ensuring high-quality genomic data for epidemiological investigations.

The WGS reagents are required for sequencing clinical, food, and environmental samples to detect and analyze disease-causing organisms. Service contracts ensure that sequencing instruments remain functional and compliant with Clinical Laboratory Improvement Amendments (CLIA) standards. Software solutions, such as BaseSpace Sequence Hub and Illumina, Inc. Analytics iCredits, allow for efficient data analysis, storage, and sharing of genomic information with public health agencies, including the CDC PulseNet program, which tracks multi-state disease outbreaks.

For public health professionals, epidemiologists, and laboratory scientists, these supplies and services ensure timely, accurate, and reliable sequencing data, supporting disease surveillance, rapid outbreak detection, and food safety investigations. For the general public, this procurement directly contributes to reducing the spread of infectious diseases, improving public health outcomes, and protecting Illinois residents from emerging health threats. By maintaining sequencing capacity and data integrity, Illinois Department of Public Health Division of Laboratories (IDPH-DOL) can proactively respond to public health emergencies and enhance statewide disease prevention efforts.

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Bulletin Reference Number 25-482DPH-OFCI-B-47168

Requesting Agency/University Illinois Department of Public Health

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

The Illinois Department of Public Health Division of Laboratories (IDPH-DOL) requires a one-year sole source contract with Illumina, Inc.

to procure Whole Genome Sequencing (WGS) reagents, instrument service, and software to support epidemiological disease investigations, newborn screening, and pathogen typing. Under this contract, Illumina, Inc. will provide essential reagents, preventative maintenance, software subscriptions, and data storage solutions necessary for continued compliance with Clinical Laboratory Improvement Amendments (CLIA) standards and participation in CDC PulseNet disease tracking.

The contract includes reagents for WGS testing, which are critical for sequencing on MiSeqDX, iSeq 100, and NextSeq 2000 instruments.

These reagents enable testing for infectious disease outbreaks, newborn genetic disorders, and environmental pathogen surveillance.

IDPH-DOL will procure reagents under this contract to maintain testing operations.

Additionally, instrument service and maintenance agreements are required for MiSeqDX (Serial Numbers: M70707, M71167), iSeq 100 (Serial Number: FS10003288), and NextSeq 2000 (Serial Numbers: VH01600, VH01606, VH01595, VH01596, VH01517). These service plans provide full coverage for parts, labor, and travel, remote technical support (up to 18x5), reagent replacement for hardware failures, annual preventative maintenance visits, software and hardware updates, and on-site response within two business days.

Illumina, Inc. will also provide BaseSpace Sequence Hub Enterprise Subscription, a cloud-based data analysis and storage solution for sequencing for 12 months. The contract includes the purchase of 5,000 iCredits for genomic data storage and processing.

This procurement ensures IDPH-DOL has uninterrupted access to critical sequencing reagents, instrument maintenance, and data analysis tools necessary to sustain public health surveillance, outbreak detection, and compliance with national genomic sequencing standards.

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Bulletin Reference Number 25-482DPH-OFCI-B-47168

Requesting Agency/University Illinois Department of Public 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?

Illumina, Inc is the sole manufacturer and exclusive provider of reagents approved for use with MiSeqDX, iSeq 100, and NextSeq 2000 sequencing instruments, which are already validated and in operation at The Illinois Department of Public Health Division of Laboratories (IDPH-DOL). No third-party vendor is licensed by Illumina, Inc. to sell these proprietary reagents, software, or maintenance services. Furthermore, preventative maintenance and repairs for these specialized instruments can only be performed by Illumina, Inc.

certified personnel, ensuring compliance with Clinical Laboratory Improvement Amendments (CLIA) standards.

Illumina, Inc. branded reagents are the only reagents compatible with the MiSeqDX, iSeq 100, and NextSeq 2000 sequencing instruments due to their proprietary chemistry, system integration, and regulatory approval requirements.

The reagents, instrument service, and software are essential for maintaining the MiSeqDX, iSeq 100, and NextSeq 2000 sequencing instruments and ensuring the accuracy, reliability, and regulatory compliance of Whole Genome Sequencing (WGS) conducted by the Illinois Department of Public Health Division of Laboratories (IDPH-DOL).

1. Reagents – The sequencing reagents are required to perform high-quality genomic analysis of clinical, environmental, and foodborne pathogen samples. These reagents are proprietary to Illumina, Inc. and are specifically designed for use with Illumina, Inc. sequencing-by-synthesis (SBS) technology. Using validated reagents ensures accurate pathogen identification, genetic variant detection, and outbreak tracking, which are critical for public health surveillance and epidemiological investigations.

2. Instrument Service – Regular preventative maintenance and repairs are necessary to ensure that sequencing instruments remain fully operational and in compliance with Clinical Laboratory Improvement Amendments (CLIA) standards. Illumina, Inc. is the only provider authorized to service these instruments, as maintenance involves calibrations, software updates, and hardware repairs that must be performed by Illumina, Inc. certified technicians. Without proper servicing, instrument failures could lead to data loss, delays in public health responses, and increased long-term repair costs.

3. Software – The Illumina, Inc. BaseSpace Sequence Hub and iCredits are required for data analysis, storage, and secure sharing of sequencing results. These software tools enable real-time genomic analysis, ensuring that sequencing data is accurately processed, stored, and transmitted to national disease surveillance programs such as the CDC PulseNet. Since sequencing data must be processed in an Illumina, Inc, validated pipeline, alternative software solutions are not compatible with the MiSeqDX, iSeq 100, or NextSeq 2000 platforms.

Without these three critical components—reagents, instrument service, and software—IDPH-DOL would be unable to conduct Whole Genome Sequencing, compromising its ability to detect and respond to infectious disease outbreaks, perform newborn screening, and meet regulatory compliance requirements.

Other reagents cannot be used with these instruments for the following reasons:

1. Proprietary Chemistry & System Optimization – Illumina, Inc. reagents are formulated to work exclusively with the MiSeqDX, iSeq 100, and NextSeq 2000’s optical detection and sequencing workflow. Third-party reagents would not be chemically compatible and could lead to instrument malfunctions or compromised sequencing accuracy.

2. Regulatory Compliance & Validation – The MiSeqDX is FDA-approved for clinical use, and its reagents are specifically validated for diagnostic and public health applications. Using non-Illumina, Inc. reagents would invalidate regulatory compliance, making results inadmissible for clinical and epidemiological purposes.

3. Software & Data Processing Integration – Illumina, Inc. sequencing workflows rely on integrated bioinformatics pipelines, such as BaseSpace Sequence Hub, to analyze data. The instruments use predefined quality control metrics and calibration settings that are tailored to Illumina, Inc. reagents, making third-party reagents incompatible with existing data analysis workflows.

The reagents, instrument service, and software are essential for maintaining the MiSeqDX, iSeq 100, and NextSeq 2000 sequencing instruments and ensuring the accuracy, reliability, and regulatory compliance of Whole Genome Sequencing (WGS) conducted by the Illinois Department of Public Health Division of Laboratories (IDPH-DOL).

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Bulletin Reference Number 25-482DPH-OFCI-B-47168

Requesting Agency/University Illinois Department of Public 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:

Illumina, Inc. is the only vendor authorized to supply, maintain, and service the MiSeqDX, iSeq 100, and NextSeq 2000 sequencing platforms used by The Illinois Department of Public Health Division of Laboratories (IDPH-DOL). No other company is licensed to sell Illumina, Inc. reagents or provide maintenance and repair services for these instruments. The reagents are proprietary and specifically engineered for Illumina, Inc. sequencing technology, ensuring compatibility, accuracy, and reliability in whole genome sequencing workflows.

The unique, quantifiable factors that require Illumina, Inc. as the sole provider include:

Exclusive Licensing & Manufacturing: Illumina, Inc. is the only company authorized to sell reagents and software for its sequencing platforms.

Instrument-Specific Reagents: Only Illumina, Inc. manufactured reagents are validated and FDA-approved for use on MiSeqDX, iSeq 100, and NextSeq 2000 instruments.

Certified Maintenance & Support: Preventative maintenance, calibration, and repairs must be performed by Illumina, Inc. certified personnel to maintain instrument warranty and regulatory compliance.

Integrated Software & Data Management: Illumina, Inc. provides BaseSpace Sequence Hub and iCredits, which are proprietary cloud-based solutions for sequencing data storage and analysis.

Because no third-party vendors are licensed to sell, service, or maintain Illumina, Inc. sequencing systems, Illumina, Inc. is the only vendor capable of meeting The Illinois Department of Public Health Division of Laboratories' (IDPH-DOL) operational and regulatory needs.

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

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 Illumina, Inc. is the only vendor licensed to manufacture, sell, and service the sequencing reagents, instruments, and software required for Whole Genome Sequencing (WGS) testing used and owned by IDPH.

6. Are there resellers or distributors?

Yes No N/A

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Bulletin Reference Number 25-482DPH-OFCI-B-47168

Requesting Agency/University Illinois Department of Public Health

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?

The Illinois Department of Public Health Division of Laboratories (IDPH-DOL) negotiated pricing with Illumina, Inc. and secured a 5% discount, contingent upon a one-year contract, on Whole Genome Sequencing (WGS) reagents and instrument service plans. This discount is reflected in the final contract pricing, ensuring cost savings for the State of Illinois. The contract includes reagents, preventative maintenance, software subscriptions, and data storage solutions required for continued regulatory compliance and operational efficiency.

The total contract value is $826,536.50, which includes:

Catalog Number: SW-411-1003: BaseSpace Sequence Hub Enterprise Annual Subscription (12-months) Catalog Number: 20042040: Illumina Analytics - 5,000 iCredits (12-months) Catalog Number: 20023959: iSeq 100 Advance Exchange for instrument Asset Number : FS10003288 (12-months) Catalog Number: 20019985: MiSeq Dx Silver Support Plan for instrument Asset Number: M71167 (12-months) Catalog Number: 20019985: MiSeq Dx Silver Support Plan for instrument Asset Number: M70707 (12-months) Catalog Number: 20040667: NextSeq 2000 Silver Support Plan for instrument Asset Number: VH01595 (12-months) Catalog Number: 20040667: NextSeq 2000 Silver Support Plan for instrument Asset Number: VH01600 (12-months) Catalog Number: 20040667: NextSeq 2000 Silver Support Plan for instrument Asset Number: VH01517 (12-months) Catalog Number: 20040667: NextSeq 2000 Silver Support Plan for instrument Asset Number: VH01596 (12-months) Catalog Number: 20040667 : NextSeq 2000 Silver Support Plan for instrument Asset Number: VH01606 (12-months) WGS Reagents (12-months)

IDPH-DOL determined that the pricing is fair and reasonable by comparing it to past procurement agreements and considering the sole-source nature of the contract. Illumina, Inc. is the only licensed vendor authorized to sell reagents, provide maintenance, and service these proprietary sequencing platforms. Alternative pricing from third-party vendors was not an option, as no other suppliers are authorized to provide Illumina Inc. specific reagents or services. The negotiated pricing ensures uninterrupted disease surveillance, newborn screening, and outbreak detection, making this contract the most economically feasible choice for the State of Illinois.

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

Yes No

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 the Illinois Department of Public Health Division of Laboratories (IDPH-DOL) is unable to procure the necessary Illumina, Inc.

sequencing reagents, the state’s ability to conduct Whole Genome Sequencing (WGS) for infectious disease surveillance, outbreak response, and newborn screening would be severely compromised.

1. Delays in Public Health Response & Disease Outbreak Tracking – WGS is critical for identifying bacterial and viral pathogens, tracking mutations, and detecting antibiotic resistance in infectious disease outbreaks. Without the required reagents, IDPH-DOL would be unable to sequence pathogens from clinical, food, and environmental samples, delaying epidemiological investigations and increasing the risk of disease spread.

2. Non-Compliance with Federal and State Health Initiatives – IDPH-DOL collaborates with the Centers for Disease Control and Prevention (CDC) PulseNet program and other national disease tracking systems. Without sequencing reagents, Illinois would fail to meet federal data-sharing and public health reporting requirements, potentially jeopardizing funding and program participation.

3. Disruption of Newborn Screening for Genetic Disorders – WGS is used to detect severe genetic conditions such as Severe Combined Immunodeficiency (SCID) in newborns. A lack of sequencing reagents would halt newborn screening operations, delaying life-saving diagnoses and treatments for affected infants.

4. A lapse in preventative maintenance and repair services for Illumina, Inc. MiSeqDX, iSeq 100, and NextSeq 2000 instruments will increase the risk of equipment failure, leading to costly emergency repairs or instrument replacements.

Without access to these reagents, IDPH-DOL would be unable to fulfill its public health mission, leading to delays in disease detection, non-compliance with federal surveillance programs, and increased costs to the state.

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Bulletin Reference Number 25-482DPH-OFCI-B-47168

Requesting Agency/University Illinois Department of Public Health

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

NA

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Bulletin Reference Number 25-482DPH-OFCI-B-47168

Requesting Agency/University Illinois Department of Public 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 Apr 25, 2025

Printed Name Joshua Geltz E-mail Address Joshua.Geltz@Illinois.gov

Phone Number 217-782-6563

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 217-299-5563 Date Apr 28, 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 04/28/2025

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

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Bulletin Reference Number 25-482DPH-OFCI-B-47168

Requesting Agency/University Illinois Department of Public Health

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

Project Title Sole Source Purchase Illumina, Inc.

Vendor Illumina, Inc.

Initial Date of Procurement Bulletin Posting 04/30/2025

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 217-622-1857

Printed Name Ellen.H.Daley@illinois.gov Date May 14, 2025

CPO E-mail Ellen.H.Daley@illinois.gov

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 Ellen.H.Daley@illinois.gov

The WGS reagents are required for sequencing clinical, food, and environmental samples to detect and analyze disease-causing organisms. Service contracts ensure that sequencing instruments remain functional and compliant with Clinical Laboratory Improvement Amendments (CLIA) standards. Software solutions, such as BaseSpace Sequence Hub and Illumina, Inc. Analytics iCredits, allow for efficient data analysis, storage, and sharing of genomic information with public health agencies, including the CDC PulseNet program, which tracks multi-state disease outbreaks.

For public health professionals, epidemiologists, and laboratory scientists, these supplies and services ensure timely, accurate, and reliable sequencing data, supporting disease surveillance, rapid outbreak detection, and food safety investigations. For the general public, this procurement directly contributes to reducing the spread of infectious diseases, improving public health outcomes, and protecting Illinois residents from emerging health threats. By maintaining sequencing capacity and data integrity, Illinois Department of Public Health Division of Laboratories (IDPH-DOL) can proactively respond to public health emergencies and enhance statewide disease prevention efforts.

Q2Answer: The Illinois Department of Public Health Division of Laboratories (IDPH-DOL) requires a one-year sole source contract with Illumina, Inc. to procure Whole Genome Sequencing (WGS) reagents, instrument service, and software to support epidemiological disease investigations, newborn screening, and pathogen typing. Under this contract, Illumina, Inc. will provide essential reagents, preventative maintenance, software subscriptions, and data storage solutions necessary for continued compliance with Clinical Laboratory Improvement Amendments (CLIA) standards and participation in CDC PulseNet disease tracking.

The contract includes reagents for WGS testing, which are critical for sequencing on MiSeqDX, iSeq 100, and NextSeq 2000 instruments. These reagents enable testing for infectious disease outbreaks, newborn genetic disorders, and environmental pathogen surveillance. IDPH-DOL will procure reagents under this contract to maintain testing operations.

Additionally, instrument service and maintenance agreements are required for MiSeqDX (Serial Numbers: M70707, M71167), iSeq 100 (Serial Number: FS10003288), and NextSeq 2000 (Serial Numbers: VH01600, VH01606, VH01595, VH01596, VH01517). These service plans provide full coverage for parts, labor, and travel, remote technical support (up to 18x5), reagent replacement for hardware failures, annual preventative maintenance visits, software and hardware updates, and on-site response within two business days.

Illumina, Inc. will also provide BaseSpace Sequence Hub Enterprise Subscription, a cloud-based data analysis and storage solution for sequencing for 12 months. The contract includes the purchase of 5,000 iCredits for genomic data storage and processing.

This procurement ensures IDPH-DOL has uninterrupted access to critical sequencing reagents, instrument maintenance, and data analysis tools necessary to sustain public health surveillance, outbreak detection, and compliance with national genomic sequencing standards.

Q3Answer: Illumina, Inc is the sole manufacturer and exclusive provider of reagents approved for use with MiSeqDX, iSeq 100, and NextSeq 2000 sequencing instruments, which are already validated and in operation at The Illinois Department of Public Health Division of Laboratories (IDPH-DOL). No third-party vendor is licensed by Illumina, Inc. to sell these proprietary reagents, software, or maintenance services. Furthermore, preventative maintenance and repairs for these specialized instruments can only be performed by Illumina, Inc. certified personnel, ensuring compliance with Clinical Laboratory Improvement Amendments (CLIA) standards.

Illumina, Inc. branded reagents are the only reagents compatible with the MiSeqDX, iSeq 100, and NextSeq 2000 sequencing instruments due to their proprietary chemistry, system integration, and regulatory approval requirements.

The reagents, instrument service, and software are essential for maintaining the MiSeqDX, iSeq 100, and NextSeq 2000 sequencing instruments and ensuring the accuracy, reliability, and regulatory compliance of Whole Genome Sequencing (WGS) conducted by the Illinois Department of Public Health Division of Laboratories (IDPH-DOL).

1. Reagents – The sequencing reagents are required to perform high-quality genomic analysis of clinical, environmental, and foodborne pathogen samples. These reagents are proprietary to Illumina, Inc. and are specifically designed for use with Illumina, Inc. sequencing-by-synthesis (SBS) technology. Using validated reagents ensures accurate pathogen identification, genetic variant detection, and outbreak tracking, which are critical for public health surveillance and epidemiological investigations.

2. Instrument Service – Regular preventative maintenance and repairs are necessary to ensure that sequencing instruments remain fully operational and in compliance with Clinical Laboratory Improvement Amendments (CLIA) standards. Illumina, Inc. is the only provider authorized to service these instruments, as maintenance involves calibrations, software updates, and hardware repairs that must be performed by Illumina, Inc. certified technicians. Without proper servicing, instrument failures could lead to data loss, delays in public health responses, and increased long-term repair costs.

3. Software – The Illumina, Inc. BaseSpace Sequence Hub and iCredits are required for data analysis, storage, and secure sharing of sequencing results. These software tools enable real-time genomic analysis, ensuring that sequencing data is accurately processed, stored, and transmitted to national disease surveillance programs such as the CDC PulseNet. Since sequencing data must be processed in an Illumina, Inc, validated pipeline, alternative software solutions are not compatible with the MiSeqDX, iSeq 100, or NextSeq 2000 platforms.

Without these three critical components—reagents, instrument service, and software—IDPH-DOL would be unable to conduct Whole Genome Sequencing, compromising its ability to detect and respond to infectious disease outbreaks, perform newborn screening, and meet regulatory compliance requirements.

Other reagents cannot be used with these instruments for the following reasons:

1. Proprietary Chemistry & System Optimization – Illumina, Inc. reagents are formulated to work exclusively with the MiSeqDX, iSeq 100, and NextSeq 2000’s optical detection and sequencing workflow. Third-party reagents would not be chemically compatible and could lead to instrument malfunctions or compromised sequencing accuracy.

2. Regulatory Compliance & Validation – The MiSeqDX is FDA-approved for clinical use, and its reagents are specifically validated for diagnostic and public health applications. Using non-Illumina, Inc. reagents would invalidate regulatory compliance, making results inadmissible for clinical and epidemiological purposes.

3. Software & Data Processing Integration – Illumina, Inc. sequencing workflows rely on integrated bioinformatics pipelines, such as BaseSpace Sequence Hub, to analyze data. The instruments use predefined quality control metrics and calibration settings that are tailored to Illumina, Inc. reagents, making third-party reagents incompatible with existing data analysis workflows.

The reagents, instrument service, and software are essential for maintaining the MiSeqDX, iSeq 100, and NextSeq 2000 sequencing instruments and ensuring the accuracy, reliability, and regulatory compliance of Whole Genome Sequencing (WGS) conducted by the Illinois Department of Public Health Division of Laboratories (IDPH-DOL).

Q4Answer: Illumina, Inc. is the only vendor authorized to supply, maintain, and service the MiSeqDX, iSeq 100, and NextSeq 2000 sequencing platforms used by The Illinois Department of Public Health Division of Laboratories (IDPH-DOL). No other company is licensed to sell Illumina, Inc. reagents or provide maintenance and repair services for these instruments. The reagents are proprietary and specifically engineered for Illumina, Inc. sequencing technology, ensuring compatibility, accuracy, and reliability in whole genome sequencing workflows.

The unique, quantifiable factors that require Illumina, Inc. as the sole provider include:

Exclusive Licensing & Manufacturing: Illumina, Inc. is the only company authorized to sell reagents and software for its sequencing platforms.

Instrument-Specific Reagents: Only Illumina, Inc. manufactured reagents are validated and FDA-approved for use on MiSeqDX, iSeq 100, and NextSeq 2000 instruments.

Certified Maintenance & Support: Preventative maintenance, calibration, and repairs must be performed by Illumina, Inc. certified personnel to maintain instrument warranty and regulatory compliance.

Integrated Software & Data Management: Illumina, Inc. provides BaseSpace Sequence Hub and iCredits, which are proprietary cloud-based solutions for sequencing data storage and analysis.

Because no third-party vendors are licensed to sell, service, or maintain Illumina, Inc. sequencing systems, Illumina, Inc. is the only vendor capable of meeting The Illinois Department of Public Health Division of Laboratories' (IDPH-DOL) operational and regulatory needs.

The total contract value is $826,536.50, which includes:

Catalog Number: SW-411-1003: BaseSpace Sequence Hub Enterprise Annual Subscription (12-months) Catalog Number: 20042040: Illumina Analytics - 5,000 iCredits (12-months) Catalog Number: 20023959: iSeq 100 Advance Exchange for instrument Asset Number : FS10003288 (12-months) Catalog Number: 20019985: MiSeq Dx Silver Support Plan for instrument Asset Number: M71167 (12-months) Catalog Number: 20019985: MiSeq Dx Silver Support Plan for instrument Asset Number: M70707 (12-months) Catalog Number: 20040667: NextSeq 2000 Silver Support Plan for instrument Asset Number: VH01595 (12-months) Catalog Number: 20040667: NextSeq 2000 Silver Support Plan for instrument Asset Number: VH01600 (12-months) Catalog Number: 20040667: NextSeq 2000 Silver Support Plan for instrument Asset Number: VH01517 (12-months) Catalog Number: 20040667: NextSeq 2000 Silver Support Plan for instrument Asset Number: VH01596 (12-months) Catalog Number: 20040667 : NextSeq 2000 Silver Support Plan for instrument Asset Number: VH01606 (12-months) WGS Reagents (12-months)

IDPH-DOL determined that the pricing is fair and reasonable by comparing it to past procurement agreements and considering the sole-source nature of the contract. Illumina, Inc. is the only licensed vendor authorized to sell reagents, provide maintenance, and service these proprietary sequencing platforms. Alternative pricing from third-party vendors was not an option, as no other suppliers are authorized to provide Illumina Inc. specific reagents or services. The negotiated pricing ensures uninterrupted disease surveillance, newborn screening, and outbreak detection, making this contract the most economically feasible choice for the State of Illinois.

1. Delays in Public Health Response & Disease Outbreak Tracking – WGS is critical for identifying bacterial and viral pathogens, tracking mutations, and detecting antibiotic resistance in infectious disease outbreaks. Without the required reagents, IDPH-DOL would be unable to sequence pathogens from clinical, food, and environmental samples, delaying epidemiological investigations and increasing the risk of disease spread.

2. Non-Compliance with Federal and State Health Initiatives – IDPH-DOL collaborates with the Centers for Disease Control and Prevention (CDC) PulseNet program and other national disease tracking systems. Without sequencing reagents, Illinois would fail to meet federal data-sharing and public health reporting requirements, potentially jeopardizing funding and program participation.

3. Disruption of Newborn Screening for Genetic Disorders – WGS is used to detect severe genetic conditions such as Severe Combined Immunodeficiency (SCID) in newborns. A lack of sequencing reagents would halt newborn screening operations, delaying life-saving diagnoses and treatments for affected infants.

4. A lapse in preventative maintenance and repair services for Illumina, Inc. MiSeqDX, iSeq 100, and NextSeq 2000 instruments will increase the risk of equipment failure, leading to costly emergency repairs or instrument replacements.

Without access to these reagents, IDPH-DOL would be unable to fulfill its public health mission, leading to delays in disease detection, non-compliance with federal surveillance programs, and increased costs to the state.