SSJF Clear Labs LG Part I.pdf

Sole Source Justification Form

Version 7.01 Page 1 of 8

Bulletin Reference Number Open Market Bid 25-482DPH-OFCDI-B-44233

Requesting Agency/University IDPH

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

Department/Bureau/Section: Illinois Department of Public Health / Division of Labs

Need Identified Date: May 31, 2024 Supply/Service Need By Date: Dec 1, 2024

Project Title: Clear Dx Instrument, Service and Reagent Sole Source

Vendor: Clear Labs, Inc

Provide a description of the supplies or services required:

This request is for a sole source contract to buy two (2) additional Clear Dx™ System LR-SR instruments and all necessary supplies for the 2 new machines being purchases and the 2 machines IDPH already owns. for the Illinois Department of Public Health (IDPH) Division of Labs (DOL), service coverage for both Clear Dx™ System LR-SR instruments, installation and training for the Clear Dx™ System LR-SR instruments, shipping and packaging for both Clear Dx™ System LR-SR instruments, Clear Dx™ System reagents and consumables.

Two (2) Clear Dx™ instruments were purchased in June of 2023 and have been implemented into the sequencing workflow.

Value: Not to Exceed Value of Initial Term, this Change Order or Amendment: 1,632,476

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: 12/1/2024

Estimated Contract End Date: 11/30/2025

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

Version 7.01 Page 2 of 8

Bulletin Reference Number Open Market Bid 25-482DPH-OFCDI-B-44233

Requesting Agency/University IDPH

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 Jun 21, 2023 Jun 20, 2024 962,476 Clear Dx™ Instrument and Reagents 38500028K Sole Source

2 Jan 12, 2024 Jan 11, 2025 1,000,400 Clear Dx™ Reagents 48500016L Sole Source

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

Section VI - Business Rationale

Version 7.01 Page 3 of 8

Bulletin Reference Number Open Market Bid 25-482DPH-OFCDI-B-44233

Requesting Agency/University IDPH

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

The Illinois Department of Public Health (IDPH) needs to procure additional Clear Lab Clear Dx™ systems and corresponding reagents to meet increasing demands and ensure consistency across its laboratories.

IDPH DOL’s current use of multiple Clear Dx™ systems demonstrates the platform’s critical role in their laboratory operations, particularly for high-throughput molecular testing and genomic analysis. With increasing demands for testing, particularly in public health scenarios like pathogen surveillance and genetic testing, acquiring two (2) additional systems is necessary to scale up capacity.

These machines can rapidly process a large volume of samples, which is essential for labs dealing with public health emergencies, disease outbreaks, or routine diagnostics. The purchase will expand the IDP DOL's ability to handle more tests in a shorter timeframe.

Uniformity across the IDPH DOL’s is crucial for ensuring consistent, reliable, and reproducible test results. Clear Lab Clear Dx™ systems operate with the same algorithms and protocols, ensuring standardized testing procedures and outcomes across all locations. This consistency is essential for the accuracy of genomic data, particularly in tracking disease outbreaks and large-scale public health surveillance.

Clear Lab Clear Dx™ systems require proprietary reagents from Clear Labs, Inc. for optimal performance. These reagents are essential for the continuous operation of both existing and new machines. Without them, the systems would be unable to perform accurate testing, making the acquisition of reagents a non-negotiable operational necessity.

Automation of the Clear Dx™ platform streamlines the entire next-generation sequencing (NGS) workflow, reducing manual labor and minimizing human error. This automation ensures consistency and reproducibility, vital for the high-stakes environment in which the IDPH DOL operates, maintaining operational efficiency and accuracy.

Clear Dx™ is the only system capable of fully automating library preparation, whole genome sequencing, and post-sequencing analysis of both SARS-CoV-2 and bacterial isolates within 18 hours. This integration reduces labor, instruments, and time, making it a cost-effective and efficient solution for the IDPH DOL’s molecular diagnostic needs.

The system’s ability to perform whole genome sequencing within 18 hours enables IDPH DOL to conduct real-time genomic surveillance for pathogens like SARS-CoV-2. This rapid testing is crucial for tracking disease spread, identifying variants, and making timely public health decisions, enhancing the department’s ability to respond quickly to emerging threats.

Version 7.01 Page 4 of 8

Bulletin Reference Number Open Market Bid 25-482DPH-OFCDI-B-44233

Requesting Agency/University IDPH

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

Product Catalog Qty 1.) Clear Dx System LR-SR 860005 2.00 This item is the actual Clear DX instrument that is needed to expand this automated sequencing technology.

2.) Clear Dx System Service Plan - 1 year 850072 2.00 This item provides service coverage for the new instrument to keep it in proper working order and calibrated. This also includes repair of the instrument if needed.

3.) Clear Labs IQ/OQ/PQ Services LR-SR System 900021 2.00 This item provides on-site instrument verification and validation services by Clear Labs personnel after installation. This ensures the instrument is ready for use for whole genome sequencing analysis.

4.) Clear Dx System and Installation Training 850067 4.00 This item is the expense to install the new instruments and train staff on how to use them.

5.) Shipping CL-IS Central NA 2.00 This is the cost of shipping the instrument to the lab.

6.) Clear Dx Packaging 850083 2.00 This is the cost of the crating and packing required to ship the instrument.

Equipment Total: $832,476.00.

Below is a list of Clear DX Reagents /Consumables- testing reagents (liquid based) and consumables (plastics, tips, ancillary items) necessary for processing of whole genome sequencing.

7.) Clear Dx™ WGS SARS-CoV-2 Reagent v3.0 and Automation Bundle 900005 Necessary for processing of whole genome sequencing.

8.) Clear Dx™ Microbial Surveillance WGS Reagent v2.0 & Automation Bundle 900015 Necessary for processing of whole genome sequencing.

9.) Clear Dx™ FlexPro Wastewater (SARS-CoV-2) WGS Reagent & Automation Bundle 900020 Necessary for processing of whole genome sequencing.

10.) Shipping

Reagent and consumable Total: $800,000 from list of Clear DX Reagents /Consumables- testing reagents (items 7-10).

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 Clear Dx™ system is the only fully automated, intelligent library preparation and Next-Generation Sequencing (NGS) platform capable of performing whole genome sequencing of both SARS-CoV-2 and bacterial isolates (Microbial Surveillance). It is the only system on the market that can perform automated bacterial isolate sample extraction, whole genome sequencing, and post-sequence analysis within 18 hours of loading a raw sample, all on a single instrument. This level of automation and integration significantly reduces labor requirements, making it essential for rapid, real-time genomic surveillance.

Version 7.01 Page 5 of 8

Bulletin Reference Number Open Market Bid 25-482DPH-OFCDI-B-44233

Requesting Agency/University IDPH

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 IDPH DOL already operates two Clear Dx™ instruments, which are used to sequence approximately 1,500 specimens annually, with plans to increase the sequencing of PulseNet organisms by 20-30% each year. Utilizing the same instruments across the labs allows for a consistent algorithm and standardized testing, ensuring accuracy and reliability in results.

Clear Labs, Inc. is the only manufacturer and authorized supplier of the Clear Dx™ system and its associated reagents and consumables in the United States. This exclusivity ensures that the IDPH DOL can maintain operational consistency and efficiency without the complications of integrating multiple systems or sourcing from different vendors.

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 agency has not considered alternative supplies or services because the IDPH DOL already operates two Clear Dx™ instruments, which are integral to their current genomic sequencing efforts, processing approximately 1,500 specimens annually. Utilizing the same instruments across all labs is crucial for maintaining a consistent algorithm and standardized testing process. This consistency ensures the accuracy and reliability of results, which is vital for the lab's operations.

Clear Labs, Inc. is the only manufacturer and authorized supplier of the Clear Dx™ system and its associated reagents and consumables in the United States. This exclusivity guarantees that the IDPH DOL can sustain operational consistency and efficiency without the complications that would arise from integrating multiple systems or sourcing from different vendors.

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?

The Illinois Department of Public Health (IDPH) has determined that the price for this procurement is fair and reasonable based on prior purchase history with Clear Labs, Inc. Based on this historical pricing and the ongoing need to maintain consistent testing protocols, IDPH has determined that the current price reflects a fair and reasonable cost for the instruments and reagents being procured.

Clear Labs, Inc is the only authorized reseller of the Clear Dx™ instruments and the reagents and consumables used for testing on their instruments. Clear Labs, Inc does not publish their pricing. However, IDPH DOL has reached out to other states across the U.S. that use the Clear DX instruments to confirm that pricing was competitive.

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

Yes No

Version 7.01 Page 6 of 8

Bulletin Reference Number Open Market Bid 25-482DPH-OFCDI-B-44233

Requesting Agency/University IDPH

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 the State of Illinois will face significant financial and operational impacts. First, the delay in acquiring additional Clear Dx™ instruments would hinder the IDPH Division of Laboratories (DOL) from expanding genomic sequencing to include other infectious diseases and microbes involved in outbreaks, particularly in long-term and congregate care facilities. This expansion is critical to addressing the growing issue of antibiotic resistance genes, which are placing increasing pressure on healthcare treatment mechanisms.

Without the approval of this sole source, the State will be unable to meet the rising demand for genomic sequencing, leading to increased costs and delays in obtaining timely test results. The current automation provided by the Clear Dx™ system reduces sample manipulation, enhancing the confidence and integrity of the testing process in a closed system. Additional instruments are crucial to managing ongoing staff shortages, allowing the lab to run smaller batches of samples and improve turnaround times by 2-3 days.

The inability to procure these instruments would exacerbate the strain on the lab's resources, delaying critical public health responses and increasing the risk of ineffective treatment outcomes in healthcare settings. The financial impact would include higher costs due to inefficiencies, potential increases in labor requirements, and the lost opportunity to reduce turnaround times, all of which would negatively affect the State’s ability to manage public health effectively.

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

No

Version 7.01 Page 7 of 8

Bulletin Reference Number Open Market Bid 25-482DPH-OFCDI-B-44233

Requesting Agency/University IDPH

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 16, 2024

Printed Name Leslie Chapman E-mail Address leslie.chapman@illinois.gov

Phone Number 618-457-5131

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 16, 2024

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 10/16/2024

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

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Bulletin Reference Number Open Market Bid 25-482DPH-OFCDI-B-44233

Requesting Agency/University IDPH

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

Project Title Clear DX Instrument, Service, and Reagent Contract

Vendor Clear Labs, Inc

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

IDPH DOL’s current use of multiple Clear Dx™ systems demonstrates the platform’s critical role in their laboratory operations, particularly for high-throughput molecular testing and genomic analysis. With increasing demands for testing, particularly in public health scenarios like pathogen surveillance and genetic testing, acquiring two (2) additional systems is necessary to scale up capacity.

These machines can rapidly process a large volume of samples, which is essential for labs dealing with public health emergencies, disease outbreaks, or routine diagnostics. The purchase will expand the IDP DOL's ability to handle more tests in a shorter timeframe.

Uniformity across the IDPH DOL’s is crucial for ensuring consistent, reliable, and reproducible test results. Clear Lab Clear Dx™ systems operate with the same algorithms and protocols, ensuring standardized testing procedures and outcomes across all locations. This consistency is essential for the accuracy of genomic data, particularly in tracking disease outbreaks and large-scale public health surveillance.

Clear Lab Clear Dx™ systems require proprietary reagents from Clear Labs, Inc. for optimal performance. These reagents are essential for the continuous operation of both existing and new machines. Without them, the systems would be unable to perform accurate testing, making the acquisition of reagents a non-negotiable operational necessity.

Automation of the Clear Dx™ platform streamlines the entire next-generation sequencing (NGS) workflow, reducing manual labor and minimizing human error. This automation ensures consistency and reproducibility, vital for the high-stakes environment in which the IDPH DOL operates, maintaining operational efficiency and accuracy.

Clear Dx™ is the only system capable of fully automating library preparation, whole genome sequencing, and post-sequencing analysis of both SARS-CoV-2 and bacterial isolates within 18 hours. This integration reduces labor, instruments, and time, making it a cost-effective and efficient solution for the IDPH DOL’s molecular diagnostic needs.

The system’s ability to perform whole genome sequencing within 18 hours enables IDPH DOL to conduct real-time genomic surveillance for pathogens like SARS-CoV-2. This rapid testing is crucial for tracking disease spread, identifying variants, and making timely public health decisions, enhancing the department’s ability to respond quickly to emerging threats.

Q2Answer: Product Catalog Qty 1.) Clear Dx System LR-SR 860005 2.00 This item is the actual Clear DX instrument that is needed to expand this automated sequencing technology.

2.) Clear Dx System Service Plan - 1 year 850072 2.00 This item provides service coverage for the new instrument to keep it in proper working order and calibrated. This also includes repair of the instrument if needed.

3.) Clear Labs IQ/OQ/PQ Services LR-SR System 900021 2.00 This item provides on-site instrument verification and validation services by Clear Labs personnel after installation. This ensures the instrument is ready for use for whole genome sequencing analysis.

4.) Clear Dx System and Installation Training 850067 4.00 This item is the expense to install the new instruments and train staff on how to use them.

5.) Shipping CL-IS Central NA 2.00 This is the cost of shipping the instrument to the lab.

6.) Clear Dx Packaging 850083 2.00 This is the cost of the crating and packing required to ship the instrument.

Equipment Total: $832,476.00.

Below is a list of Clear DX Reagents /Consumables- testing reagents (liquid based) and consumables (plastics, tips, ancillary items) necessary for processing of whole genome sequencing.

7.) Clear Dx™ WGS SARS-CoV-2 Reagent v3.0 and Automation Bundle 900005 Necessary for processing of whole genome sequencing.

8.) Clear Dx™ Microbial Surveillance WGS Reagent v2.0 & Automation Bundle 900015 Necessary for processing of whole genome sequencing.

9.) Clear Dx™ FlexPro Wastewater (SARS-CoV-2) WGS Reagent & Automation Bundle 900020 Necessary for processing of whole genome sequencing.

10.) Shipping

Reagent and consumable Total: $800,000 from list of Clear DX Reagents /Consumables- testing reagents (items 7-10).

Clear Labs, Inc. is the only manufacturer and authorized supplier of the Clear Dx™ system and its associated reagents and consumables in the United States. This exclusivity ensures that the IDPH DOL can maintain operational consistency and efficiency without the complications of integrating multiple systems or sourcing from different vendors.

Clear Labs, Inc. is the only manufacturer and authorized supplier of the Clear Dx™ system and its associated reagents and consumables in the United States. This exclusivity guarantees that the IDPH DOL can sustain operational consistency and efficiency without the complications that would arise from integrating multiple systems or sourcing from different vendors.

Clear Labs, Inc is the only authorized reseller of the Clear Dx™ instruments and the reagents and consumables used for testing on their instruments. Clear Labs, Inc does not publish their pricing. However, IDPH DOL has reached out to other states across the U.S. that use the Clear DX instruments to confirm that pricing was competitive.

Without the approval of this sole source, the State will be unable to meet the rising demand for genomic sequencing, leading to increased costs and delays in obtaining timely test results. The current automation provided by the Clear Dx™ system reduces sample manipulation, enhancing the confidence and integrity of the testing process in a closed system. Additional instruments are crucial to managing ongoing staff shortages, allowing the lab to run smaller batches of samples and improve turnaround times by 2-3 days.

The inability to procure these instruments would exacerbate the strain on the lab's resources, delaying critical public health responses and increasing the risk of ineffective treatment outcomes in healthcare settings. The financial impact would include higher costs due to inefficiencies, potential increases in labor requirements, and the lost opportunity to reduce turnaround times, all of which would negatively affect the State’s ability to manage public health effectively.