BRAND NAME JUSTIFICATION

Bio-Rad QX200 Droplet Digital PCR System

ALP Tracking Number: HFP-2026-133843

1. Description of the Requirement

The Office of Applied Microbiology and Technology (OAMT) requires replacement of an aging Bio-Rad QX200 Droplet Digital PCR (ddPCR) system, including droplet generator and droplet reader components, to support ongoing research and method development activities related to hepatitis A virus (HAV) detection in food matrices.

The estimated value of this acquisition is approximately $38,000

2. Brand Name Specification

This requirement is for the Bio-Rad QX200 Droplet Digital PCR System (including compatible droplet generator and reader components).

This brand-name restriction is justified in accordance with FAR 11.105.

3. Minimum Technical Requirements

The Government’s minimum technical requirements are for a droplet digital PCR system that:

Utilizes droplet-based partitioning technology consistent with previously validated RTddPCR methods

Is fully compatible with Bio-Rad QX200 droplet generation and reading workflows Is compatible with QX Manager Software version 2.2 Standard Edition, including existing analysis templates and data output formats Produces data outputs (e.g., droplet amplitude, cluster separation, concentration calculations) that are directly comparable to existing validated datasets Supports continuity of validated RTddPCR methods for HAV detection in food matrices without requiring revalidation Is interoperable with external laboratory collaborators currently using the Bio-Rad

QX200 platform

The Government’s minimum need is not simply a digital PCR system, but one that ensures methodological continuity, data comparability, and uninterrupted research progress. This acquisition is necessary to replace an aging and increasingly unreliable QX200 system currently used for ongoing research activities. The existing system has experienced performance degradation and poses a risk of failure that would disrupt ongoing method development and data generation efforts.

The system is required to support active research on HAV detection in food matrices, including studies that are currently in progress and rely on consistent instrumentation for data integrity. Without replacement of the system, the Government would be unable to continue these activities without interruption, resulting in delays to research that supports regulatory and public health decision-making.

Therefore, the acquisition is necessary to maintain operational capability and ensure continuity of ongoing research, and is not a matter of convenience.

4. Rationale for Brand Name Restriction

OAMT is currently conducting active research and comparative method development studies evaluating reverse transcription quantitative PCR (RTqPCR) against reverse transcription droplet digital PCR (RTddPCR) for HAV detection in complex food matrices.

The RTddPCR methods under evaluation have been developed, optimized, and partially validated specifically using the Bio-Rad QX200 hardware configuration and QX Manager Software 2.2 Standard Edition. These methods include platform-specific assay optimization parameters, droplet amplitude thresholding approaches, and inhibition mitigation strategies.

Existing datasets generated during this work are directly tied to QX200 output formats and performance characteristics. Use of a different platform would result in non-comparable data due to differences in partitioning technology, fluorescence signal interpretation, and analysis software.

OAMT is also engaged in collaborative and comparative studies with external laboratories utilizing the Bio-Rad QX200 platform. Maintaining the same platform is necessary to ensure consistency of results and validity of inter-laboratory comparisons. Use of an alternative platform would require redevelopment and revalidation of RTddPCR methods, as existing assays have been optimized and partially validated specifically on the Bio-Rad QX200 system. Revalidation would require significant staff time, laboratory resources, and repeated testing across multiple food matrices to re-establish analytical sensitivity, specificity, inhibition performance, and reproducibility.

This effort is estimated to require approximately 6–12 months of additional work, resulting in measurable cost and delaying ongoing research activities that support regulatory and public health decision-making. During this period, existing datasets would not be directly comparable, and collaborative studies with external laboratories would be disrupted.

The use of an alternative digital PCR platform, including newer Bio-Rad platforms such as QX ONE or systems from other manufacturers, would require full or partial method revalidation. This would include generation of new performance data across multiple food matrices, reassessment of inhibition effects, and re-establishment of analytical sensitivity and reproducibility. Such efforts are estimated to require approximately 6–12 months and would delay ongoing research activities.

For these reasons, only the Bio-Rad QX200 system meets the Government’s minimum need for continuity, comparability, and support of ongoing validated research activities.

This restriction is based on technical necessity and protection of active research integrity and is not due to vendor preference.

5. Unique Capabilities of the Bio-Rad QX200

The Bio-Rad QX200 system provides specific capabilities required to meet the Government’s minimum needs that are not fully met by alternative platforms:

Established method validation baseline: All current RTddPCR methods for HAV detection have been developed and optimized specifically on the QX200 platform

Droplet generation consistency: The QX200 droplet formation process produces droplet characteristics that are integral to existing assay performance and thresholding approaches

Software compatibility: QX Manager Software 2.2 is configured with existing analysis templates, thresholds, and workflows that are not directly transferable to other platforms

Data continuity: Historical datasets were generated using QX200-specific output formats, making direct comparison dependent on continued use of the same system

Inter-laboratory standardization: External collaborators are using the QX200 platform, requiring consistency in instrumentation to ensure valid comparative results

Other commercially available systems utilize different partitioning technologies, data output formats, and analysis workflows, which would require method redevelopment or bridging studies.

6. Market Research Summary

Market research identified several commercially available digital PCR systems, including:

Thermo Fisher QuantStudio Absolute Q Digital PCR System Stilla Naica Digital PCR System Bio-Rad QX ONE Digital PCR System

These alternatives were evaluated and determined to be insufficient for the following reasons:

Different partitioning technologies (e.g., chip-based or microfluidic systems versus droplet-based), resulting in different assay performance characteristics

Incompatible data output formats, preventing direct comparison with existing validated datasets

Different software environments, requiring redevelopment of analysis workflows and thresholds

Need for bridging studies or full method revalidation, including reassessment of sensitivity, inhibition, and reproducibility across food matrices

Newer digital PCR platforms from the same manufacturer, including the Bio-Rad QX ONE system, do not meet the Government’s minimum requirements. While these systems provide digital PCR capability, they utilize different hardware configurations, droplet generation processes, and software environments that are not directly compatible with the existing QX200-based methods and datasets. As a result, use of a newer system would produce data that is not directly comparable to existing validated datasets and would require redevelopment and revalidation of methods.

While these systems are capable of performing digital PCR, they do not meet the Government’s minimum requirement for continuity of validated methods and data comparability without additional validation effort.

The QX200 system is proprietary to Bio-Rad; however, authorized distributors may provide the system.

7. Market Research Methodology

Market research for this requirement was conducted by:

REDACTED, Management & Program Analyst, Office of Applied Microbiology and Technology (OAMT)

REDACTED, Research Microbiologist / Technical Point of Contact, Office of Applied Microbiology and Technology

Market research was performed between March 12-23, 2026

The following market research techniques were used:

Review of manufacturer technical documentation, product specifications, and published application notes for commercially available digital PCR systems (including Bio-Rad, Thermo Fisher Scientific, and Stilla Technologies) to assess compatibility with existing QX200-based methods

Review of vendor white papers and peer-reviewed publications describing platform-specific performance characteristics and workflows

Consultation with internal subject matter experts and laboratory personnel currently using the QX200 system to evaluate method compatibility and data comparability requirements

Consideration of interoperability requirements for ongoing collaboration with external laboratories utilizing the Bio-Rad QX200 platform

Informal vendor engagement, including product information provided by manufacturer representatives regarding system capabilities and software compatibility

In addition, available product literature and technical documentation were reviewed to assess whether alternative systems could meet the Government’s minimum requirements without requiring method redevelopment or revalidation.

No alternative sources were identified that could meet the Government’s minimum requirements without requiring significant additional validation, time, and resource investment.

Based on the conducted market research, it was determined that alternative systems could not meet the Government’s minimum requirements without requiring redevelopment or revalidation of existing methods.

8. Conclusion

Based on the ongoing validated research activities and the requirement to preserve methodological continuity, restriction to the Bio-Rad QX200 Droplet Digital PCR System is necessary to meet the Government’s minimum technical needs.

Accordingly, restriction to the Bio-Rad QX200 Droplet Digital PCR System is necessary to satisfy the Government’s minimum needs and is based on technical requirements directly linked to the program’s requirement to support ongoing HAV method development, ensure scientific validity of comparative studies, and avoid disruption to research that may inform regulatory or public health applications.

This justification restricts the requirement to the specified brand name in accordance with

FAR 11.105.

Prepared By:

Name:REDACTED

Title: Management & Program Analyst / COR

Office: Office of Applied Microbiology and Technology (OAMT)

Date: 4/22/2026

REDACTED