BioRad QX200 Droplet Digital PCR System

Statement of Need Purchase of a BioRad QX200 Droplet Digital PCR System Purpose The Government requires the purchase of one (1) BioRad QX200 droplet digital PCR system to support DNA and RNA analyses focused on microbial contaminant identification, detection, quality control and quantification for genomic microbiology research conducted by the Office of Applied Microbiology and Technology (OAMT). The system will be used to determine viral nucleic acid identification and concentration post extraction of viral genome target(s) from food and produce wash water prior to downstream applications including next-generation sequencing (NGS) and whole genome microarray, and comparison to results obtained from alternate detection systems such as qPCR. This requirement represents the replacement of an aging BioRad QX200 droplet digital PCR system that is the platform currently in use to establish laboratory validated workflows, data systems, and ongoing research activities. Background OAMT (Division of Food Safety Genomics) currently operates a heavily used and aging QX200 droplet digital system dedicated to the experiment analyses and methods development for the detection and quantification of RNA derived from foodborne viruses such as hepatitis A virus. This instrumentation is integrated into validated standard operating procedures (SOPs), quality control workflows, and ongoing genomic research protocols within the foodborne virus research/methods development program. BioRad QX200 droplet digital PCR system is required to ensure compatibility with existing instrumentation, proprietary QX200 consumables, comparison to validated analytical methodologies, and established updated data systems. Use of an alternative manufacturer’s platform would require revalidation of laboratory methods and could adversely impact data comparability, workflow continuity, and ongoing research, methods development activities. Due to the use of proprietary consumables and validated methods specific to the QX200 platform, alternative systems are not considered technically acceptable without significant revalidation effort. Minimum Technical Requirements 1. Supply Requirement – QX200 Droplet Digital PCR System The Contractor shall provide one (1) QX200 Droplet Digital PCR System configured application of established methods and development of new methods development for the detection and quantification of RNA derived from foodborne viruses, as well as for DNA and RNA quantification and quality control analysis. 1.1 System Configuration The system shall: The system shall be a Bio-Rad QX200 Droplet Digital PCR system that is fully compatible with existing QX200 instrumentation, consumables, and validated laboratory workflows. Include manual droplet generator, droplet reader, computer, software, one year warranty with instrument purchase, and associated component consumables, for EvaGreen or probe-based digital PCR systems. Include delivery, installation and training, and initial operational verification. 1.2 Functional Capabilities The system shall: Perform droplet generation and quantitative analysis of DNA and RNA samples. Generate quantitative concentration measurements. Produce droplet sampling, partitioning, size segregation/exclusion, and counting for digital analysis of positive and negative samples/droplets with digital and graphic/image outputs suitable for intra- and inter sample quantitative analyses and comparisons for quantity distribution profiles. Provide results in formats relevant for downstream applications such as next-generation sequencing (NGS), whole genome microarray, and qPCR analyses and workflows. 1.3 Performance Characteristics The system shall: Process up to ninety-six (96) samples per run. Deliver complete analyses for a 96-samples run in 2 to 3 hours depending on the configuration of output, and any associated preliminary analyses. Require no more than 5 µL of sample input per analysis. Provide reproducible droplet sizing, partitioning, within run quality analyses, and quantification of results consistent with manufacturer specifications. 1.4 Software Requirements The system shall include manufacturer-provided software capable of: Automated data acquisition and analysis. Will include but not limited to tabular formatted (e.g. excel) and distribution profiles in both chart and graph formats, in both digital and image outputs suitable for intra- and inter sample quantitative analyses and comparisons for quantity distribution profiles. Concentration calculation and droplet size exclusion. Data exported in formats compatible with existing laboratory data systems. 1.5 Compatibility Requirements The system shall: Be fully compatible with existing QX200 Droplet Digital PCR system instrumentation. Utilize proprietary QX200 Droplet Digital PCR system consumables currently in use within the laboratory. Integrate with validated laboratory standard operating procedures (SOPs), quality control thresholds, and established data workflows. Compatibility with existing Government-owned QX200 instrumentation, QX200 proprietary consumables, and validated laboratory methods, existing datasets, and established data analysis workflows is a minimum technical requirement necessary to maintain data integrity and continuity of laboratory operations. 1.6 Delivery and Acceptance The Contractor shall: Deliver the system to the location specified in the contract during normal Government business hours. Coordinate installation with the Government point of contact. Confirm system operational status following installation. Final acceptance will occur upon successful installation and verification that the system meets the requirements stated herein. 2. Maintenance Requirement – QX200 Droplet Digital Reader Service Plan for Droplet Digital Reader w/Man DG OS. The Contractor shall provide a one (1) year service plan following the expiration of the manufacturer warranty, …