Acquisition of an Applied Biosystems QuantStudio 3 Real-Time PCR System

Requirements:

To ensure continuity of research, NIAMS proposes the acquisition of an Applied Biosystems QuantStudio 3 Real-Time PCR System. qPCR is a core technology used for nucleic acid amplification, quantification, and analysis and supports a wide range of research applications, including gene expression studies, pathogen detection, transcript quantification, and validation of experimental results. The QuantStudio 3 is the closest replacement to the current StepOnePlus systems, allowing researchers to maintain established workflows and consistency in experimental design and data interpretation. The QuantStudio 3 offers several operational advantages, including user-friendly software, compatibility with both Mac and PC platforms, touchscreen operation, and the ability to function as a standalone instrument or in conjunction with a computer. Its thermal block design is similar to the existing systems, minimizing the learning curve for users and supporting a broad range of genomic applications. In addition, the manufacturer offers trade-in credit for the current instruments, reducing the overall acquisition cost while providing access to a fully supported platform with available parts and technical support. Acquiring the QuantStudio 3 at this time will help prevent interruptions to research activities, maintain reliable and consistent data generation, and ensure that NIAMS laboratories have access to a supported and dependable qPCR platform.

4.1 PRODUCT FEATURES/SALIENT CHARACTERISTICS The contractor shall provide one Applied Biosystems QuantStudio 3 Real-Time PCR System or an equal system that meets all the following minimum requirements. 4.1.1. System Features/Benefits The system shall: • Utilize a platform providing 1 TB or storage space for data sharing at user discretion • be used with online scientific apps • come with desktop-based software, allowing single-plate run setup and analysis.

4.1.2. Technical specifications – Instrument The instrument shall: • have a 96 well 0.1 ml plate block format and the option to run fast protocols <30 minutes • not require a field service engineer for set up by end user. Set up should be easy for end user – directly out of the box. • not require a computer for installation • use an RNase P verification plate to verify performance • not require dye calibration upon installation • have dimensions fo 27 x 50 x 40 cm and be designed to maximize horizonal and vertical bench space • be capable of analyzing 96 samples simultaneously in various formats incluing both 96-well plates, 8-tube strips and individual tubes • the 96-well block should be made of at least 3 separated Peltier elements – VeriFlex Blocks. The maximum temperature difference programmable across the block should be 10 degrees C. 5 degrees C should be the maximum difference in temperature allowed between adjacent blocks. • Support reaction volumes of 10-30 uL on 0.1mL the 96-well block • Be factory calibrated with FAM, SYBR Green 1, VIC, NED, ABY, JUN, TAMRA, and ROX dyes • Have melt or dissociation curves that take place in steps with deltaT varying between 0.015 degrees C and 3.66 degrees C • Have a maximum block ramp rate of 9.0 degrees C/sec for the 0.1 mL block • Have a block with a temperature range of 4-99.9 degrees celcius • Have a heated cover with temperature range of 50-110 degreesC 2

• Have a long-lasting bright white LED source with median lifetime of at least 60,000 hours • Have a CMOS imager for data acquisition and collects data for each filter combination in less than 2 seconds • be used with 120-240 V outlets without modification or special plug requirements • Include a heated lid assembly to heat tops of sample plates and minimize reaction evaporation.

 4.1.3 Technical specifications – Instrument onboard computer The system shall: • Possess the capability to run in stand-alone mode, without an attached computer • Include a touchscreen interface and store protocols for quick starts with no computer needed • Have a touchscreen interface that enables viewing amplification plots and filtering them by sample, target and task • Have a touchscreen interface that facilitates uploading of protocols or downloading of run files via a USB, local network and the Connect platform • Have a touchscreen interface that allows uploading of protocols and run files directly to the Connect platform • Contain onboard storage with memory capacity of 10 GB for storing 1,000-5,000 standard absolute quantification run files, and be designed for run protection in case of power outages • Be able to be customized through the touchscreen for time zones and service/calibration notification settings • Have a touchscreen interface that supports the creation of local user accounts with PIN-protected access that can be linked to the Connect platform to online accounts on thermofisher.com • Have a touchscreen interface that allows creation and running of protocols as guests • Have a touchscreen interface that allows for editing of protocols at all stages of the reaction cycle as well as block settings, temperature settings duration, ramp rate, etc. • Have a touchscreen interface that allows a template to be loaded from a USB, local network or the Connect platform • Have a touchscreen interface that allows user to enter reagent information • Have a touchscreen interface that allows a run to be paused and during that pause for the block temperature to be set as well as for the drawer to be opened and closed • Have a touchscreen interface that allows editing of sample and target assignments • Have a touchscreen interface that allows the repeat of a previous run 3 • Have a touchscreen interface that allows users to perform dye calibrations and view results on the touchscreen • Have a touchscreen interface that allows RNase P verification runs and automatically provides pass/fail results • Have a touchscreen interface that allows a user to run a self-verification test • Have a touchscreen interface that allows the user to view the cure QC assessment after calibration and RNase P plate runs are finished • Have a touchscreen interface that allows progress monitoring.

 4.1.4 Performance Requirements The instrument shall: • Complete 40-cycle real-time PCR runs using fluorogenic 5’ nuclease assay and Fast chemistry in a standard 96-well plate in less than 30 minutes as well as being able to run in standard ramping mode with standard chemistry • Include an OptiFlex system that combines four coupled excitation, and emission filter sets to allow multiplexing up to four unique wavelengths • Support at least two reaction chemistries-TaqMan® Probes and SYBR Green dye • Have real-time quantitative PCR installation specifications to be able to distinguish between 5,000 and 10,000 template copies at a 99.7% confidence level.

 4.1.5 Software Requirements The software shall: • Allow flexible customization of run protocols • Allow the creation of secure templates that are locked with a password to limit modification of run setup • Provide run monitoring of connected instruments • Include preoptimized run protocols for applications like standard curve, relative standard curve, relative quantification of gene expression, and SNP genotyping with TaqMan® or SYBR Green chemistries • Include a copy of free software to analyze data for absolute and relative quantification, SNP detection and other assays. • Collect information on both TaqMan and SYBR assays in the same run • Have a genotyping optimization tool that uses real-time data • Provide raw fluorescence data and multicomponent data for troubleshooting • Allow conversion of protocols for the Applied Biosystems StepOnePlus and 7500 to the QuantStudio 3 system protocols • Allow batch analysis of up to 500 experiments simultaneously • Can control the instrument and analyze data from a remote computer on the same network 4 • Provide status monitoring of connected instruments and real-time plots STATEMENT OF NEED (SON) • Have the ability to send user notifications when a run is started, stopped or has an error • Allow registered users of the Connect platform to monitor any connected instrument • Allow users to run an assay plate without performing plate setup prior to beginning of run and to correct plate set up after the run • Allow export of all run results to excel and save graphs as .jpg files • Provide the ability to import a standard curve from one plate for analysis of another plate of the same instrument type • Allow for the selection of endogenous controls for gene expression experiments • Include statistical analysis tools including box-whisker plots, scatter plots and heat maps • Allow preselection of data to export and the location of the exported file • Allow for command-line functions for batch exporting of analyzed run files • Allow users to save predefined analysis settings for auto-exporting run data into format of choice • Contain online high-resolution melt application so user can specify number of clusters/variants and save defined controls and analysis setting.

 4.1.6 Instrument Ecosystem The instrument ecosystem shall: • Be part of a desktop ecosystem that consists of a suite of qPCR applications. Instrument data can be grouped (multi-plate) for relative quantitation, SNP genotyping, standard curve, HRM analysis, and presence/absence analysis. • Be part of the Connect platform • Be able to connect to the Connect platform for run setup download and data uploads • Allow a run to be monitored by a web browser or mobile device • Allow batch-analysis of up to 500 experiments simultaneously through an online relative quantitation module • Provide an endogenous control selection tool for gene expression experiments in both the desktop and online quantitation software • Contain statistical anaylsis tools with both the desktop and online quantitation software • Contain a genotyping optimization tool that uses real-time data to pick the best cycle number for calling genotype in both the desktop and online genotyping software • Allow the user to specify number of clusters/variants and save defined controls and analysis settings with both desktop and online software.

 4.1.7.  Design 5 The system shall: • Have an application programming interface (API) included that allows programming routines to be developed for controlling the instrument • Be cUL, UL, CE, C-TICK, and WEEE compliant • Be developed and manufactured in a facility with quality system requirements that comply with ISO 13485 standards and ISO 9001 standards 4.1.8 Gene expression profiling • Users shall be able to select from more than 61,000 predesigned human, mouse and rat Applied BiosystemsTMTaqMan® Assays.

 4.1.9 Able to accept the trade-in of Model STEPONEPLUS. Serial number 272008444 4.1.10 Must be compatible with protocols from Applied Biosystems StepOnePlus Real Time PCR (qPCR) allowing for consistency in experimental set-up 4.2 DELIVERY / INSTALLATION The contractor shall deliver and install the equipment within thirty (30) calendar days after receipt of award.