VERSANT® kPCR Molecular System Dynamic Assay Protocols Online Training

Welcome to the VERSANT® kPCR Molecular System Dynamic Assay Protocols Online Training. Dynamic Assay Protocols allow for: The integration of third party assays on the VERSANT kPCR Molecular System The combination of multiple assays from a single specimen in a single PCR plate Select Next to continue. Describe the features that support dynamic protocols on the VERSANT kPCR Molecular System Identify common operator errors that can occur when running dynamic protocols Navigate the software screens used to run a dynamic protocol Upon successful completion of this course, you will be able to: Select Next to continue. Congratulations. You have completed the VERSANT kPCR Molecular System Dynamic Assay Protocols online training course. Listed below are the key points that have been presented. Take time to review the material before you proceed to the final quiz. Describe the features that support dynamic protocols on the VERSANT kPCR Molecular System User Defined Number of SP and No SP Calibrator/Controls Post SP Loading of Analyte Reagent Rack Multiple Assays Per Plate Eluate Splitting Optional Universal Negative Control Delivery Optional Internal Control Delivery Navigate the software screens used to run a dynamic protocol Steps to run dynamic assay protocols on the SP module: Load the sample carriers. From protocol list, select the appropriate dynamic protocol. Enter the appropriate information on the Dynamic Assay Run Setup screen. On the Worklist Editor screen, either enter test orders or verify orders have been received from the LIS. Load the tip carrier. Load the SP reagents. When prompted by the software, load the No SP reagents. Review the Sample Preparation report. Identify common operator errors that can occur when running dynamic protocols. Identify common operator errors that can occur when running dynamic protocols Incorrectly transferring patient IDs to a non-Siemens AD module False negative patient results due to wells being processed with sample preparation errors False low patient results due to a delay in loading the post-process analyte reagent rack Delay in reporting results due to the test definition template being over-written with results Select Next to continue. Dynamic assay protocols enable the integration of third party assays on the VERSANT kPCR Molecular System. Several features allow you to run these assays:  User Defined Number of SP and No SP Calibrator/Controls Post SP Loading Step Multiple Assays Per Plate Eluate Splitting Universal Negative Control and Internal Control Delivery (Optional) Features of Dynamic Assay Protocols Learn about the features of dynamic assay protocols. Slide NumberText BlocksCalloutsAudio ScriptImage File1 Dynamic assay protocols enable the integration of third party assays on the VERSANT kPCR Molecular System. Several features allow for this:  User Defined Number of SP and No SP Calibrator/Controls Post SP Loading Step Multiple Assays Per Plate Eluate Splitting Optional Universal Negative Control Delivery Optional Internal Control Delivery     Select Next to continue.   Note: If audio does not automatically start, select the play arrow in the top left to begin.Dynamic assay protocols enable the integration of third party assays on the VERSANT kPCR Molecular System. This slideshow will describe several features of dynamic assays that allow for this integration. Select next to continue. 2 User Defined Number of SP and No SP Calibrator/Controls Many third party assays are designed for manual processing and therefore do not have the stability to have analyte reagents at room temperature during sample preparation. Dynamic Protocols allow users to replace the analyte reagent rack near the end of the sample preparation process to load calibrator/controls which are not intended to go through the sample preparation process.   SP Controls: Loaded at the start of the sample preparation process Transferred to the Deep Well Plate, extracted, and then eventually loaded on the PCR plate. No SP Controls: Loaded at the end of the sample preparation process Go directly to the PCR plate                    During run setup in the software, the operator enters the number of calibrator and controls which will go through the sample preparation process on their way to the PCR plate and the number that will be loaded at the end.   Select Next to continue.     Select each number to review the corresponding text. Callouts SP Rack No SP Rack Deep Well Plate PCR Plate Many third party assays are designed for manual processing and therefore do not have the stability to have analyte reagents at room temperature during sample preparation. These reagents cannot be loaded at the start of the run. To allow for this, Dynamic Protocols allow users to replace the analyte reagent rack near the end of the sample preparation process. When the sample preparation process is nearly complete and the samples have been eluted, the system is going to prompt the user to exchange the analyte reagent rack. The graphic illustrates the concept of how the system processes calibrators and controls depending on when they are loaded on the system. Depending on user input, calibrator and controls will be loaded on different analyte reagent racks but will eventually reach the PCR plate. Calibrators and controls loaded on the SP rack at the beginning of the run will be transferred to the Deep Well Plate, extracted, and then will eventually be loaded on the PCR plate. Calibrators and controls loaded on the No SP rack toward the end of the run will go directly to the PCR plate. During run setup in the software, the operator enters the number of calibrator and controls which will go through the sample preparation process on their way to the PCR plate and the number that will be loaded at the end. Select next to continue.3Post SP Loading Step   On this slide we are demonstrating when different types of reagents should be loaded.   Items loaded on the SP rack carrier: Internal control (optional) The PK Universal Negative Control (optional) Calibrators and controls Items loaded on the No SP rack carrier: Master Mix tube (combination of Primer/Probe and Enzyme Mix) Calibrators and controls   Select Next to continue.   On this slide we are demonstrating when different types of reagents should be loaded. Calibrators and controls can be loaded on either the SP or the No SP Rack Carrier. Internal control and the PK will be loaded on the SP rack carrier, as well as the Universal Negative Control which is new for dynamic assays and will be discussed later in the presentation. The user is required to combine the Primer/Probe and Enzyme Mix into a Master Mix tube which is loaded on the No SP rack carrier. Select next to continue.4Multiple Assays Per Plate   Many third party assay vendors have assay families which use the same amplification thermal profile and analysis settings – allowing multiple assays to be loaded on the same PCR plate.   Dynamic assays allow the user to run up to 6 assays on a single PCR plate.     Select Next to continue.   The next feature that we’ll discuss is the ability to run multiple assays on one plate. Many third party assay vendors have assay families which use the same amplification thermal profile and analysis settings, which would allow multiple assays to be loaded on the same PCR plate. All of these assays will then eventually go through the same amplification and detection analysis. Dynamic assays allow the user to run up to 6 assays on a single PCR plate. The number of assays is entered in the software by the operator during the run setup. The next slide will explain how it is possible to run either 3 or 5 assays on one plate. Select next to continue.5Multiple Assays Per Plate – Merged Assays   It is possible to run 3 or 5 assays by merging regions.   To run 3 assays: Select to run 4 assays Merge 2 of the regions together   To run 5 assays: Select to run 6 assays Merge 2 of the regions together   Select Next to continue. There is an option to merge regions to run different numbers of assays. For example, if the operator wants to run 3 assays, then in the software they would select to run 4 assays and merge 2 of those regions. In a set of merged regions, the second region will use the same controls as those assigned to the first region. Another option is to duplicate an assay in multiple regions. Duplicate regions differ from merged regions in that duplicate regions do not use the same controls. You can only merge 2 assay regions, so if a third region is assigned to the same assay, it will be a duplicate. Select next to continue.6 Eluate Splitting      In order to get more information out of a single sample, dynamic protocols provide that capability by splitting the eluate instead of the sample.    One aliquot from a sample that is processed in the deep well plate and then when it’s time to prepare the PCR plate, that one aliquot is divided among the assays that it was assigned to.     Select Next to continue.   Select each number to review the corresponding text.   Callouts Sample Rack Deep Well Plate PCR Plate Next we’ll discuss the ability to split the eluate. A customer’s preference is to get more information out of a single sample. Dynamic protocols provide that capability by splitting the eluate instead of the sample. You can have one aliquot from a sample that is processed in the deep well plate and then when it’s time to prepare the PCR plate, that one aliquot is divided among the assays that it was assigned to. During setup, the user is able to select which tests will be requested for each sample. Select next to continue.7 Optional Universal Negative Control Delivery      Dynamic assay protocols allow for an optional universal negative control to be used. This single control is processed as a sample and is split to each assay region.     Select Next to continue.   Select each number to review the corresponding text. Callouts SP Rack Deep Well Plate PCR Plate Another feather of Dynamic Assay Protocols is the ability for a Universal Negative Control to be extracted and amplified with all assays in a single run. The control is loaded on the SP rack and is transferred into the deep well plate. After sample processing, the control is automatically dispensed into the first SP control well in the PCR plate for each assay. Most negative controls use the same matrix. So instead of having to load multiple negative control tubes, one for each assay, with this feature one tube can be loaded which will be split amongst all the assay regions. Select next to continue.8 Optional Internal Control Delivery     Many third party assays come with an internal control.  Dynamic assay protocols allow the user to automate the delivery of the internal control to the deep well plate.     Select Next to continue.   Select each number to review the corresponding text. Callouts SP Rack Deep Well Plate PCR Plate Internal Control is not delivered to the PCR plate (includes No SP controls) Another new optional feature of Dynamic Assay Protocols is the ability for an Internal Control to be added to all controls and samples that go through the sample preparation process on the deep well plate. The internal control is not delivered directly to the PCR plate, therefore the internal control has to be manually added to any calibrators or controls that do not go through the sample preparation process. Select next to continue.9Summary   Several features that enable the integration of third party assays in dynamic assay protocols are: User Defined Number of SP and No SP Calibrator/Controls Post SP Loading Step Multiple Assays Per Plate Eluate Splitting Optional Universal Negative Control Delivery Optional Internal Control Delivery When complete, select the X in the upper-right corner to close the window and continue. Dynamic assay protocols enable the integration of third party assays on the VERSANT kPCR Molecular System. This slideshow described several features of dynamic assays that allow for this integration. Steps to run dynamic assay protocols on the SP module: Load the sample carriers. From protocol list, select the appropriate dynamic protocol. Enter the appropriate information on the Dynamic Assay Run Setup screen. On the Worklist Editor screen, either enter test orders or verify orders have been received from the LIS. Load the tip carrier. Load the SP reagents. When prompted by the software, load the No SP reagents. Review the Sample Preparation report. Running Dynamic Assay Protocols Learn how to run dynamic assay protocols. Instructions:If media does not automatically start, select the play arrow to begin.Flash File:/content/generator/Course_90008291/SIM_kPCR_DynamicAssayProtocols1/SIM_kPCR_DynamicAssayProtocols1.htmHTML5 File:/content/generator/Course_90008291/SIM_kPCR_DynamicAssayProtocols_HTML5_800x600/index.htmlPDF File: Integrating Third Party Assays on the System Learn factors to consider when simultaneously running third party assays on the system. Slide NumberText BlocksCalloutsAudio ScriptImage File1 Several factors should be considered when simultaneously running third party assays on the VERSANT kPCR Molecular System.   These include factors regarding:  Sample Preparation Process Amplification Thermal Profiles  Internal Control Target (Optional) Negative Control Matrix (Optional)    Select Next to continue. Note: If audio does not automatically start, select the play arrow in the top left to begin.Several factors should be considered when simultaneouslyrunning third party assays on the VERSANT kPCR Molecular System. This slideshow will describe some of these factors. Select Next to continue.2Sample Preparation Process   When setting up a dynamic assay run, required volumes are not user configurable.  Therefore, the required volumes for a given assay must be compatible with those hard coded values. In the example shown on the slide, three Altona assays are being looked at – CMV, EBV, and STEC. The application guides for these three assays show that each of these assays requires the same master mix volume, which is 20 uL, and the same sample or control volume, which is 10 uL.  The total PCR volume is 30 uL for each of these assays. The three tables shown on the right side of the slide were taken from the Reference Section of the kPCR version 3.1 Application Guide Addendum.  These tables display information on the output volumes to the PCR plate for each of the Dynamic Assay Preparations currently available in the software.   Select Next to continue. In this example, in order to run these three assays simultaneously, the only assay preparation that would work is Dynamic Assay Preparation 2 since that preparation has 20 uL master mix output and also meets the requirement of these assays to have 10 uL of control or sample output.The first factor can help determine if third party assays can be run simultaneously on the system is regarding the sample preparation process. When setting up a dynamic assay run in the software, required volumes are not user configurable. The volumes are hard coded in the test definitions. Therefore, the required volumes for a given assay must be compatible with those hard coded values. In the example shown on the slide, three Altona assays are being looked at – CMV, EBV, and STEC. The application guides for these three assays show that each of these assays requires the same master mix volume, which is 20 uL, and the same sample or control volume, which is 10 uL. The total PCR volume is 30 uL for each of these assays. The three tables shown on the right side of the slide were taken from the Reference Section of the kPCR version 3.1 Application Guide Addendum. These tables display information on the output volumes to the PCR plate for each of the Dynamic Assay Preparations currently available in the software. In this example, the only assay preparation that would work is Dynamic Assay Preparation 2 since that preparation has 20 uL master mix output, which is required by the Altona assays that are being looked at. Dynamic Assay Preparation 2 also meets the requirement of these assays to have 10 uL of control or sample output. Therefore in this example, the operator must choose to run Dynamic Assay Preparation 2 when running these particular Altona assays simultaneously on the system. Select next to continue.3Amplification Thermal Profiles   On the AD module, you can only define one thermal profile for the plate.  If multiple assays are run together, they must have the same thermal profiles.   In the example shown on the slide, CMV and EBV have exactly the same thermal profile.  STEC however is not compatible due to time duration differences.   The previous slide demonstrated how these assays all require the same sample preparation volumes and would be compatible with Dynamic Assay Preparation 2.  However, here we demonstrate that thermal profile must also be considered.  Based on the thermal profile evaluation, only CMV and EBV could be run together at the same time.   Another option for this example would be to run all three assays together, and then after the sample preparation process, manually pipette the STEC samples to a different PCR plate.  The two PCR plates could then be run on two different AD modules, each with its own thermal profile.   Select Next to continue. The second compatibility check that can help determine if a third party assay can be run on the system is the thermal profile of the PCR plate. On the AD module, you can only define one thermal profile for the plate. If multiple assays are run together, they must have the same thermal profiles. In the example shown on the slide, CMV and EBV have exactly the same thermal profile. STEC however is not compatible due to time duration differences. On the previous slide, we discussed how these assays all require the same sample preparation volumes and would be compatible with Dynamic Assay Preparation 2. However, here we demonstrate that thermal profile must also be considered. Based on the thermal profile evaluation, only CMV and EBV could be run together at the same time. Another option for this example would be to run all 3 assays together, and then after the sample preparation process, manually pipette the STEC samples to a different PCR plate. The two PCR plates could then be run on two different AD modules, each with its own thermal profile. Select next to continue.4Internal Control and Negative Control Matrix (Optional)    Internal Control: Delivered to all the wells in the deep well plate at the beginning of the sample preparation procedure.  Since there is only one internal control, the operator needs to make sure that the internal control target is the same across all the assays.   Universal Negative Control: Delivered to each assay region. The operator needs to know if the background matrix of the negative control is compatible with all the assays being run together.   Select Next to continue. Select each number to review the corresponding text. Callouts Internal Control Checkbox Universal Negative Control Checkbox This slide discusses a couple of factors involving controls. These are optional because using internal control and universal negative control is optional. There is one internal control that is delivered to all the wells in the deep well plate at the beginning of the sample preparation procedure. Since there is only one internal control, the operator needs to make sure that the internal control target is the same across all the assays. Similarly, there is one universal negative control that is delivered to each assay region. The operator needs to know if the background matrix of the negative control is compatible with all the assays being run together. The operator should keep these points in mind when deciding which assays to run together and whether to run an internal control and/or a negative control. Select next to continue.5 Summary   Several factors be considered when running a third party assays together at the same time on the VERSANT kPCR Molecular System: Sample Preparation Process Amplification Thermal Profiles  Internal Control (Optional) Negative Control Matrix (Optional)   When complete, select the X in the upper-right corner to close the window and continue. This slideshow described several factors that should be considered when running third party assays together at the same time on the VERSANT kPCR Molecular System. Common operator errors that can occur when running dynamic assay protocols include: Incorrectly transferring patient IDs to a non-Siemens AD module False negative patient results due to wells being processed with sample preparation errors False low patient results due to a delay in loading the post-process analyte reagent rack Delay in reporting results due to the test definition template being over-written with results Common Operator Errors Learn about common operator errors that can occur when running dynamic assay protocols. Slide NumberText BlocksCalloutsAudio ScriptImage File1Common operator errors that can occur when running dynamic assay protocols include: Incorrectly transferring patient IDs to a non-Siemens AD module False negative patient results due to wells being processed with sample preparation errors False low patient results due to a delay in loading the post-process analyte reagent rack Delay in reporting results due to the test definition template being over-written with results   Select Next to continue. Note: If audio does not automatically start, select the play arrow in the top left to begin.This slideshow will describe several common errors that can occur when running dynamic assay protocols. Select next to continue.2 Incorrectly transferring patient IDs to a non-Siemens AD module     Event:  Incorrect patient results due to a mis-matched patient ID.   Cause:  Incorrect AD setup due to user error when manually transferring information from run report to a Non-Siemens AD module   Mitigation:  To prevent incorrect patient results due to a mismatched patient ID, always confirm that the correct patient ID is entered in the well name.     Select Next to continue. The first common error we will discuss is incorrectly transferring patient IDs when using a non Siemens Amplification Detection module. Customers can use their dynamic assay plate maps on any AD module. Non Siemens AD modules will not have the capability to read the kPCR plate maps, therefore the patient IDs will have to be entered manually, which leads to the risk of manual entry errors. Select next to continue.3False negative patient results due to wells being processed with sample preparation errors   Event:  Incorrect patient results due to false negatives (No Ct is reported rather than “Invalid Well”)   Cause:  The operator is unaware of sample preparation errors since they are not reported in the final AD results report.   Mitigation:  Do not allow the system to process wells with sample preparation errors.  The operator is alerted to sample preparation errors on several software screens: Run Complete window Sample Preparation Run Report Plate Setup Comments Box on the AD Module Any wells with sample preparation errors must be clearly marked indicating a "Not in Use" status along with a Sample Preparation Error comment before they are sent to the LIS.  Refer to the “Identifying and marking wells with Sample Preparation Errors” section of the Application Guide Addendum for detailed instructions on how to mark wells as not in use.   Select Next to continue. The next error is false negative patient results due to the operator not being aware of sample preparation errors. Sample preparation errors are displayed several times throughout the process, but are not automatically reported in the final AD results report. The screens on which the operator is alerted to sample preparation errors are the Run Complete window, the Sample Preparation Run Report, and the Plate Setup Comments Box on the AD Module. It is the operator’s responsibility to ensure that the system does not process wells with sample preparation errors. Any wells with sample preparation errors must be clearly marked indicating a Not in Use status along with a Sample Preparation Error comment before they are sent to the LIS. Refer to the “Identifying and marking wells with Sample Preparation Errors” section of the Application Guide Addendum for detailed instructions on how to mark wells as not in use. Select next to continue.4False low patient results due to a delay in loading the post-process analyte reagent rack   Event:  False low patient results.   Cause:  The operator does not immediately load post-process analyte reagent rack, resulting in a delay and potential decay of eluate on the system.   Mitigation: When you see the system prompt, immediately replace the SP controls in the control carrier with the No SP controls.   The Sample Preparation Run Report displays the time from the prompt displaying on the screen to the time when the operator loads the No SP analyte reagent carrier on the system is displayed.  The operator would have to determine if this time is too long for the assay being run.     Select Next to continue. Select the number to review the corresponding text. Callouts The time it took the operator to load the No SP controls. Another potential operator error is false low patient results caused by not immediately loading the post-process (or No SP) analyte reagent rack. A delay in loading the No SP rack could lead to decay of the eluate on the system, depending on the assay that is run. In the Sample Preparation Run Report, the time from the prompt displaying on the screen to the time when the operator loads the No SP analyte reagent carrier on the system is displayed. The operator would have to determine if this time is too long for the assay being run. Select next to continue.5Delay in reporting results due to the test definition template being over-written with results   Event:  Delay In Reporting Patient Results   Cause:  A user’s test definition template is written over with results. The next time the user uses the template with a sample size greater than the overwritten results, wells exceeding the previous size will not be reported.   Mitigation:  Before starting a new run on the AD Module, select File > Save As, and enter a name for the run.  The name cannot match the name of any existing dynamic assay protocols.     Select Next to continue. The last potential issue we will discuss is a delay in reporting patient results. This could happen if a test definition template is over written with results. To avoid this issue, before starting a new run on the AD module, the operator should always save the run with a new file name using the save as feature. Select next to continue.6 Summary   Common operator errors can occur when running dynamic assay protocols include:   Incorrectly transferring patient IDs to a non-Siemens AD module False negative patient results due to wells being processed with sample preparation errors False low patient results due to a delay in loading the post-process analyte reagent rack Delay in reporting results due to the test definition template being over-written with results   When complete, select the X in the upper-right corner to close the window and continue. This slideshow described several common errors that can occur when running dynamic assay protocols.