Digital LightCycler® System User Assistance Publication version 1.1 Software version 1.
Publication information Publication version Software version Revision date Change description 1.0 1.0 February 2022 First version 1.1 1.0 September 2022 US-specific publication version with added US-specific compliance information. u What is new in US-specific publication version 1.1 (13) y Revision history Edition notice This publication is intended for users of the Digital LightCycler® System.
General attention To avoid serious or fatal injury, ensure that you are familiar with the system and safety information before you use the system. r Pay particular attention to all safety precautions. r Always follow the instructions in this publication. r Do not use the instruments in a way that is not described in this publication. r Store all publications in a safe and easily accessible place.
Open-source and commercial software Digital LightCycler® System may include components or modules of commercial or open-source software. For further information on the intellectual property and other warnings, as well as licenses pertaining to the software programs included in Digital LightCycler® System, refer to the electronic distribution included with this product.
To view the full text of the 2014/53/EU declaration of conformity, go to the Roche DiaLog global website (dialogportal.roche.com) and choose the eLabDoc link. If you are unable to access Roche DiaLog, contact a Roche Service representative. Compliance with the applicable directives is provided by means of the declaration of conformity. This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant to Part 15 of the FCC Rules.
Roche Molecular Systems, Inc. 1080 US Highway 202 South Branchburg, NJ 08876 USA Made in Switzerland Roche Diagnostics GmbH Sandhofer Strasse 116 68305 Mannheim Germany Distributed in the United States by: Roche Diagnostics 9115 Hague Road Indianapolis, IN 46256 USA Roche affiliates A list of all Roche affiliates can be found at: www.roche.com/about/business/roche_worldwide.htm eLabDoc Electronic user documentation can be downloaded using the eLabDoc e-service on Roche DiaLog: dialogportal.roche.
Table of contents Table of contents Publication information 2 Contact adresses 5 Intended use 9 Symbols and abbreviations 9 What is new in US-specific publication version 1.
Table of contents 15 16 Performing a development workflow without unassigned sample setup Performing a development workflow with unassigned sample setup Projects in the development software Run profiles in the analyzer software Entering run information for a development run in the analyzer software Runs in the development software Editing lane settings via copy and paste in the development software Clustering in the development software Analyses in the development software Unassigned sample setups in
Intended use The Digital LightCycler® System supports a semiautomated workflow to run Polymerase Chain Reaction (PCR) based Nucleic Acid Testing (NAT). The system performs digital endpoint PCR analysis of microfluidic partitions, combining the functionalities of instrumentation, consumables, reagents, and data management to provide an efficient workflow from sample partitioning to result interpretation.
Symbols used in the publication Symbol Explanation o List item u Cross-reference to another topic w Figure, used in figure titles and crossreferences to figures y Table, used in table titles and crossreferences to tables z Equation, used in cross-references to equations k Code example, used in code titles and crossreferences to codes Tip, used for extra information on correct use or for useful hints Extra information within a task Result of an action within a task Frequency of a task Durat
Symbol Explanation Distributed by Serial number Catalog number Unique device identifier Lot number Caution Protective earth Consult operating instructions Temperature limits Humidity limits Keep upright Fragile handle with care Keep dry y Symbols used on product Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Symbol Explanation Do not stack Keep away from sunlight Used to indicate that the equipment is suitable for alternating current only; to identify relevant terminals Expiry date To indicate that the device requires a prescription to use y Symbols used on product Abbreviations The following abbreviations are used.
Abbreviation Definition in.
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Safety 1 General safety information ........................................................................ 17 Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Table of contents 17 General safety information Introduction.............................................................................. 19 Safety classifications............................................................. 20 Safety precautions ................................................................. 21 Installation and transport......................................... 21 Safe and proper use of the system ...................... 21 Operating conditions ..............................
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General safety information 19 Introduction General attention To avoid serious or fatal injury, read this publication thoroughly before you use the system. r Pay particular attention to all safety precautions. r Always follow the instructions in this publication. r Do not use the system in a way that is not described in this publication. r Keep this publication in a safe place to ensure that it is not damaged and remains available for use.
Safety classifications Safety classifications The safety precautions and important user notes are classified according to the applicable standards. Familiarize yourself with the following meanings and icons: Safety alert r The safety alert symbol is used to alert you to potential physical injury hazards. Obey all safety messages that follow this symbol to avoid possible damage to the system, injury, or death.
General safety information 21 Safety precautions In this section Installation and transport (21) Safe and proper use of the system (21) Operating conditions (22) Electromagnetic compatibility (23) Installation and transport Errors in installation Error during installation of a new system or new parts can cause malfunctions. r Leave installation activities to Roche Service representatives. Damage during transport Damage during transport can cause malfunctions.
Safety precautions u List of available consumables and reagents (186) Operating conditions Unsuitable operating conditions Operation outside of the specified ranges may lead to incorrect processing or malfunction of the system. r Consult the specifications. r Use the system indoors only. Avoid proximity to heat sources and high radiation, and avoid humidity outside of the specified range. r Ensure that the system’s ventilation openings always remain unobstructed.
General safety information 23 Electromagnetic compatibility The system complies with the emission and immunity requirements described in the parts IEC 61326-2-6 and IEC 61326-1. The system complies with the emission requirements described in FCC CFR 47, Part 15 Class A. The system has been designed and tested to CISPR 11 Class A. In a domestic environment, the system may cause electromagnetic interference, in which case you must take measures to mitigate the interference.
Safety precautions Electromagnetic fields Strong electromagnetic fields can result in degradation of the system performance. r Evaluate the electromagnetic environment before operating the system. r Do not use portable radio frequency (RF) communications equipment (including peripherals such as antenna cables and external antennas) closer than 30 cm to any part of the system, including cables specified by the manufacturer.
General safety information 25 Warning messages Electrical safety Electric shock Removing the covers of electronic equipment can cause electric shock. r Do not remove any cover of the system except those covers specified in the instructions. r Do not exchange or remove any part of the instruments. Leave replacement or repair of all instrument parts to Roche Service representatives. Fire and burns Alcohol is a flammable substance.
Caution messages Caution messages In this section Personal injury (26) Incorrect, invalid, or delayed results (27) Waste handling (33) Personal injury Sharps, rough edges, and/or moving parts Personal injury and infection due to sharps, rough edges, and/or moving parts. r Laboratory best practices can reduce the risk of injury. r Be aware of your laboratory environment, wellprepared, and follow this publication.
General safety information Moving drawers 27 The nanowell plate drawer of the partitioning engine and the nanowell plate stack drawer of the analyzer open and close during operation. An opening drawer may strike you. A closing drawer may pinch your fingers. r Keep away from the nanowell plate drawer of the partitioning engine and the nanowell plate stack drawer of the analyzer during operation.
Caution messages Improper handling of nanowell plates Scratches, finger prints, dust, or other artifacts on the nanowell plate lanes compromise the image integrity, which may cause incorrect, invalid, or delayed results. r Open the packing of the nanowell plates only immediately before use. r Do not leave the nanowell plates in the open for any length of time. r Do not touch the nanowell plate lanes. r Handle the nanowell plates by the long sides of the nanowell plate frames only.
General safety information Contamination of the partitioning engine 29 The partitioning fluid bottles and the liquid waste bottles are indistinguishable by their overall appearance. Loading a liquid waste bottle in the position of the partitioning fluid bottle may contaminate the partitioning engine, which may cause incorrect, invalid, or delayed results. r Store partitioning fluid bottles and liquid waste bottles in a way to allow for proper distinction.
Caution messages Leakage of sample material from nanowell plates Pipetted and partitioned nanowell plates do not have a physical barrier against leakage of the reaction mixtures from the nanowell plates. Leakage of the reaction mixtures from the nanowell plates may contaminate the laboratory, which may cause incorrect, invalid, or delayed results. r After unloading the nanowell plates from the analyzer, immediately place them in a resealable plastic bag that you keep sealed.
General safety information Invalidated controls 31 If you invalidate a nanowell plate lane that contains a control, the system automatically invalidates all final results of the sample setup for the affected targets, which may cause delayed results. r Take extra care to avoid wrongly invalidating a nanowell plate lane that contains a control. r If you must invalidate a nanowell plate lane that contains a control, consider the implications for the final results of the sample setup.
Caution messages Weak passwords Weak passwords may allow unauthorized access to the system, data manipulation or loss, or unauthorized access to personal information, which may cause incorrect, invalid, or delayed results. r Use strong passwords. r Do not share passwords. r Do not write down passwords. r Do not share user accounts. r As an administrator, ensure that the global password policy configured in the analyzer software enforces safe password handling.
General safety information Unprotected export files 33 Insecure transfer or storage of backup files and archive files may allow for data manipulation, which may cause incorrect, invalid, or delayed results. r Ensure that backup files and archive files are transferred securely, are stored in a secure location, and are protected from any unauthorized access and disaster.
Notices Notices In this section Delay (34) Loss of supplies (35) Unauthorized access to personal information (36) Damage to the instruments (36) Delay Incorrect loading of the partitioning engine The partitioning fluid bottles and the liquid waste bottles are indistinguishable by their overall appearance. Loading a liquid waste bottle in the position of the partitioning fluid bottle may contaminate the partitioning engine, which may cause a time delay.
General safety information 35 Loss of supplies Incorrect loading of the partitioning engine The partitioning fluid bottles and the liquid waste bottles are indistinguishable by their overall appearance. Loading a partitioning fluid bottle in the position of the liquid waste bottle contaminates the partitioning fluid and the partitioning fluid bottle. r Store partitioning fluid bottles and liquid waste bottles in a way to allow for proper distinction.
Notices Unauthorized access to personal information Compromised data security Unrestricted physical access to the system and attached infrastructure, and unprotected IT infrastructure may allow for infection with malicious software, manipulation of system components, or misuse of the system. Infection with malicious software, manipulation, or misuse may cause incorrect, invalid, or delayed results, or unauthorized access to personal information.
General safety information Mechanical stress 37 Shock, vibration, or pressure can damage the system. r Keep sources of vibration away from the instruments. 1 General safety information r Do not place objects on top of the instruments. Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Safety labels on the system Safety labels on the system In this section About safety labels on the system (38) List of safety labels on the system (38) Location of safety labels on the partitioning engine (39) Location of safety labels on the analyzer (40) About safety labels on the system The system has warning labels to draw your attention to areas of potential hazard. The following list explains the meanings of the labels at the locations where you find the labels.
General safety information 39 No heavy load There is a risk of instrument damage near this label. Do not place heavy objects on the instrument part. Location of safety labels on the partitioning engine Safety labels on the partitioning engine (front view with open nanowell plate drawer) 1 General safety information w Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Safety labels on the system 1 General safety information Location of safety labels on the analyzer w Safety labels on the analyzer (front view with open nanowell plate stack drawer) w Safety labels on the analyzer (side view) Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
General safety information 41 Safety information for disposal r Dispose of the system according to local regulations. For more information, contact your Roche Service representative. 1 General safety information Disposal Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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User Assistance 2 Using the User Assistance......................................................................... 45 Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Table of contents 45 Using the User Assistance 2 In this chapter 47 Overview of User Assistance functions ......................... 49 Accessing the User Assistance from the software ... 51 Accessing the User Assistance online........................... 52 Accessing the User Assistance offline........................... 53 Searching in the User Assistance.................................... 54 2 Using the User Assistance About the User Assistance.............................................
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Using the User Assistance 47 About the User Assistance The User Assistance supports you in your daily work. It is available in different formats (e.g., online, offline,...). The functionalities provided by the user interface are similar across all formats. The User Assistance window is divided into a main panel and a detail panel.
About the User Assistance Recently viewed To get a list of the most recent topics that you have viewed. Favorites 2 Using the User Assistance To store your frequently used topics for direct access at any time. Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Using the User Assistance 49 Overview of User Assistance functions Enlarging images You can enlarge an image by choosing the button beside it. The image is displayed in a callout in which you can further zoom in using the zoom slider. Browsing history You can use the and navigation buttons to go backwards and forwards in your browsing history. At the end of some topics, there is a list of links to other topics that contain related information. You can go back to the original topic using the button.
Overview of User Assistance functions Viewing descriptions of terms The button in text indicates that you can view information about the term to the button’s left. When you choose the button, a callout is displayed containing a description of the term. Downloading a PDF You can download the publication to your computer in PDF format using the Download PDF button. Download PDF Giving feedback In the User Assistance online, at the bottom of each topic, you can give feedback on that topic.
Using the User Assistance 51 Accessing the User Assistance from the software If you need support while you are using the software, you can access the User Assistance directly within the software. i Some features are not available in the User Assistance integrated in the software. r To access the User Assistance from the analyzer software and the web application 1 In the global information area of the analyzer software button.
Accessing the User Assistance online Accessing the User Assistance online When accessing the User Assistance online, the latest content is always available. i d If you have no internet access, contact your Roche representative for a standalone version of the User Assistance.
Using the User Assistance 53 Accessing the User Assistance offline You can use the standalone User Assistance offline on your PC. No internet connection is required. i d To get the installer for the standalone User Assistance, contact your Roche representative. m PC m Installer for standalone User Assistance r To access the User Assistance offline 1 Copy the installer for the standalone User Assistance to your PC.
Searching in the User Assistance Searching in the User Assistance Use the search function in the User Assistance to find information directly. Search options There are 2 search options in the User Assistance: • Text search: Searches the text entered in the search field. • Faceted search: Limits the number of search results using filters. You can combine both search options.
Using the User Assistance 55 r To perform a search in the User Assistance 1 In the User Assistance, choose the Search in this publication tab. 2 To perform a simple search, enter full or partial text entries, and then choose the button. Search results Type Topic Search in this publication 3 To perform a faceted search, choose the button. f The filter drop-down lists are displayed. 4 From the drop-down lists, choose one or more search filters.
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System description 3 Overview of the system ............................................................................... 59 4 Overview of the instruments ..................................................................... 69 5 Overview of the software components.................................................. 81 6 Overview of the supplies .......................................................................... 157 7 Overview of orders, run prerequisites, and results.......................
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Table of contents 59 Overview of the system 3 In this chapter 61 Overview of the workflows ................................................. 63 Overview of the system architecture and the data flow.............................................................................................. 65 Overview of the connections ............................................. 67 3 Overview of the system Overview of the system........................................................
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Overview of the system 61 Overview of the system The system is a nucleic acid quantification system that uses digital PCR technology (dPCR). The system partitions a sample into a large number of nanowells to allow for absolute quantification of a target nucleic acid sequence without a standard curve. The system allows for a wide range of applications, e.g.
Overview of the system • About merged lanes Software components: The software components (partitioning engine software, analyzer software, web application, and development software) control the instruments and/or allow you to plan, perform, and analyze your runs. Merged lanes emulate the partitioning of a larger sample volume into a higher number of nanowells. The system treats the nanowells of a set of merged lanes as if they belong to 1 nanowell plate lane.
Overview of the system 63 Overview of the workflows The system supports 2 distinct workflows (diagnostic workflow and development workflow) for different purposes. About the diagnostic workflow The diagnostic workflow is designed for diagnostic purposes. In diagnostic workflows, you work with the following system components: • • • Web application Partitioning engine Analyzer As part of a diagnostic workflow, the nanowell plates are processed in a diagnostic run on the analyzer.
Overview of the workflows The supplies for a development workflow are partly provided by Roche (e.g., master reagents, nanowell plates) and partly by the laboratory (e.g., primers and probes). For development workflows, there are the following 2 options to plan the sample setup (i.e., the reaction mixtures and their distribution on the nanowell plates for the development run): • Without unassigned sample setup: – You plan the sample setup outside of the development software.
Overview of the system 65 Overview of the system architecture and the data flow The following illustration gives an overview of the system architecture and the data flow. The following applies: • The database of the system is located on the analyzer. • • The data transfer between the system components takes place either via direct connection or via LAN. For diagnostic workflows, result calculation is done on the analyzer.
Overview of the system architecture and the data flow • • Partitioning engine Analyzer In a development workflow, you work with the following system components: • Development software • Partitioning engine Analyzer 3 Overview of the system • Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Overview of the system 67 Overview of the connections You can connect the system to an LIS, to AVENIO Connect, and/or to an external device via EDI. The system behavior depends on the type of connection. About LIS connection If the system is connected to an LIS, the following applies to the diagnostic workflow: • The web application can receive the orders automatically from the LIS (LIS orders). • The results are sent back from the web application to the LIS (manually or automatically).
Overview of the connections • • • • Start development run: An EDI user must be logged on and the requested run profile must exist on the analyzer. Start diagnostic run: An EDI user must be logged on. Query analyzer status: Possible without EDI user logged on. Query workflow status: An EDI user must be logged on. 3 Overview of the system You cannot work locally on the analyzer if it is controlled remotely via EDI. Roche Diagnostics Digital LightCycler® System · Software version 1.
Table of contents 69 Overview of the instruments 4 In this chapter 71 Overview of the analyzer ..................................................... 74 About the hand-held barcode readers .......................... 77 About the mouse.................................................................... 78 About the external keyboard ............................................. 79 4 Overview of the instruments Overview of the partitioning engine................................
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Overview of the instruments 71 Overview of the partitioning engine The partitioning engine partitions the samples into the nanowells on the nanowell plates and seals the nanowells with partitioning fluid.
Overview of the partitioning engine Use your finger or a touch screen stylus on the touch screen monitor. u Overview of the partitioning engine software (83) About the nanowell plate drawer The nanowell plate drawer holds 1 nanowell plate during partitioning. The design of the nanowell plate drawer and the beveled corner of the nanowell plate ensure the correct orientation of the nanowell plate in the nanowell plate drawer. i Do not try to close the nanowell plate drawer manually.
Overview of the instruments 73 u Starting up the partitioning engine (231) u Shutting down the partitioning engine (437) u Restarting an unresponsive partitioning engine (506) About the power inlet About the LAN port About the USB ports The power inlet is located at the back of the partitioning engine. The LAN port is located at the back of the partitioning engine. To access the LAN port, remove the cover. The partitioning engine has 2 USB ports to connect external storage devices, e.g.
Overview of the analyzer Overview of the analyzer The analyzer performs thermal cycling and image acquisition.
Overview of the instruments 75 The design of the nanowell plate stack drawer and the beveled corners of the nanowell plates ensure the correct orientation of the nanowell plates in the nanowell plate stack drawer. i Do not try to close the nanowell plate stack drawer manually. Instead, follow the loading and unloading procedures for the analyzer.
Overview of the analyzer u Resolving an alarm of the analyzer (527) About the power inlet About the LAN port The power inlet is located on the right side of the analyzer next to the power switch. The LAN port is located at the back of the analyzer. About the components inside the analyzer A The nanowell plate handler transfers the nanowell plates between the nanowell plate stack drawer, the thermal cycler units, the nanowell plate park position, and the detection unit.
Overview of the instruments 77 About the hand-held barcode readers You can connect hand-held barcode readers to the analyzer, to the computer running the web application, and to the computer running the development software. Instead of manually entering the IDs, e.g., sample IDs and nanowell plate IDs, use a hand-held barcode reader to scan the barcode labels. Connect the hand-held barcode reader to a USB port on the right side of the analyzer.
About the mouse About the mouse You can connect a mouse to the analyzer. Instead of using the touch screen, use the mouse to work with the analyzer software. Connect the mouse to a USB port on the right side of the analyzer. Contact your local IT support for installation and configuration of the mouse. 4 Overview of the instruments u About the USB ports (75) Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Overview of the instruments 79 About the external keyboard You can connect an external keyboard to the analyzer. Instead of using the virtual keyboard in the analyzer software, use the external keyboard for data entry. Connect the external keyboard to a USB port on the right side of the analyzer. Contact your local IT support for installation and configuration of the external keyboard.
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Table of contents 81 Overview of the software components Overview of the partitioning engine software ............. 83 About the global information area of the partitioning engine software................................... 83 About the work area of the partitioning engine software ........................................................... 85 Overview of the web application...................................... 89 About the global information area of the web application .........................
5 Overview of the software components 82 Table of contents About the Navigation area of the development software............................................... 127 About the work area of the development software .......................................................................... 127 Tabs in the development software ....................... 129 About the tabs in the development software............................................................... 129 About the run tabs ....................
Overview of the software components 83 Overview of the partitioning engine software A You access the partitioning engine software and operate the partitioning engine via the user interface.
Overview of the partitioning engine software Initialize Instrument u Initializing the partitioning engine (505) Prime Instrument u Priming the partitioning engine (232) Copy Logs to USB u Copying the logs from the partitioning engine to an external storage device (504) Event Viewer u Displaying the event viewer in the partitioning engine software (503) Information u To display the system information in the partitioning engine software (452) Shut Down Instrument u Shutting down the partitioning eng
Overview of the software components i 85 Do not partition nanowell plates if the partitioning engine is disconnected from the analyzer. The partitioning information will be lost and you will not be able to run the nanowell plates on the analyzer. About the work area of the partitioning engine software The work area is the center of your activities when working with the partitioning engine software. The work area displays the panels.
Overview of the partitioning engine software Green: The nanowell plate lane was partitioned successfully. Red: Partitioning of the nanowell plate lane failed. The nanowell plate lane is flagged and invalidated. For invalid nanowell plate lanes, the following applies: • The contained reaction mixture is flagged and invalidated: – For a sample, the final results will be invalid. – For a control, the final results of all associated targets or samples will be invalid.
Overview of the software components 87 About the Liquids panel The Liquids panel displays the following information about the partitioning fluid bottle and the liquid waste bottle: • Expiry date of the partitioning fluid A B C E • • • • Fill percentage Fill level Fill status Lot number of the partitioning fluid F D The fill status is color-coded: A Expiry date of the partitioning fluid B Fill percentage of partitioning fluid bottle C Fill level and status of partitioning fluid bottle D Lot number
Overview of the partitioning engine software About the event viewer The event viewer displays a list of the events with event severity and event code. An event can have the following severity: • Information • • Warning Error If an error event occurs, a corresponding message is displayed in the global information area. To display the event viewer, in the global information area, choose the button. From the drop-down menu, choose the Event Viewer command.
Overview of the software components 89 Overview of the web application The web application is a dedicated application to plan and to start diagnostic workflows and to review the results. The web application is the interface between the system and a connected LIS. You access and operate the web application in a browser window.
Overview of the web application A C B D F G E A Application version E Serial number of the connected analyzer B URL for analyzer connection F LIS connection indicator C Dashboard button G Logon indicator D Screen name H User Assistance H 5 Overview of the software components The global information area is always displayed and contains the following elements: • • • Application version URL for the connection to the analyzer Dashboard button • • • • Screen name Serial number of the conn
Overview of the software components 91 u Logging off from the web application (438) u Change password (237) u To change my password at logon in the web application (238) About the User Assistance To display the User Assistance, choose the button. The User Assistance is context-sensitive and displays information about the screen you are currently using. u About the User Assistance (47) About the dashboard of the web application When you log on to the web application, the dashboard is displayed.
Overview of the web application A 5 Overview of the software components E B F G C H I D J K A Orders column G Batch tile for batch in Ready to start run status B Sample setups column H Batch tile for batch in Pending partitioning status C Run in progress column I D Results column J Completed batches tile (displays the number of completed batches) E View orders tile K Batch tile for batch after run finished Batch tile for batch in Processing status F Create sample setup tile (disp
Overview of the software components • 93 Results column: Displays a batch tile per processed but not completed batch, and the Completed batches tile if there are completed batches on the system. i A batch is processed if the run on the analyzer is finished. A batch is completed if all results are complete, i.e., released and sent. The batch tiles are ordered consecutively in the Sample setups column and the Results column with the newest batch at the top.
Overview of the web application – Processing ({percent}%) (with "{percent}" replaced by the percentage of the run that has already elapsed) • For processed but not completed batches, the number of results with the result status (with "{count}" replaced by the applicable number): – {count} pending to be released – {count} pending to be sent – {count} completed i The {count} completed result status on the batch tile summarizes the results that are in Send queued status or Sent status on the Samples ta
Overview of the software components 95 In this section About the Orders screen (95) About the Edit orders screen (96) About the Sample setup screen (97) About the Results of screen (100) About the Completed batches screen (104) About the Orders screen If assignment mode is enabled, the Orders screen lists the orders that are not allocated. If assignment mode is disabled, the Orders screen lists all orders.
Overview of the web application If you choose rows on the Orders screen in assignment mode, the number of orders, needed nanowell plate lanes, and needed nanowell plates is calculated and displayed at the top right of the table. Alternatively, to display the same information in the Selected orders dialog box, choose the Selection overview button. If you choose too many rows for 12 nanowell plates, the number of orders, needed nanowell plate lanes, and needed nanowell plates is displayed in red.
Overview of the software components 97 The Edit orders screen comprises the Add sample ID card, the Sample IDs card, and the Analysis package and test card. To display the Edit orders screen, on the Orders screen in assignment mode, choose the Add/edit order button. If orders are selected on the Orders screen, they are displayed on the Edit orders screen. A B C If no orders are selected on the Orders screen, only the available analysis packages are displayed on the Edit orders screen.
Overview of the web application A B C The Sample setup screen displays the following information: • Batch name (used as name of the diagnostic run on the analyzer) • Estimated run duration on the analyzer • Sample setup in plate view: – 1 column per nanowell plate with column header and column footer – 1 tile per nanowell plate lane On the Sample setup screen, to deselect all tiles, press Esc.
Overview of the software components 99 About the Plate: combo box A B C D E The Plate: combo box displays the currently available information about the nanowell plate: • Position of the nanowell plate in the sample setup • Nanowell plate ID • • • Nanowell plate information Invalidation status of nanowell plate Partitioning information You cannot enter the nanowell plate ID of a nanowell plate that is expired, has the wrong type, is already part of a sample setup, and/or is already partitioned.
Overview of the web application About the Sample settings: combo box A B C D E F G H A Position of nanowell plate lane in sample setup B Sample ID C Analysis package information The Sample settings: combo box displays the currently available information about the nanowell plate lane: • Position of the nanowell plate lane in the sample setup • Sample ID • Analysis package information • • • • Notes Invalidation status of nanowell plate lane Dilution factor Kit ID • Partitioning flags If you choo
Overview of the software components A B D C 101 E G H F I A Screen name and run name F Notes indicator B Details of sample setup G Row with tabs C Drop-down list for analysis packages H Row with columns headers D Run details I E Color-coded screen header w Results of screen On the Results of screen, the results are ordered as follows: 1. By analysis package: To access the results for a specific analysis package, choose the analysis package from the drop-down list. 2.
Overview of the web application 3. By columns: The information is ordered in columns. You can sort by columns. To reach the result that you want to access, navigate through this hierarchy or use the search function. About header colors The header on the Results of screen has the same color as the tiles in the Results column on the dashboard: Light-green: • • • There are results that are not released and/or sent yet. The batch is processed, but not completed.
Overview of the software components i 103 The {count} completed result status on the batch tile summarizes the results that are in Send queued status or Sent status on the Samples tab on the Results of screen. u About the batch tiles (93) On the Results of screen in the web application, the result status for samples is displayed in the Status column on the Samples tab. To display a callout with the status legend, in the Status column header on the Samples tab, choose the icon.
Overview of the web application u About final results (173) u About color-coding of final results for samples (149) About the notes indicator The notes indicator is displayed in the Notes column on the Controls tab and the Samples tab. The notes indicator indicates if a sample or control has notes: No notes. There are notes. To add, edit, or delete notes, choose the notes indicator.
Overview of the software components 105 Searching on the Completed batches screen To search for runs by batch information, enter the search term in the Search field. 5 Overview of the software components To search for runs by sample IDs that were processed in the run, select the Search by sample ID check box and enter the sample ID in the Search field. Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Overview of the analyzer software Overview of the analyzer software You access the analyzer software and operate the analyzer via the user interface.
Overview of the software components A B C D E F G H A Plates button F User Assistance B Button to open and close the nanowell plate stack drawer G Shutdown button C Message indicator H Connection indicator D Logon indicator I E Log on button or Log off button J Screenshot button w I 107 J Analyzer status indicator Global information area of the analyzer software About the Plates button • • • • Shutdown button User Assistance Connection indicators Analyzer status indicator • Scre
Overview of the analyzer software You do not need to be logged on to open or close the nanowell plate stack drawer. u Loading the analyzer (225) u Unloading the analyzer (227) About the message indicator To display the messages panel and to hide it again, choose the message indicator. The message indicator is color-coded if a user is logged on to the analyzer software. If no user is currently logged on, the message indicator is unavailable.
Overview of the software components 109 The User Assistance is context-sensitive and displays information about the panel you are currently using. u About the User Assistance (47) About the shutdown button To shut down the analyzer and the analyzer software, button. choose the The button is only available if the nanowell plate stack drawer is closed and the analyzer is in Analyzer not initialized status, Analyzer ready status, or Analyzer paused status.
Overview of the analyzer software • • • • Backup Analyzer paused Error Analyzer connected • • • • Analyzer disconnected Analyzer performing maintenance Analyzer offline Analyzer starting up • • • Analyzer pre-initialized Analyzer shutting down Software starting up If the analyzer status changes, the analyzer status indicator is updated immediately.
Overview of the software components A B The work area contains the following elements: • Tabs C • • • • D 111 Navigation bar with back button, forward button, and breadcrumb Panel Software version Date and time E A Navigation bar B Tabs C Panel D Software version E Date and time A tab groups related tasks, e.g., all administration tasks. It depends on your user role which tasks you can access from the tabs.
Overview of the analyzer software – The blue element in the breadcrumb is the current location. – Choose an element of the breadcrumb to go back to that location. About the panels in the analyzer software A panel in the analyzer software is an organizational unit within a tab and groups information and related software functions.
Overview of the software components B G C H D E I F J K A Plates button G Manual entry button B Nanowell plate stack H Open drawer button / Close drawer button C Color-coding of nanowell plate type I D Status of loaded nanowell plate J Run profile button for development runs E Error indicator for nanowell plate K Sample setup button for diagnostic runs Error indicator and error description for run prerequisites F Table of nanowell plates with position, nanowell plate ID, and nanowell p
Overview of the analyzer software About the nanowell plate status Depending on the outcome of the checks, a loaded nanowell plate can be in the following statuses: • Barcode scan failed • Invalid barcode • • • • Duplicate barcode Expired Results already exist Not partitioned • Valid For each plate that is not in Valid status, an error indicator is displayed. To display a callout with additional information, choose the error indicator.
Overview of the software components 115 About the Sample setup panel The Sample setup panel displays the sample setup for a diagnostic run that was received from the web application. The Sample setup panel is read-only.
Overview of the analyzer software i The nanowell plates on the Sample setup panel are displayed in the same order as in the sample setup in the web application, not in the actual loading order on the analyzer. This is to facilitate the verification of the loaded sample setup against the sample setup report from the web application. The Sample setup panel is displayed automatically after loading the analyzer if the prerequisites for a diagnostic run are met.
Overview of the software components 117 If the denoted positions of a nanowell plate do not match, the numbers in the column header differ. If a nanowell plate was invalidated by the partitioning engine or in the web application, and is not loaded on the analyzer, a hyphen is displayed in the brackets instead of the position of the nanowell plate in the stack. (The column for the nanowell plate is still displayed on the Sample setup panel.
Overview of the analyzer software E F G H I J K L A M B C N 5 Overview of the software components D A Temperature of the step [in °C] H Incubation program B Temperature curve I C Duration of the step [in seconds] J Number of PCR cycles D Temperature chart of the run K Mandatory cooling program E Add program button L Run profile name F Name of the program M Detection formats G Delete program button N Estimated run duration depending on number of samples w Amplification progra
Overview of the software components • About amplification programs 119 Duration: 120 s A run profile can contain up to 5 amplification programs. An amplification program can contain 2 or 3 steps. A 2-step amplification program is a sequence of 2 steps with different temperatures and durations, and the number of PCR cycles that the analyzer repeats the sequence.
Overview of the analyzer software About the cooling program Each run profile contains a mandatory cooling program at the end that cannot be edited or deleted. The values for the cooling program are as follows: • Name: Cooling • • Temperature: 40 °C Duration: 30 s About the detection formats 5 Overview of the software components The detection formats define the channels, the dye per channel, and the integration time for the detection of fluorescence by the analyzer.
Overview of the software components A B C 121 The Monitoring panel is displayed automatically after a run is started on the analyzer. D button to edit the run name and/or to add run The notes is only displayed during a development run.
Overview of the analyzer software A B D C E F G H 5 Overview of the software components I A Message indicator F Icon indicating information message B Icon indicating unconfirmed message G Icon indicating warning message C Detail panel H Icon indicating error message D Sort, filter, configure columns, and export I Icon indicating confirmed message E Messages table w Messages panel u Audit trails in the analyzer software (449) u Messages in the analyzer software (509) About the severit
Overview of the software components 123 Unconfirmed message Confirmed message If there is no icon displayed in the Status column, the message does not need confirmation. u Displaying and confirming messages in the analyzer software (511) About the Administration panel The Administration panel displays the task buttons to perform administrator tasks.
Overview of the analyzer software • • The last selected folder is retained: The folder you selected the last time for a function is preselected the next time the folder browser is displayed for the same function. If you create a folder, the folder name can consist of 1 to 30 characters. The name must not contain the following characters: ?*<>/\:"|’ i Do not create folders in network shares in a folder browser.
Overview of the software components 125 About the virtual keyboard Use the virtual keyboard for data entry. Whenever input is required, the virtual keyboard is displayed automatically. To toggle between the alphanumeric and the numeric keyboard, choose the 123 button or the Text button, respectively. To hide the virtual keyboard, choose the button. The layout of the virtual keyboard depends on the active language package in the analyzer software.
Overview of the development software Overview of the development software The development software is a dedicated software to plan development runs, to analyze development runs and diagnostic runs, and to create analysis packages. A project in the development software can contain up to 50 analyses, allowing for an iterative approach. i In the development software, the language of the user interface and the User Assistance is determined by the Windows language settings.
Overview of the software components 127 In this section About the Navigation area of the development software (127) About the work area of the development software (127) Tabs in the development software (129) Plate view and table view in the development software (138) About the Navigation area of the development software The Navigation area of the development software provides menus and commands that are always available.
Overview of the development software • • • Tab navigation buttons Buttons Cards A B 5 Overview of the software components C E D A Tabs D Sample setup plate view card B Tab navigation buttons E Run settings card C Buttons w Work area of the development software In the work area, several tabs of the same sort can be displayed (e.g., several clustering tabs). You can arrange the tabs in the work area: • To close a tab, choose its button.
Overview of the software components 129 About the tab navigation buttons Use the tab navigation buttons to access the tabs: • To scroll the tabs to the right or left, choose the button or the button, respectively. • To navigate to a certain tab, choose the button. From the drop-down list, choose the tab. • To close all tabs, choose The button and the all tabs are visible. > Close all tabs.
Overview of the development software workflow, i.e., choose the affected tab entries from top to bottom in the Navigation area. This is because later steps in the workflow (e.g., an analysis) may be affected by the recalculation of an earlier step (e.g., a clustering). About the tab commands To display the tab commands, in the Navigation area, choose the button next to the tab entry in the corresponding menu. The availability of commands depends on the status of your project.
Overview of the software components 131 u Runs in the development software (309) About the clustering tabs A clustering tab displays the clustering for one combination of master mix reagent and nanowell plate type across all runs of a project.
Overview of the development software Merged lanes are listed individually on a clustering tab and their scatter plots are displayed separately. u List of naming placeholders (154) u Clustering in the development software (338) About the clustering data table The clustering data table on the Clustering data card displays the samples included in the clustering.
Overview of the software components 133 The Legend buttons display or hide the dye to target name mapping and a legend for the color-coding of the scatter plots. The Scale buttons display a linear or a logarithmic scale for the fluorescence axes. The Heatmap buttons display or hide the scatter plots as heatmaps.
Overview of the development software About the Settings combo box The Settings combo box displays the current clustering settings and allows you to change them: • Clustering method A • • • • B C Clustering parameters Scatter plot type Channels displayed in the scatter plots Axis ranges for the scatter plots The availability of the clustering parameters depends on the selected clustering method.
Overview of the software components • • 135 Linkage (for absolute quantification analysis only) Statistics To display a panel, choose the corresponding button. The panels only display results for samples that are included in the analysis. Merged lanes are analyzed together. Therefore, a set of merged lanes has 1 entry on an analysis tab. The sample ID in the Sample ID columns on the panels is a link to the run tab of the run in which the sample was processed.
Overview of the development software u About color-coding of controls (148) u Displaying the bar charts (400) About the button for the analysis settings To display the Settings combo box for the analysis settings, choose the button. u Analyses in the development software (358) About the Settings combo box The Settings combo box displays the current analysis settings and allows you to change them.
Overview of the software components A B C D 137 By default, the sample setup tabs are named "Sample Setup" and numbered consecutively. You can rename sample setup tabs via the tab commands. In the Navigation area, the sample setup tabs are listed in the Unassigned sample setup menu. You can display the unassigned sample setup on the sample setup tab either in plate view or in table view. E F To display the Run settings card or the Lane settings card, choose the corresponding button.
Overview of the development software About the breadcrumb At the top of the panels, an analysis package tab always displays the breadcrumb for the steps that you must perform in the given order to create an analysis package: • Edit • • • General settings Test definition MMx settings To display the panel for a step, choose a button from the breadcrumb.
Overview of the software components 139 About plate view By default, the development software displays all sample setups in plate view. In plate view, 1 column per nanowell plate and 1 tile per nanowell plate lane is displayed. To perform an action on a selected tile, choose the tile. To select several tiles, press Shift or Ctrl while choosing tiles. To select all tiles, choose the the plate view.
Overview of the development software About configuring table view j In table view, you can configure which columns are displayed. u Configuring table columns (142) m Sample setup tab or run tab in plate view r To configure plate view 1 In the development software, in the Navigation area, choose a run from the Runs menu or an unassigned sample setup from the Unassigned sample setup menu. 2 If the sample setup is displayed in table view, choose the button.
Overview of the software components 141 I The reset does not apply to the project coloring options. 8 Choose the Confirm button. 5 Overview of the software components f The plate view is updated. Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Common software functions Common software functions In this section Working with tables (142) Color-coding (148) Sample setups in plate view (150) About callouts (154) List of naming placeholders (154) Working with tables The analyzer software, the web application, and the development software offer similar functions for data in tables.
Overview of the software components 143 3 Choose the Configure columns button. f The Configure columns callout is displayed. 4 Adjust the visibility of the table columns: • To display a column, choose the column from the Available columns table and choose the button. • To hide a column, choose the column from the Visible columns table and choose the button. I You cannot hide columns that are marked with an icon.
Common software functions If a search produces no matches, consider if the search term is only contained in not searchable or hidden columns. You cannot search and filter a table simultaneously. Searching a table disables any previously applied filter. About filtering Filter a table to reduce the number of entries. There are 2 types of filters: • Default filters: – The analyzer software and the development software include predefined default filters for each table.
Overview of the software components 145 2 To display the table entries that contain a search term, do the following: • In the field at the top of the table, enter your search term. • Choose the button. I If there are no matches, the search term may be contained in not searchable or hidden columns only. 3 To display all table entries again, do the following: • Clear the field. • Choose the button. • Alternatively, from the filter drop-down list, choose the All default filter.
Common software functions I If you apply a custom filter only, the filter will be lost when you navigate to a different location in the software. To keep a custom filter permanently, you must save it. 7 To save the custom filter, do the following: • Choose the Save button. • Choose the Save view as field and enter a name for the filter. • Choose the Save button. f The custom filter is added to the filter drop-down list of the table. r To delete a custom filter 1 Navigate to a table.
Overview of the software components j 147 m In the analyzer software: Access to the panel that displays the table (depending on user role) r To export a table as Excel file in the analyzer software 1 Optionally, to export to an external storage device, connect the external storage device to the analyzer. 2 In the analyzer software, navigate to the table. 3 At the top of the table, choose the button. f The Export to Excel dialog box is displayed. 4 Optionally, enter a different file name.
Common software functions Color-coding The software components of the system share a common color-coding concept. If your color vision is impaired, refer to the texts and/or icons in the software components to obtain the same information.
Overview of the software components 149 Blue: Negative control Pink: Positive control for absolute quantification analysis Copy number control for CNV analysis Variant control for indel analysis Brown: Wild type control for indel analysis Orange: Internal control for absolute quantification analysis Example: Tile header for controls in sample setups in plate view u Sample setups in plate view (150) About color-coding of final results for samples When a final result is displayed in the web application or
Common software functions Blue: Normal Dark pink: High Gray: Invalid Color-coding for indel analysis The web application and the development software use the following color-coding for final results of an indel analysis: Pink: Variant positive Blue: Variant negative Gray: Invalid Sample setups in plate view 5 Overview of the software components The web application, the analyzer software, and the development software display sample setups in plate view.
Overview of the software components A B C 151 A sample setup in plate view consists of the following elements: • Letters (A to H) on the left denoting the position of the nanowell plate lane • 1 column per nanowell plate with column header and column footer • 1 tile per nanowell plate lane, i.e., reaction mixture A sample setup in plate view can contain up to 12 columns for the 12 nanowell plates that can be processed in 1 run on the analyzer.
Common software functions Each column has a column header and a column footer. A C The column header displays the position of the nanowell plate in the sample setup (1 to 12). In the analyzer software, the column header additionally displays the position of the nanowell plate in the stack in the nanowell plate stack drawer, e.g., 1(1). If available, the column footer displays the last 5 digits of the nanowell plate ID and is color-coded according to nanowell plate type.
Overview of the software components • • • 153 If there are master mix reagents with the same name from different analysis packages, they are considered and colored differently. The tiles for unused nanowell plate lanes are white and empty. The tiles for invalidated nanowell plate lanes are grayed out. u About color-coding of controls (148) In the development software, you can configure which information is displayed on a tile and how the tiles are colored.
Common software functions "A1". The position is also used as name for the set of merged lanes. i The positions of the nanowell plate lanes and sets of merged lanes are derived from plate view. However, the same denominations are used whenever the position is displayed, e.g., in table view. About callouts A callout is a context-specific element that provides additional information. A callout always points to the software element it belongs to.
Overview of the software components • RunType = Type of the run, i.e., "Diagnostic" or "Development" MMx = Name of the master mix reagent TypeOfReport = Type of problem report (i.e., "Basic", "Advanced", "Extended", or "Complete") 5 Overview of the software components • • 155 Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Table of contents 157 Overview of the supplies 6 Consumables ........................................................................... 159 Nanowell plates ........................................................... 159 Liquid waste bottles................................................... 160 Reagents and controls ......................................................... 162 IVD kits............................................................................ 162 Master reagents ............
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Overview of the supplies 159 Consumables Consumables are for single use only. Do not reuse consumables. Dispose of consumables according to local regulations. In this section Nanowell plates (159) Liquid waste bottles (160) Nanowell plates Nanowell plates hold the reaction mixtures.
Consumables To facilitate the target detection for samples with a low concentration of target molecules, the software components allow merged lanes to emulate nanowell plate lanes with an even higher number of nanowells. u About color-coding of nanowell plates (148) u About merged lanes (62) Universal nanowell plates Universal nanowell plates have white labels. High resolution nanowell plates High resolution nanowell plates have violet labels.
Overview of the supplies 161 The fill status of the liquid waste bottle is displayed in the Liquids panel in the partitioning engine software. Empty liquid waste bottles are delivered together with the partitioning engine. They are marked as liquid waste bottle on the RFID tag. When a liquid waste bottle is full, discard it together with the liquid waste. Do not empty and reuse a liquid waste bottle. Instead, use empty or expired partitioning fluid bottles as liquid waste bottles.
Reagents and controls Reagents and controls Reagents and controls enable the processing of samples, the detection of targets, and the monitoring of the process. Dispose of reagents and controls according to local regulations. In this section IVD kits (162) Master reagents (162) Partitioning fluid (163) Primers, probes, and dyes (164) Controls (165) IVD kits For IVD workflows, the Roche-provided IVD kits contain the mandatory master mix reagents (with primers and probes) and controls.
Overview of the supplies 163 A DNA master reagent and an RNA master reagent are available for DNA and RNA applications, respectively. The master reagents have a barcode label with the master reagent ID. You can enter the master reagent ID in the sample setup in the web application and the development software. The master reagents have an expiry date. Do not use expired master reagents.
Reagents and controls The partitioning engine monitors the loaded partitioning fluid for the expiry date and for the onboard stability. You must exchange the partitioning fluid when the expiry date or the onboard stability is exceeded (whichever happens first). You cannot use expired partitioning fluid on the partitioning engine. The date when the partitioning fluid will expire is displayed on the Liquids panel in the partitioning engine software.
Overview of the supplies 165 For details about preparing the reaction mixtures, refer to the Instructions for Use of the IVD kits and the master reagents. About dyes The dyes are part of the probes. If the target nucleic acid sequence is present, the dyes fluoresce and can be detected by the system. For IVD workflows, the IVD kits contain probes with system-compatible dyes. For LDT workflows and development workflows, ensure that your probes contain system-compatible dyes only.
Reagents and controls • IVD workflows: – Controls are mandatory. – Controls are part of the Roche-provided IVD kits. • LDT workflows: – It depends on the settings in the analysis packages if the sample setup contains controls. – It is the responsibility of the issuers of the analysis packages to include controls. – You must prepare your own user-defined controls in advance. • Development workflows: – It is your responsibility to add controls to the sample setup.
Table of contents 167 Overview of orders, run In this chapter 7 About orders ............................................................................ 169 About run prerequisites....................................................... 172 About final results.................................................................. 173 Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Overview of orders, run prerequisites, and results 169 About orders For diagnostic workflows, orders tell the system which tests to perform on which samples. There are no orders for development workflows. An order is the distinct combination of 1 sample ID with 1 test. If more than 1 test is assigned to the same sample ID, each combination of sample ID and test constitutes a separate order. Orders are exclusively managed in the web application.
About orders • • Released Sent As soon as an order is in Executed status, a result exists for that order in the web application. An order is in Released status if the corresponding result is released. An order is in Sent status if the corresponding result is sent. u About the Orders screen (95) 7 Overview of orders, run prerequisites, and results About allocation of orders Orders that are not yet assigned to a sample setup are called not allocated orders.
Overview of orders, run prerequisites, and results • • • 171 On the Orders screen, LIS is displayed in the Requester name column. On the Sample IDs card on the Edit orders screen, tests from LIS orders are displayed in blue font. You cannot delete LIS orders, i.e., you cannot deassign the test from an LIS order. You can add orders for sample IDs that are part of LIS orders. I.e.
About run prerequisites About run prerequisites You can only start a diagnostic run or a development run on the analyzer if the corresponding run prerequisites are met. You can use different types of nanowell plates together in 1 run. However, you cannot start a run if nanowell plates for a diagnostic run and nanowell plates for a development run are loaded together on the analyzer.
Overview of orders, run prerequisites, and results 173 About final results Final results are the outcomes of your workflows. The system displays final quantitative and final qualitative results. The final results for samples consider the corresponding control results.
About final results About results of diagnostics workflows After an order is processed in a diagnostic workflow, the corresponding final results are calculated automatically and displayed on the Results of screen in the web application. • If configured, the final quantitative results are displayed in the Result column (with the corresponding unit in the Unit column). • The final qualitative results are displayed in the Final result column.
Table of contents 175 Maintenance overview 8 About maintenance............................................................... 177 8 Maintenance overview In this chapter Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Maintenance overview 177 About maintenance Maintenance ensures safe and reliable operation of the system. Do not carry out any maintenance actions that are not described in this publication. Automatic maintenance actions You can schedule automatic archiving and automatic backups on the system.
About maintenance 8 Maintenance overview u About preventive maintenance (482) Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Table of contents 179 In this chapter 9 System specifications ........................................................... 181 General specifications............................................... 181 General specifications of the system ....... 181 General specifications of the analyzer..... 181 General specifications of the partitioning engine .......................................... 182 Electric power supply ................................................
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Specifications 181 System specifications In this section General specifications (181) Electric power supply (182) Environmental conditions for the system (183) Dimensions and weight (183) Required space (184) Radio equipment specifications (185) Supported characters in ASTM messages (185) List of available consumables and reagents (186) General specifications In this section General specifications of the system (181) General specifications of the analyzer (181) General specifications of the partitioning
System specifications General specifications of the partitioning engine The partitioning engine has the following general specifications: Partitioning engine Up to 5 minutes for 1 nanowell plate Throughput Up to 60 minutes for 12 nanowell plates y General specifications of the partitioning engine Electric power supply In this section Electric power supply for the analyzer (182) Electric power supply for the partitioning engine (182) Electric power supply for the analyzer The electric power supply
Specifications International (Europe) 183 US / Canada 100-240 V AC ± 10% Input voltage 50-60 Hz Input frequency 1.6 A Input current Output voltage 24 V DC Output current 5A Installation category Installation Installation Category II (IEC 61010-1) Protection class Protection Class I y Power supply (AC adapter) of the partitioning engine i Only use the power supply (AC adapter) that is delivered together with the partitioning engine.
System specifications In this section Dimensions and weight of the analyzer (184) Dimensions and weight of the partitioning engine (184) Dimensions and weight of the analyzer The analyzer has the following dimensions and weight: International (Europe) US Height 90 cm 35.4 in Width 100 cm 39.4 in Depth 60 cm (without monitor) 23.
Specifications International (Europe) 185 US Front 30 cm 12 in Back 0 cm 0 in Left side 50 cm 20 in Right side 30 cm 12 in Top 50 cm 20 in y Space required around the analyzer Space required around the partitioning engine Do not operate the partitioning engine if there is insufficient free space around it.
System specifications If you connect the system to an LIS via the ASTM protocol, only use characters in the range of 0x21 (exclamation mark "!") to 0x7D (closing curly bracket "}") of the CP-1252 character encoding for sample IDs. List of available consumables and reagents Below is a list of globally available consumables and reagents. For ordering information, contact your local sales representative.
Specifications 187 Computer specifications In this section Specifications for the development software (187) Specifications for the web application (187) Specifications for the development software Minimum Operating system: Windows 10 Computer Monitor resolution Recommended Intel i5 processor Intel i7 processor or higher 8 GB RAM 16 GB RAM or more 1366 × 768 1920 × 1080 y Specifications for the development software Specifications for the web application Specification Browser Firefox ESR 91.
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Operation 10 Overview of routine tasks......................................................................... 191 11 Frequently performed tasks..................................................................... 219 12 Before routine operation........................................................................... 229 13 Routine operation of diagnostic workflow......................................... 241 14 Routine operation of development workflow....................................
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Table of contents 191 Overview of routine tasks 10 In this chapter 193 Overview of development workflow without unassigned sample setup ................................................... 194 Overview of development workflow with unassigned sample setup ................................................... 195 Diagnostic workflow (quick reference) ......................... 196 Development workflow without unassigned sample setup (quick reference) .......................................
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Overview of routine tasks 193 Overview of diagnostic workflow Diagnostic workflow Partitioning engine • Prepare reaction mixtures • Pipette nanowell plates 5 Web application 1 Get orders 2 Create and confirm sample setup 3 Create sample setup report Partition nanowell plates 6 Load analyzer 7 Verify sample setup 8 Start run 9 Unload analyzer Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Overview of development workflow without unassigned sample setup Overview of development workflow without unassigned sample setup Development workflow without unassigned sample setup Development software 10 Overview of routine tasks 1 • Plan development run • Prepare reaction mixtures • Pipette nanowell plates Partitioning engine 2 6 • Open or create project • Import raw data file • Add lane settings 7 • Adjust clustering • Perform analyses 8 Review results 9 • Create or update analysis
Overview of routine tasks 195 Overview of development workflow with unassigned sample setup Development workflow with unassigned sample setup 3 1 Open or create project 2 • Create unassigned sample setup • Create sample setup report • Prepare reaction mixtures • Pipette nanowell plates Partitioning engine 4 8 • Import raw data file • Assign sample setup to run 9 • Adjust clustering • Perform analyses 10 Review results 11 • Create or update analysis package • Export analysis package Analyz
Diagnostic workflow (quick reference) Diagnostic workflow (quick reference) Step 1 Description Web application If orders are not exclusively received from an LIS: Create and import the orders list and/or create the orders. To create and import an orders list, do the following: 1. Create a CSV file for the orders. 2. In the Orders column on the dashboard, choose the View orders tile. 3. On the Orders screen, choose the Import order list button. 4.
Overview of routine tasks Step 3 197 Description Web application Enter or scan the nanowell plate IDs. On the Sample setup screen, do the following for each nanowell plate: 1. To display the Plate: combo box, choose the column header twice. 2. In the Plate ID field, scan or enter the nanowell plate ID. 3. Choose the Confirm button. 4 Web application If required, enter or scan the kit IDs and/or enter sample notes.
Diagnostic workflow (quick reference) Step 8 Description Prepare the reaction mixtures. 1. Prepare the reaction mixtures. 2. Refer to the sample setup report to identify the nanowell plates and to allocate the reaction mixtures to the nanowell plate lanes. For details about preparing the reaction mixtures and pipetting, refer to the Instructions for Use of the reagents and controls. 9 Partitioning engine Pipette and partition the nanowell plates. 1.
Overview of routine tasks Step 13 199 Description Analyzer Unload the analyzer. 1. When the run is finished, in the global information area, choose the button. 2. Remove the nanowell plate stack from the nanowell plate stack drawer. 3. Choose the button. 4. Dispose of the nanowell plates according to local regulations. u Unloading the analyzer (227) 14 Web application If required, release and/or send the results.
Development workflow without unassigned sample setup (quick reference) Development workflow without unassigned sample setup (quick reference) The following table provides you with a quick reference of how to perform a development workflow without unassigned sample setup. u For a quick reference for a development workflow with unassigned sample setup, refer to Development workflow with unassigned sample setup (quick reference) (208). Step 1 Description Prepare the reaction mixtures. 1.
Overview of routine tasks Step 5 201 Description Analyzer Optionally, duplicate or import a run profile. To duplicate a run profile, do the following: 1. On the Manage run profiles panel, choose a run profile. 2. Choose the Duplicate button. 3. In the Edit run profile name dialog box, enter a name for the run profile. 4. Choose the Save button. To import a run profile, do the following: 1. On the Manage run profiles panel, choose the Import button. 2.
Development workflow without unassigned sample setup (quick reference) Step 8 Description Analyzer Optionally, change the run name and/or enter run notes. 1. In the middle of the Monitoring panel, next to the run name, choose the button. 2. In the dialog box, in the Run name field, enter a new run name. 3. In the Edit notes field, enter run notes. 4. Choose the Confirm button. u Entering run information for a development run in the analyzer software (307) 9 Analyzer Unload the analyzer. 1.
Overview of routine tasks Step 11 203 Description Development software Create a project or open a project. To open a project: 1. On the Start page tab, choose the Open file button. 2. Navigate to the dpcrPrj file and choose the Open button. To create a project: 1. If you exported the raw data file to an external storage device, connect the external storage device to the computer running the development software. 2. In the Windows Explorer, double-click the raw data file of the development run.
Development workflow without unassigned sample setup (quick reference) Step 14 Description Development software Add the lane settings. 1. On the run tab, choose the Lane settings button. 2. Choose one or several tiles (in plate view) or rows (in table view). 3. On the Lane settings card, choose the Sample ID field. Scan or enter the sample ID. If required, press Enter. 4. Optionally, edit the dilution factor for the sample. 5. In the MMx field, enter the name of the master mix reagent. 6.
Overview of routine tasks Step 17 205 Description Development software Optionally, work with sample groups. 1. On the run tab, choose the Sample groups button. 2. Add and/or edit sample groups. 3. Save the project. u Working with sample groups in the development software (328) 18 Development software Check and adjust the clustering. 1. Choose the clustering from the Clustering menu. 2. Choose the button. 3. In the Settings combo box, adjust the clustering settings. 4. Choose the button. 5.
Development workflow without unassigned sample setup (quick reference) Step 19 Description Development software Perform the analyses. To add an analysis, do the following: 1. From the Navigation area, choose Analysis > . Choose the analysis type. 2. In the Settings combo box, choose the samples and choose the Update analysis button. 3. Optionally, add and/or edit sample groups. 4. On the other tabs in the Settings combo box, enter the settings required for the analysis type. 5.
Overview of routine tasks Step 20 207 Description Development software Optionally, create or update an analysis package. To create an analysis package: 1. From the Navigation area, choose Analysis package > > Create analysis package. 2. In the Create analysis package dialog box, enter a name for the analysis package and the type of nanowell plate. Choose the Confirm button. 3. On the panels of the analysis package tab, enter the required information. 4.
Development workflow with unassigned sample setup (quick reference) Development workflow with unassigned sample setup (quick reference) The following table provides you with a quick reference of how to perform a development workflow with unassigned sample setup. u For a quick reference for a development workflow without unassigned sample setup, refer to Development workflow without unassigned sample setup (quick reference) (200).
Overview of routine tasks Step 3 209 Description Development software Add the nanowell plates. 1. On the sample setup tab, from the Plate type drop-down list, choose the nanowell plate type. 2. Optionally, scan or enter the nanowell plate ID. If required, press Enter. 3. Save the project. u Adding run settings and lane settings to unassigned sample setups in the development software (406) 4 Development software Set the detection formats. 1. Choose the Detection formats button. 2.
Development workflow with unassigned sample setup (quick reference) Step 6 Description Development software Add the lane settings. 1. On the sample setup tab, choose the Lane settings button. 2. Choose one or several tiles (in plate view) or rows (in table view). 3. On the Lane settings card, choose the Sample ID field. Scan or enter the sample ID. If required, press Enter. 4. Optionally, edit the dilution factor for the sample. 5. In the MMx field, enter the name of the master mix reagent. 6.
Overview of routine tasks Step 10 211 Description Prepare the reaction mixtures. 1. Prepare the reaction mixtures. 2. Refer to the sample setup report to identify the nanowell plates and to allocate the reaction mixtures to the nanowell plate lanes. For details about preparing the reaction mixtures and pipetting, refer to the Instructions for Use of the reagents and controls. 11 Partitioning engine Pipette and partition the nanowell plates. 1.
Development workflow with unassigned sample setup (quick reference) Step 14 Description Analyzer Optionally, duplicate or import a run profile. To duplicate a run profile, do the following: 1. On the Manage run profiles panel, choose a run profile. 2. Choose the Duplicate button. 3. In the Edit run profile name dialog box, enter a name for the run profile. 4. Choose the Save button. To import a run profile, do the following: 1. On the Manage run profiles panel, choose the Import button. 2.
Overview of routine tasks Step 17 213 Description Analyzer Optionally, change the run name and/or enter run notes. 1. In the middle of the Monitoring panel, next to the run name, choose the button. 2. In the dialog box, in the Run name field, enter a new run name. 3. In the Edit notes field, enter run notes. 4. Choose the Confirm button. u Entering run information for a development run in the analyzer software (307) 18 Analyzer Unload the analyzer. 1.
Development workflow with unassigned sample setup (quick reference) Step 20 Description Development software Import the raw data file of the development run. 1. If the raw data file was exported to an external storage device, connect the external storage device to the computer running the development software. 2. From the Navigation area, choose Runs > > Import. 3. Navigate to the raw data file and choose the Open button. 4.
Overview of routine tasks Step 23 215 Description Development software Optionally, work with sample groups. 1. On the run tab, choose the Sample groups button. 2. Add and/or edit sample groups. 3. Save the project. u Working with sample groups in the development software (328) 24 Development software Check and adjust the clustering. 1. Choose the clustering from the Clustering menu. 2. Choose the button. 3. In the Settings combo box, adjust the clustering settings. 4. Choose the button. 5.
Development workflow with unassigned sample setup (quick reference) Step 25 Description Development software Perform the analyses. To add an analysis, do the following: 1. From the Navigation area, choose Analysis > . Choose the analysis type. 2. In the Settings combo box, choose the samples and choose the Update analysis button. 3. Optionally, add and/or edit sample groups. 4. On the other tabs in the Settings combo box, enter the settings required for the analysis type. 5. Choose the button.
Overview of routine tasks Step 26 217 Description Development software Optionally, create or update an analysis package. To create an analysis package: 1. From the Navigation area, choose Analysis package > > Create analysis package. 2. In the Create analysis package dialog box, enter a name for the analysis package and the type of nanowell plate. Choose the Confirm button. 3. On the panels of the analysis package tab, enter the required information. 4.
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Table of contents 219 Frequently performed tasks 11 In this chapter 221 Loading the analyzer ............................................................ 225 Unloading the analyzer........................................................ 227 11 Frequently performed tasks Partitioning the nanowell plates....................................... Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Frequently performed tasks 221 Partitioning the nanowell plates You must partition the pipetted nanowell plates in the partitioning engine before you can process them on the analyzer. i The stability of the reaction mixtures between partitioning of a nanowell plate and processing it on the analyzer has been tested for 90 minutes. The design of the drawer of the partitioning engine and the beveled corner of the nanowell plates ensure the correct orientation of the nanowell plate in the drawer.
Partitioning the nanowell plates • • • Information about the partitioning fluid Invalid nanowell plate lanes Partitioning flags Without this information, the validation of the nanowell plate fails during loading on the analyzer and the nanowell plate cannot be processed. In a diagnostic workflow, the information is also sent to the web application. In a development workflow, the analyzer includes the information in the raw data file of the run.
Frequently performed tasks 223 r To partition a nanowell plate 1 Ensure that the connection indicator in the global information area indicates that the partitioning engine is connected to the analyzer. 2 On the Plate Setup panel, choose the Load button. f The nanowell plate drawer opens. 3 Place a pipetted nanowell plate in the nanowell plate drawer with the beveled corner at the back right. I Do not try to close the nanowell plate drawer manually by pushing against it.
Partitioning the nanowell plates 6 Check the partitioning status of the nanowell plate lanes by means of the color of the partitioning indicators: • Check that the partitioning indicators for all nanowell plate lanes that contain reaction mixtures are green or red. • If partitioning indicators of nanowell plate lanes that contain reaction mixtures remain gray, discard the nanowell plate according to local regulations.
Frequently performed tasks 225 Loading the analyzer You must load the partitioned nanowell plates on the analyzer. i The stability of the reaction mixtures between partitioning of a nanowell plate and processing it on the analyzer has been tested for 90 minutes. For diagnostic runs, do not load nanowell plates on the analyzer that you invalidated in the web application. You cannot start the diagnostic run while invalidated nanowell plates are loaded.
Loading the analyzer 3 To close the nanowell plate stack drawer, choose the button. I Do not try to close the nanowell plate stack drawer manually by pushing against it. 11 Frequently performed tasks 4 Wait until the automatic scanning of the barcode labels of the nanowell plates is finished. f The nanowell plates are displayed on the Plates panel. Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Frequently performed tasks 227 Unloading the analyzer Unload the analyzer when a run is finished. Always unload the analyzer before you shut down the analyzer. CAUTION! Moving drawer The nanowell plate stack drawer of the analyzer opens and closes during operation. An opening drawer may strike you. A closing drawer may pinch your fingers. r Keep away from the nanowell plate stack drawer during operation. r Do not try to close the nanowell plate stack drawer manually by pushing against it.
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Table of contents 229 Before routine operation 12 In this chapter 231 Priming the partitioning engine........................................ 232 Logging on to the web application ................................. 234 Starting up the analyzer ...................................................... 235 Logging on to the analyzer software .............................. 236 Change password .................................................................. 237 Starting the development software ..
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Before routine operation 231 Starting up the partitioning engine You must start up the partitioning engine before use. n 5 minutes r To start up the partitioning engine 1 At the back of the partitioning engine, press the power switch. 2 Wait until the partitioning engine is initialized and primed and is in Ready status. 12 Before routine operation 3 Ensure that the connection indicator in the global information area indicates that the partitioning engine is connected to the analyzer.
Priming the partitioning engine Priming the partitioning engine You can prime the partitioning engine when required or on demand. Priming flushes the fluid system inside the partitioning engine with partitioning fluid to ensure it is free of air bubbles. The partitioning engine primes automatically directly after startup. The partitioning engine requires priming after 24 hours without activity or after shutdown. When priming is required, the Prime button is available on the Plate Setup panel.
Before routine operation 233 2 To prime the partitioning engine on demand, in the > Prime global information area, choose Instrument. 12 Before routine operation 3 Wait until priming is complete and the partitioning engine is in Ready status. Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Logging on to the web application Logging on to the web application You must log on to the web application before use. To log on to the web application, you need diagnostic operator user role or diagnostic approver user role. User accounts are managed in the analyzer software. You log on to the web application with the same user account that you use in the analyzer software.
Before routine operation 235 Starting up the analyzer You must start up the analyzer and log on before use. During startup, the analyzer transfers all loaded nanowell plates to the nanowell plate stack drawer and displays the Plates panel. In this case, you must unload the analyzer before further use. u Unloading the analyzer (227) n 10 minutes d m User name and password r To start up the analyzer 1 On the right side of the analyzer, press the power button.
Logging on to the analyzer software Logging on to the analyzer software If you logged off from the analyzer software or if you were logged off automatically, you must log on again before you can use the analyzer. d m User name and password r To log on to the analyzer software 1 In the global information area of the analyzer software, choose the Logon button. 2 In the Logon dialog box, enter your user name and password. 3 Choose the Confirm button.
Before routine operation 237 Change password In the Change password dialog box, you change your password. All users, regardless of their user roles, can change their own passwords. The new password applies to the analyzer software and the web application. CAUTION! Weak passwords Weak passwords may allow unauthorized access to the system, data manipulation or loss, or unauthorized access to personal information, which may cause incorrect, invalid, or delayed results. r Use strong passwords.
Change password 2 Enter your current password. Enter the new password twice. I Passwords are case-sensitive. 3 Choose the Confirm button. f The new password applies to the analyzer software and the web application. r To change my password at logon in the analyzer software 1 In the global information area of the analyzer software, choose the Logon button. 2 In the Logon dialog box, enter your user name and password. 3 Choose the Logon button. f The Change password dialog box is displayed.
Before routine operation 239 2 In the Logon dialog box, enter your user name and password. I Use the same user account as for the analyzer software. 3 Choose the Logon button. f The Change password dialog box is displayed. 4 Enter your new password twice. I Passwords are case-sensitive. 12 Before routine operation 5 Choose the Confirm button. f The new password applies to the analyzer software and the web application. Roche Diagnostics Digital LightCycler® System · Software version 1.
Starting the development software Starting the development software You must start the development software before use. On the start page of the development software, the last 5 projects or raw data files that you worked with are listed in the Open a recently used file list. The project or file that you worked with last is listed at the top. When you open a raw data file from the start page, a new project for that file is created automatically.
Table of contents 241 Routine operation of diagnostic workflow Performing a diagnostic workflow................................... 243 Orders in the web application........................................... 250 Ordering in the web application ........................... 250 Editing not allocated orders in the web application ..................................................................... 252 Sample setups in the web application...........................
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Routine operation of diagnostic workflow 243 Performing a diagnostic workflow Perform a diagnostic workflow for diagnostic purposes.
Performing a diagnostic workflow j m Diagnostic operator user role m To send results manually: Diagnostic approver user role m Analysis packages imported and enabled in analyzer software r To perform a diagnostic workflow 13 Routine operation of diagnostic workflow 1 If orders are not exclusively received from an LIS, in the web application, create and import an orders list as described in Ordering in the web application (250): • Create a CSV file for the orders.
Routine operation of diagnostic workflow 245 f The column footers are color-coded according to nanowell plate type. 4 On the Sample setup screen, for each nanowell plate, assign the nanowell plate IDs: • To display the Plate: combo box, choose the column header twice. • In the Plate ID field, scan or enter the nanowell plate ID. • Choose the Confirm button.
Performing a diagnostic workflow 7 On the Sample setup screen, choose the Confirm button. I Ensure that you confirm the sample setup. Otherwise the sample setup is lost when you leave the Sample setup screen. f The sample setup is confirmed. f In the Sample setups column on the dashboard, the batch tile of the sample setup is displayed in Pending partitioning status.
Routine operation of diagnostic workflow 247 Pipette and partition the nanowell plates on the partitioning engine as described in Partitioning the nanowell plates (221): • Pipette the reaction mixtures into the inlet ports of the first nanowell plate. • Choose the Load button. • Place the nanowell plate in the nanowell plate drawer. • Choose the Start button. • When the nanowell plate drawer opens, check that all nanowell plate lanes that contain reaction mixtures are partitioned.
Performing a diagnostic workflow 13 Verify the displayed sample setup against the sample setup report from the web application. 14 To start the run, choose the Start run button. f In the analyzer software, the Monitoring panel is displayed. f In the web application, in the Run in progress column on the dashboard, the batch tile is displayed in Processing status. f The expected run duration is displayed in the analyzer software and in the web application.
Routine operation of diagnostic workflow 249 • Select the results from the list and choose the Release button. • In the Confirmation dialog box, enter your password and choose the Release button. f The results are released. 18 If required, a user with diagnostic approver user role must send the results in the web application as described in Sending results manually in the web application (267): • In the Results column on the dashboard, choose the batch tile.
Orders in the web application Orders in the web application For diagnostic workflows, orders tell the system which tests to perform on which samples. In this section Ordering in the web application (250) Editing not allocated orders in the web application (252) Ordering in the web application If orders are not exclusively received from an LIS, you must import an orders list and/or create orders manually in the web application.
Routine operation of diagnostic workflow • • 251 If the orders list contains duplicate orders. If there is already a not allocated order in the web application that matches an order in the orders list. If the import fails for 1 order of the orders list, no order is imported from the orders list.
Orders in the web application 2 Choose the Add/edit order button. f The Edit orders screen is displayed. 3 To add the sample IDs, do the following: • On the Add sample ID card, choose the Sample ID field. • Scan or enter the sample ID. • Choose the Add button. I The sample ID can consist of 1 to 25 characters. Do not press Enter after entering the sample ID. The Enter key does not work. 13 Routine operation of diagnostic workflow f The sample ID is added to the Sample IDs card.
Routine operation of diagnostic workflow 253 You edit orders by assigning and/or deassigning tests from sample IDs. Because an order is the combination of a sample ID and a single test, editing orders results in the following: • If you assign an additional test to a sample ID, you create an additional order for the same sample ID. • If you deassign a test from a sample ID, you delete the order. For LIS orders, the following applies: • • You cannot delete LIS orders in the web application.
Orders in the web application • On the Analysis package and test card, assign complete analysis packages, i.e., all tests of the analysis packages. Alternatively, expand the analysis packages and assign selected tests only (if possible). I You can create orders for sample IDs that were received as part of an LIS order.
Routine operation of diagnostic workflow 255 Sample setups in the web application A sample setup in the web application comprises the orders that are processed together in a diagnostic run on the analyzer.
Sample setups in the web application u List of naming placeholders (154) d j u Prerequisites for a diagnostic run (172) m Orders in the web application (received from LIS, imported as orders list, and/or added manually) m Diagnostic operator user role r To create a sample setup in the web application 1 In the web application, in the Orders column on the dashboard, choose the Create sample setup tile. f The Orders screen in assignment mode is displayed. f The table lists all not allocated orders.
Routine operation of diagnostic workflow 257 6 CAUTION! Risk of compromised image integrity. Avoid scratches, finger prints, dust, or other artifacts on the nanowell plate lanes. For each nanowell plate of the sample setup, do the following: • To display the Plate: combo box, choose the column header twice. • In the Plate ID field, scan or enter the nanowell plate ID. • Choose the Confirm button.
Sample setups in the web application I You cannot generate a sample setup report before the sample setup is confirmed. f The sample setup is confirmed. f The dashboard is displayed. f A batch tile in Pending partitioning status is created and displayed in the Sample setups column. f The assigned orders are in Allocated status. Editing sample setups in the web application You can edit sample setups in the web application.
Routine operation of diagnostic workflow 259 3 To edit the sample settings for a nanowell plate lane, do the following: • To display the Sample settings: combo box, choose the tile twice. • Edit the sample settings. • Choose the Confirm button. 4 To change the batch name and/or enter run notes, do the following: • In the top center of the Sample setup screen, button. choose the • In the Run information dialog box, change the batch name and/or enter run notes. • Choose the Confirm button.
Sample setups in the web application • Plate view of the sample setup as on the Sample setup screen (plus the dilution) By default, sample setup reports are named Diagnostic Sample Setup Report - BatchName.pdf u List of naming placeholders (154) u About the Sample setup screen (97) d m Sample setup in the web application j m Diagnostic operator user role m Optionally, external storage device, e.g.
Routine operation of diagnostic workflow 261 Entering run information for a diagnostic run in the web application Before and during a diagnostic run, you can enter run information in the web application. Run information comprises the following: • Run name: The name of the sample setup that is used as run name on the analyzer. The run name can consist of 1 to 25 characters. The run name must not contain the following characters: ?*<>/\:"|’ Run notes: Additional information that is listed on the Run notes t
Entering run information for a diagnostic run in the web application 2 In the top center of the Sample setup screen, button. choose the f The Run information dialog box is displayed. 3 Change the run name and/or enter run notes. I The run name can consist of 1 to 25 characters. The run name must not contain the following characters: ?*<>/\:"|’ 4 Choose the Confirm button.
Routine operation of diagnostic workflow 263 Results in the web application Results are the outcome of your diagnostic workflows. It depends on the configuration of your system if you must release and/or send results manually to the LIS.
Results in the web application 3 Choose the Controls tab or the Samples tab. 4 In the Notes column, choose the indicator of the result. f The Sample notes dialog box is displayed. 5 To close the Sample notes dialog box again, choose the Cancel button. I Only choose the Confirm button if you are logged on with diagnostic operator user role. 13 Routine operation of diagnostic workflow r To add result notes 1 In the web application, in the Results column on the dashboard, choose a batch tile.
Routine operation of diagnostic workflow 265 2 Choose the Controls tab or the Samples tab. 3 In the Notes column, choose the indicator of the result. f The Sample notes dialog box is displayed. 4 Edit the result notes and choose the Confirm button. 1 In the web application, in the Results column on the dashboard, choose a batch tile. f The Results of screen is displayed. 2 Choose the Controls tab or the Samples tab. 3 In the Notes column, choose the result.
Results in the web application To release results manually, you need diagnostic operator user role. To complete the batch, the results must be sent additionally. Results for orders with analysis packages in In validation status are complete immediately after the diagnostic run finishes. You cannot release such results or send them to the LIS.
Routine operation of diagnostic workflow 267 Sending results manually in the web application If results are not sent automatically, you must send the results manually to the LIS. You can only send results that are already released, either automatically or manually by a user with diagnostic operator user role (depending on system configuration). To send results, you need diagnostic approver user role.
Results in the web application 4 To send the results, choose the Send button. f The Confirmation dialog box is displayed. 5 Enter your password and choose the Send button. f The result status changes to Send queued or icon or an Sent, respectively, marked with an icon in the Status column (depending on LIS connection status). f Your user name is added to the Send by column.
Routine operation of diagnostic workflow 269 • For completed batches, choose the {count} completed batches tile. Choose a batch and choose the View button. f The Results of screen of the batch is displayed. 3 Choose the Report button. f A dialog box is displayed. 4 Select to open or save the report. Choose the OK button. I The available options and details depend on your browser and computer configuration. 5 Optionally, disconnect the external storage device.
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Table of contents 271 Routine operation of development workflow Performing a development workflow without unassigned sample setup ................................................... 275 Performing a development workflow with unassigned sample setup ................................................... 283 Projects in the development software............................ 294 About projects in the development software ... 294 Working with projects in the development software ..........................
14 Routine operation of development workflow 272 Table of contents Working with sample groups in the development software............................................... 328 Editing lane settings via copy and paste in the development software.......................................................... 335 Clustering in the development software ....................... 338 About clustering in the development software ..........................................................................
About unassigned sample setups in the development software............................................... 402 Working with unassigned sample setups in the development software ....................................... 405 Adding run settings and lane settings to unassigned sample setups in the development software............................................... 406 Creating a sample setup report of an unassigned sample setup in the development software ....................................................
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Routine operation of development workflow 275 Performing a development workflow without unassigned sample setup In a development workflow without unassigned sample setup, you plan the sample setup outside of the development software. After the development run, you import the raw data file of the run into the development software and then add the sample setup information to the run.
Performing a development workflow without unassigned sample setup r To perform a development workflow without unassigned sample setup 1 Prepare the reaction mixtures. I For details about preparing the reaction mixtures and pipetting, refer to the Instructions for Use of the reagents and controls. 14 Routine operation of development workflow 2 CAUTION! Risk of incorrect results. Take care to avoid pipetting errors.
Routine operation of development workflow 277 4 In the analyzer software, on the Plates panel, do the following: • Verify that all nanowell plates have status Valid. • Verify the displayed nanowell plates against the planned sample setup. 5 Choose the Run profile button. f The Manage run profiles panel is displayed.
Performing a development workflow without unassigned sample setup 9 Optionally, change the name of the development run and/or add run notes as described in Entering run information for a development run in the analyzer software (307): • On the Monitoring panel, next to the run name, choose the button. • In the dialog box, in the Run name field, enter a new run name. • In the Edit notes field, enter run notes. • Choose the Confirm button.
Routine operation of development workflow 279 If the raw data file was exported to an external storage device, connect the external storage device to the computer running the development software. • In the Windows Explorer, double-click the raw data file of the development run. • Save the project as described in To save a project in the development software (296). • Optionally, disconnect the external storage device. f The run tab is displayed.
Performing a development workflow without unassigned sample setup 18 For each master mix reagent, in the Target and dye settings table, do the following: • Choose a tile (in plate view) or a row (in table view). • Disable the dyes that are not contained in the master mix reagent. • Optionally, rename the targets. • Save the project. 14 Routine operation of development workflow I A change applies to all tiles that use the same master mix reagent.
Routine operation of development workflow 281 22 Add analyses as described in Analyses in the development software (358): • From the Navigation area, choose Analysis > . Choose the analysis type. • In the Settings combo box, choose the samples and choose the Update analysis button. • Optionally, add and/or edit sample groups. • On the other tabs in the Settings combo box, enter the settings required for the analysis type. • Choose the button. • Save the project.
Performing a development workflow without unassigned sample setup • Save the project. 14 Routine operation of development workflow 25 Optionally, update an analysis package as described in Working with analysis packages (429): • From the Analysis package menu, choose the analysis package. • On the panels of the analysis package tab, edit the information. • From the Analysis package menu, choose the analysis package. • Choose > Update version.
Routine operation of development workflow 283 Performing a development workflow with unassigned sample setup In a development workflow with unassigned sample setup, you plan the sample setup in the development software. After the development run, you import the raw data file of the run into the development software and then assign the sample setup information to the run.
Performing a development workflow with unassigned sample setup r To perform a development workflow with unassigned sample setup 14 Routine operation of development workflow 1 In the development software, open a project as described in Working with projects in the development software (295): • On the Start page tab, choose the Open file button. • Navigate to the dpcrPrj file of the project and choose the Open button.
Routine operation of development workflow 285 5 On the Run settings card, set the detection formats for the development run: • Choose the Detection formats button. • In the Detection format combo box, disable the channels for dyes that are not contained in any of the master mix reagents used in the development run. • For each enabled channel, choose the dye from the drop-down list. • To edit the integration times, choose the Advanced Settings check box.
Performing a development workflow with unassigned sample setup • Save the project. I If you enter the same lane settings for multiple tiles or rows, the nanowell plate lanes are automatically merged. 9 For each master mix reagent, in the Target and dye settings table, do the following: • Choose a tile (in plate view) or a row (in table view). • Disable the dyes that are not contained in the master mix reagent. • Optionally, rename the targets. • Save the project.
Routine operation of development workflow 287 Pipette and partition the nanowell plates on the partitioning engine as described in Partitioning the nanowell plates (221): • Pipette the reaction mixtures into the inlet ports of the first nanowell plate. • Choose the Load button. • Place the nanowell plate in the drawer. • Choose the Start button. • When the nanowell plate drawer opens, check that all nanowell plate lanes that contain reaction mixtures are partitioned. • Remove the nanowell plate.
Performing a development workflow with unassigned sample setup 14 Routine operation of development workflow 18 Optionally, on the Manage run profiles panel, duplicate or import a run profile as described in Working with run profiles on the Manage run profiles panel in the analyzer software (299): • To duplicate a run profile, choose a run profile and choose the Duplicate button. Enter a name for the run profile and choose the Save button. • To import a run profile, choose the Import button.
Routine operation of development workflow 289 22 CAUTION! Risk of contamination of the laboratory. Pack the used nanowell plates in a resealable plastic bag. When the run is finished, unload the analyzer as described in Unloading the analyzer (227): • In the global information area, choose the button. • Remove the nanowell plate stack from the drawer. • Choose the button.
Performing a development workflow with unassigned sample setup • • • • From the Runs menu, choose the run. > Assign existing sample setup. Choose Choose the unassigned sample setup and choose the Confirm button. Save the project. I If no unassigned sample setup can be assigned, you must add the lane settings directly to the run.
Routine operation of development workflow 291 28 Check and adjust the clustering, as described in Adjusting the clustering in the development software (342): • From the Clustering menu, choose the clustering. button. • Choose the • In the Settings combo box, adjust the clustering settings. • Choose the button. • If required, adjust the thresholds in the scatter plots. Choose the Calculate button. • Save the project.
Performing a development workflow with unassigned sample setup 14 Routine operation of development workflow 30 Alternatively, edit analyses as described in Analyses in the development software (358): • From the Analysis menu, choose the analysis. • Choose the button. • In the Settings combo box, edit the analysis settings. • Choose the button. • Save the project.
Routine operation of development workflow 293 u Related topics • Development workflow with unassigned sample setup (quick reference) (208) • Partitioning the nanowell plates (221) • Loading the analyzer (225) • Unloading the analyzer (227) • Projects in the development software (294) • Run profiles in the analyzer software (298) • Entering run information for a development run in the analyzer software (307) • Runs in the development software (309) • Editing lane settings via copy and paste in the developm
Projects in the development software Projects in the development software In the development software, a project comprises associated data, for example, data belonging to the same research topic.
Routine operation of development workflow 295 By default, projects are named "Project" and numbered consecutively. A project has a .dpcrPrj file extension. Working with projects in the development software You can create, open, save, and close a project. Always save your projects before closing. 1 In the development software, do one of the following: • On the Start page tab, choose the Create new project button. > New • In the Navigation area, choose File > project.
Projects in the development software r To open a project in the development software 1 In the development software, do one of the following: • On the Start page tab, choose the project from the list of recent items. • On the Start page tab, choose the Open file button. • In the Navigation area, choose File > > Open. • In the Windows Explorer, double-click the dpcrPrj file. 2 If required, navigate to a dpcrPrj file and choose the Open button.
Routine operation of development workflow 297 r To close a project in the development software 1 To close a project, do one of the following: • In the Navigation area, choose File > > Close. • In the top right of the software window, choose the button. 2 In the Close dialog box, choose the Exit button. f The project and the instance of the development software are closed.
Run profiles in the analyzer software Run profiles in the analyzer software For development runs, run profiles contain the run parameters for the analyzer. The run profiles are listed on the Manage run profiles panel. You can edit the run profiles on the Edit run profile panel.
Routine operation of development workflow Detection formats Program Temperature Duration Number of cycles Channel 2 / FAM UNG 50 °C 120 s 1 Channel 3 / HEX Denaturation 95 °C 20 s 1 RT Step 1 55 °C 180 s 1 RT Step 2 65 °C 720 s 1 RT Inactivation 95 °C 15 s 1 Amplification Step 1: 95 °C Step 1: 15 s 40 Step 2: 58 °C Step 2: 30 s 40 °C 30 s Cooling 299 1 y Default RNA run profile A run profile can be locked or unlocked, which is indicated in the Manage run profiles pane
Run profiles in the analyzer software You can export run profiles to and import from a network share or external storage device. You can only start a run from the Manage run profiles panel if the prerequisites for a development run are met. u Prerequisites for a development run (172) d 14 Routine operation of development workflow j m To import a run profile: Run profile (.
Routine operation of development workflow 301 4 In the Edit run profile name dialog box, enter a new name for the run profile. I The name can consist of 1 to 20 characters. The name must not contain the following characters: ?*<>/\:"|’ 5 Choose the Save button. f The run profile is displayed with the changed name in the Run profiles table. r To duplicate a run profile in the analyzer software 1 In the analyzer software, choose Routine > Development run > Manage run profiles.
Run profiles in the analyzer software f The Monitoring panel is displayed. r To delete a run profile in the analyzer software 1 In the analyzer software, choose Routine > Development run > Manage run profiles. f The Manage run profiles panel is displayed. 2 From the Run profiles table, choose a run profile. I You can only delete unlocked run profiles. You can delete several run profiles simultaneously. 3 Choose the Delete button.
Routine operation of development workflow 303 2 In the analyzer software, choose Routine > Development run > Manage run profiles. f The Manage run profiles panel is displayed. 3 Choose the Import button. f The Import run profiles dialog box is displayed. 4 In the folder browser, navigate to the folder of the run profile. 5 In the file browser, choose the run profile. I You can import several run profiles simultaneously.
Run profiles in the analyzer software You can only start a run from the Edit run profile panel if all changes to the run profile are saved and if the prerequisites for a development run are met. u Prerequisites for a development run (172) About the detection formats The detection formats define the channels, the dye per channel, and the integration time for the detection of fluorescence by the analyzer.
Routine operation of development workflow 305 5 To add a program, choose the button. From the drop-down menu, choose the program. I It depends on the location in the run profile which programs you can add. f The new program is added to the left. 6 To delete a program, choose the button. I You cannot delete the cooling program at the end of the run profile. 8 To edit the detection formats, do the following: • To disable a channel, clear the Enabled check box.
Run profiles in the analyzer software 3 Choose the Run button. I The Run button is only available if there are no unsaved changes in the run profile and if the prerequisites for a development run are met. Alternatively, you can start the development run from the Manage run profiles panel. f The development run is started. 14 Routine operation of development workflow f The Monitoring panel is displayed. Roche Diagnostics Digital LightCycler® System · Software version 1.
Routine operation of development workflow 307 Entering run information for a development run in the analyzer software During a development run, you can enter run information on the Monitoring panel of the analyzer software. Run information comprises the run name and run notes. By default, a development run is named "Batch_YYYYMMDDhhmmss" with the date and time the development run was started on the analyzer.
Entering run information for a development run in the analyzer software 2 Change the run name and/or enter run notes. I The run name can consist of 1 to 25 characters. The run name must not contain the following characters: ?*<>/\:"|’ 14 Routine operation of development workflow 3 Choose the Confirm button. Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Routine operation of development workflow 309 Runs in the development software At the end of each run, a raw data file is generated that contains the run parameters and fluorescence values. You import the raw data files as runs into the development software for data analysis. You can import the raw data files of up to 600 samples into the development software. Merged nanowell plate lanes are still processed separately. Therefore, each merged lane is listed individually on a run tab.
Runs in the development software Raw data files are then imported as runs into the development software and are listed in the Runs menu. The raw data is the basis for clustering and analyses.
Routine operation of development workflow 311 For a development run, the lane settings are not contained in the raw data file. The lane settings can either be assigned to the run from an unassigned sample setup or they can be added directly to the run.
Runs in the development software The position of a set of merged lanes in a sample setup is denoted by the lowest position of the included nanowell plate lanes. Example: If the nanowell plate lanes A1, B1, and C1 are merged, the position of the set of merged lanes is denoted as "A1". The position is also used as name for the set of merged lanes.
Routine operation of development workflow 313 Alternatively, you can change the run name in the development software after import of the raw data file. u Working with raw data files and runs in the development software (317) About export Even if automatic export of the raw data files is configured, manual export of the raw data files is always possible. If no automatic export of the raw data files is configured or if automatic export fails, you must export the raw data files manually.
Runs in the development software 4 Enter a new name for the run and choose the Save button. I The name can consist of 1 to 20 characters. The name must not contain the following characters: ?*<>/\:"|’ f The new name is displayed on the Development results panel. r To export the raw data of a development run manually from the analyzer software 1 Optionally, to export to an external storage device, connect the external storage device to the analyzer.
Routine operation of development workflow 315 4 Choose the Confirm button. f The run is deleted from the table on the Development results panel. Exporting raw data files of diagnostic runs from the web application For diagnostic runs, you can export the raw data files from the web application if the export conditions are met. If no automatic export of the raw data files is configured or if automatic export fails, you must export the raw data files manually.
Runs in the development software • d j Alternatively, you can export and save the raw data file for later import into the development software. m Optionally, external storage device, e.g.
Routine operation of development workflow 317 r To export and save the raw data file of a diagnostic run from the web application 1 Optionally, to export to an external storage device, connect the external storage device to the computer running the web application. 2 In the web application, in the Results column on the dashboard, choose the {count} completed batches tile. f The Completed batches screen is displayed. 3 Choose the run and choose the Export button. f A dialog box is displayed.
Runs in the development software • • Nanowell plate IDs Detection formats An unassigned sample setup is partially matching, if the following parameters match between the unassigned sample setup and the development run: • Number of nanowell plates • Nanowell plate types • • Order of the nanowell plates Detection formats After an unassigned sample setup is assigned to a development run, the following applies: • The unassigned sample setup is deleted from the Unassigned sample setup menu in the Navig
Routine operation of development workflow 319 f The run tab is displayed in the work area. f In the Navigation area, the run is listed in the Runs menu. f 1 default clustering per combination of master mix reagent and plate type is added to the project and listed in the Clustering menu. 4 Save the project. r To import the raw data file into a project in the development software 1 In the development software, open the project as described in Working with projects in the development software (295).
Runs in the development software r To view the run profile of a run in the development software 1 In the Navigation area, choose the run from the Runs menu. Choose > View run profile. f The run profile is displayed in the same format as on the Edit run profile panel in the analyzer software. f The run profile is view only. You cannot edit the run profile. 2 To display the channel, dye, and integration time settings, choose the Detection formats button.
Routine operation of development workflow 321 2 Navigate to a folder and choose the OK button. f A CSV file per nanowell plate lane is exported to the folder. f The first row in the CSV files contains the column headers, i.e., the legend. r To delete a run from a project in the development software 1 In the Navigation area, choose the run from the Runs menu. Choose > Remove. 2 In the Warning dialog box, choose the Confirm button. I You cannot restore the run, but you can open or import the run again.
Runs in the development software An unassigned sample setup is partially matching, if the following parameters match between the unassigned sample setup and the development run: • Number of nanowell plates • Nanowell plate types • • Order of the nanowell plates Detection formats After an unassigned sample setup is assigned to a development run, the following applies: • The unassigned sample setup is deleted from the Unassigned sample setup menu in the Navigation area.
Routine operation of development workflow 323 5 Save the project. List of columns on the Sample setup table view card i The entry in the MMx ID field on the Lane settings card is not displayed on the Sample setup table view card. If you change a lane setting on the Lane settings card, the corresponding column on the Sample setup table view card (and the entry on the tile in plate view) is updated accordingly. If the update is delayed, close the tab and reopen it from the Navigation area.
Runs in the development software Example: A dilution factor of 2 (i.e., a dilution of 1:2) means half of the reaction mixture consists of sample. By default (dilution of 1:1), the development software calculates the quantitative results in relation to the volume of the reaction mixture. If you enter a dilution factor, the development software automatically uses it as a multiplication factor to calculate the quantitative results in relation to the sample volume.
Routine operation of development workflow MMx lot number column Additional identifying information, e.g., the lot number of the master reagent or master mix reagent, as entered in the MMx lot number field on the Lane settings card. MMx expiry date column The expiry date, e.g., of the master reagent or the master mix reagent, as entered in the MMx expiry date field on the Lane settings card. Merging column 325 Indicates if the nanowell plate lane belongs to a set of merged lanes.
Runs in the development software • • • • ID of master mix reagent or master reagent Expiry date of master mix reagent or master reagent Lot number of master mix reagent or master reagent Target and dye settings • Notes and sample preparation notes The following applies to lane settings: • • • • 14 Routine operation of development workflow • Changes to a master mix reagent, e.g.
Routine operation of development workflow 327 6 To add a new master mix reagent to the project and assign it to the selected tiles or rows, do the following: • Choose the MMx field. • Enter the name of the master mix reagent. • Press Enter. f The master mix reagent is displayed on the selected tiles or in the selected rows. f By default, in plate view, all tiles with the same master mix reagent are displayed with the same color.
Runs in the development software I Only the dyes for channels that were enabled in the run settings are displayed. At least 1 target must be enabled for each master mix reagent. Disabled targets are excluded from clustering and analysis later in the development workflow. Ensure that you disable empty channels. 11 To map the targets to the dyes, rename the targets: • Choose the Target field. • Enter the name of the target. • Press Enter.
Routine operation of development workflow Sample groups and merged lanes 329 If merged lanes belong to a sample group, always all lanes of the set of merged lanes belong to the sample group because the merged lanes contain the same sample. If you add a merged lane to a sample group, all other merged lanes of the same set are added automatically to the sample group. If you merge a lane that is part of a sample group, all other merged lanes of the same set are added automatically to the sample group.
Runs in the development software 3 On the Sample groups card, choose the New button. f A sample group is created that contains the selected samples and is listed on the Sample groups card. f Sample groups are numbered consecutively. 14 Routine operation of development workflow 4 Save the project.
Routine operation of development workflow 331 3 On the Sample groups card, choose the button of the sample group you want to add the samples to. f The new samples and the samples already belonging to the sample group are selected. 4 On the Sample groups card, choose the Update button. I Without this step, the samples are not added to the sample group! f The sample group contains both the old and the newly added samples.
Runs in the development software 2 On the Sample groups card, choose the sample group. f The samples belonging to the sample group are selected. 3 Press and hold Ctrl. Select and/or deselect samples for the sample group. I Pressing Ctrl keeps the selected samples. If you just select a sample without pressing Ctrl, all other samples are deselected. 4 On the Sample groups card, choose the Update button. I Instead of updating a sample group, consider deleting it and creating a new one.
Routine operation of development workflow 333 2 On the Sample groups card, choose the sample group. 3 Choose the Rename button. f The Edit sample group name dialog box is displayed. 4 Enter the new name and choose the Save button. f The new name of the sample group is displayed on the Sample groups card.
Runs in the development software 2 On the Sample groups card, choose the sample group. 3 Choose the Delete button. f The Warning dialog box is displayed. 4 Choose the Confirm button. I You cannot restore deleted sample groups. f The sample group is deleted from the Sample groups card. 14 Routine operation of development workflow 5 Save the project.
Routine operation of development workflow 335 Editing lane settings via copy and paste in the development software Instead of adding and/or editing lane settings manually, you can copy and paste them between unassigned sample setups and/or runs of the same project in the development software.
Editing lane settings via copy and paste in the development software • You can copy several tiles from the same nanowell plate and choose 1 tile only in the target setup if there are enough tiles below the selected tile in the target setup. The tiles are pasted starting from the selected tile towards the end of the nanowell plate.
Routine operation of development workflow • 337 Optionally, to undo the paste operation, choose the Undo button. 14 Routine operation of development workflow 7 Save the project. Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Clustering in the development software Clustering in the development software Clustering differentiates between positive and negative nanowells.
Routine operation of development workflow 339 The development software adds, updates, and/or deletes the clustering tabs when you do one of the following: • Open a raw data file as a new project: – Clustering tabs are added. • Import a raw data file into an existing project: – All samples with a combination of master mix reagent and nanowell plate type that matches an existing clustering are added to that clustering tab. – For all other samples, clustering tabs are added.
Clustering in the development software Lane column Columns for number of positive nanowells The position of the sample in the sample setup. The Pos. NWs {0}-{1} columns display the number of positive nanowells of the sample determined from the current clustering settings. The Clustering data card contains a separate Pos. NWs {0}-{1} column per dye that is enabled in the lane settings on the run tab.
Routine operation of development workflow 341 The quality indicator does not distinguish between the channels, but is calculated across all channels of a nanowell plate lane. u List of clustering settings in the development software (342) Flags column The flags associated with the sample. Changing the display options for the scatter plots in the development software By default, all samples that are listed on the Clustering data card on a clustering tab are displayed in the scatter plots.
Clustering in the development software • • To hide the Navigation area, choose the button. To hide or display the Clustering data card, choose the Table button above the scatter plots. 6 To display the scatter plots for different channels next to each other, choose the View buttons. 7 To hide or display the dye to target name mapping and a legend for the color-coding of the scatter plots, choose the Legend buttons.
Routine operation of development workflow 343 To display the clustering settings, in the top right corner button. on the clustering tab, choose the Clustering drop-down list Determines the clustering method: • Automatic The clustering is calculated as if all scatter points originated from one nanowell plate lane. • Automatic (individual) The clustering is calculated separately for each nanowell plate lane.
Clustering in the development software Sensitivity specificity field For the Custom option of the clustering parameters only: Editable value between 0.0000 and 1.0000 that determines the balance between sensitivity and specificity: • 0.0000 = maximum sensitivity • 1.0000 = maximum specificity The lower the value, the closer the threshold is set to the negative cluster. Default value = 1.
Routine operation of development workflow 345 If 2 targets compete for reaction components, the fluorescence of nanowells that contain both targets is lower in both channels than the fluorescence of nanowells that contain 1 of the targets only. If 2 targets cross-react, a positive reaction in 1 channel raises the baseline for the negative nanowells in the other channel.
Clustering in the development software Graph drop-down list Determines the type of scatter plots used to visualize the fluorescence intensities: • 1D scatter plot • • 2D scatter plot 3D scatter plot Default value = 1D scatter plot In a 1D scatter plot, the fluorescence intensity of a channel is plotted against the nanowell index that is randomized for visualization purposes only.
Routine operation of development workflow 347 Select channels table Allows you to include or exclude channels from the scatter plots. For the 2D scatter plot plot type or the 3D scatter plot plot type, you must enable the corresponding number of channels. Axis ranges group box In the Min. field and the Max. field, enter the start and end values for the intensity-axes of the scatter plots (e.g., the y-axis of the 1D scatter plot). To reset the axis ranges, choose the Reset button.
Clustering in the development software r To adjust the clustering settings for the Automatic clustering method or the Automatic (individual) clustering method 1 In the development software, in the Navigation area, choose the clustering from the Clustering menu. f The clustering tab is displayed. 2 In the top right corner, choose the button. f The Settings combo box is displayed.
Routine operation of development workflow 349 f The scatter plots and the values on the Clustering data card are recalculated and displayed. 11 Save the project. r To adjust the clustering settings for Automatic - External seed data clustering method 1 Optionally, if the seed data file is stored on an external storage device, connect the external storage device to the computer running the development software.
Clustering in the development software Adjusting the clustering settings and thresholds for manual clustering For the manual clustering method, you can adjust the plot type, the enabled channels, and the axis ranges in the clustering settings. In the scatter plots, you must adjust the thresholds manually. With the Manual clustering method, you can adjust the thresholds manually in 1D scatter plots and 2D scatter plots only.
Routine operation of development workflow • • • • 351 To adjust the thresholds in a 2D scatter plot with the Threshold button (manual clustering) (352) To adjust the thresholds in a 2D scatter plot with the Lasso button (manual clustering) (353) To adjust the thresholds in a 2D scatter plot with the Spider button (manual clustering) (354) To calculate the values in the clustering data table for a 3D scatter plot (manual clustering) (355) r To adjust the threshold in a 1D scatter plot (manual clustering)
Clustering in the development software r To adjust the thresholds in a 2D scatter plot with the Threshold button (manual clustering) 1 Adjust the clustering settings as described in To adjust the clustering settings for the Manual clustering method (350). Choose the 2D scatter plot option. f The values on the Clustering data card are deleted. f The scatter plots including threshold indicators (dashed lines) are displayed. f The Threshold button for the manual clustering is selected.
Routine operation of development workflow 353 r To adjust the thresholds in a 2D scatter plot with the Lasso button (manual clustering) 1 Adjust the clustering settings as described in To adjust the clustering settings for the Manual clustering method (350). Choose the 2D scatter plot option. f The values on the Clustering data card are deleted. f The scatter plots including threshold indicators (dashed lines) are displayed. f The Threshold button for the manual clustering is selected.
Clustering in the development software f The values on the Clustering data card are calculated and displayed. 5 Save the project. r To adjust the thresholds in a 2D scatter plot with the Spider button (manual clustering) 14 Routine operation of development workflow 1 Adjust the clustering settings as described in To adjust the clustering settings for the Manual clustering method (350). Choose the 2D scatter plot option. f The values on the Clustering data card are deleted.
Routine operation of development workflow 355 r To calculate the values in the clustering data table for a 3D scatter plot (manual clustering) 1 Adjust the clustering settings as described in To adjust the clustering settings for the Manual clustering method (350). Choose the 3D scatter plot option. f The values on the Clustering data card are deleted. f The scatter plot is displayed. f The scatter points are color-coded. 2 To turn the 3D-view, click in the scatter plot. Drag and drop the view.
Clustering in the development software Exporting custom clustering parameters as seed data files You can export the custom clustering parameters from an automatic clustering as a seed data file to transfer the clustering parameters to another automatic clustering and to use them in analysis packages. A seed data file is specific for the nanowell plate type. A seed data file is exported as signed XML file and is named PlateType_SeedData_YYYYMMDDhhmmss.sdxml with the date and time of the export.
Routine operation of development workflow 357 4 Choose the Export seed data button. I You can only export a seed data file from an automatic clustering with custom clustering parameters. 5 Navigate to a folder. Optionally, enter a different name for the seed data file. Choose the Save button. f The SDXML file is exported.
Analyses in the development software Analyses in the development software Analyses determine the final qualitative and quantitative results. i Merged lanes are analyzed together. Therefore, a set of merged lanes has 1 entry on an analysis tab.
Routine operation of development workflow 359 r To delete an analysis 1 In the Navigation area, choose the analysis from the Analysis menu. Choose > Delete. 2 In the Warning dialog box, choose the Confirm button. f The analysis is deleted from the project. r To rename an analysis 1 In the Navigation area, choose the analysis from the Analysis menu. Choose > Rename. 2 In the dialog box, enter the new name. 3 Choose the Save button. f The analysis tab is renamed.
Analyses in the development software f Navigation > Analysis > > Abs Quant > The settings are ordered on tabs in the Settings combo box. The availability of settings on a tab depends on the current settings on the other tabs. Sample selection tab On the Sample selection tab, choose the samples for the analysis. The table lists all samples of the project with the sample IDs as entered in the lane settings on the run tabs.
Routine operation of development workflow 361 the analyzer but the tests were not included in the analysis package. By default, such positions are analyzed as samples, not as controls. The table on the right of the tab lists the defined controls for the selected combination of master mix reagent and target. Controls are target-specific: If the control for a target is invalid, the system automatically invalidates the final results for that target for all samples of the same run.
Analyses in the development software Lower limit field and Upper limit field The fields define the valid concentration range for the internal control. The lower limit must be lower than the upper limit. Default values: • Lower limit = 1.0000 cp/µl • Upper limit = 1000.0000 cp/µl Target limits tab On the Target limits tab, optionally enter the limit of detection and/or the limits of quantification.
Routine operation of development workflow 363 The lower limit of quantification must be lower than the upper limit of quantification. The lower limit of quantification must be higher than the lower limit of detection. Default values: • Limit of quantification = disabled • Lower limit of quantification = 0.0000 cp/µl • Upper limit of quantification = 50000.
Analyses in the development software u List of columns on the Sample setup table view card (323) MMx column The used master mix reagent as entered in the lane settings on the run tab. u List of columns on the Sample setup table view card (323) Lane column The position of the sample or control in the run. Merged icon.
Routine operation of development workflow 365 u List of flags (489) Sample type column Color-coding and icon for the control type. u About color-coding of controls (148) Merged lanes column Name of the set of merged lanes as displayed in the lane settings on the run tab. Total copies column Absolute number of target molecules in the sample or control. Initial result column Initial (qualitative) result for the target. For samples, initial results are regardless of the corresponding control results.
Analyses in the development software Dilution factor column Dilution factor as entered in the lane settings on the run tab. u List of columns on the Sample setup table view card (323) Run name column Run name on the analyzer in which the sample or control was processed. The run name is used as name of the run tab in the development software. 14 Routine operation of development workflow Conc. 68% CI min. column and Conc. 68% CI max.
Routine operation of development workflow 367 Raw values are regardless of applied limits. For samples, raw values are also regardless of the corresponding control results. Result overview panel The Result overview panel summarizes the results per target for each sample or control for the selected master mix reagent. Run name on the analyzer in which the sample or control was processed. The run name is used as name of the run tab in the development software.
Analyses in the development software 14 Routine operation of development workflow Linkage panel Linkage is the occurrence of different targets that are located on the same target molecule and therefore in the same nanowell: • If 2 targets are unlinked, the targets are all located on different target molecules. The fraction of double-positive nanowells is the product of the fraction of nanowells positive for target 1 and the fraction of nanowells positive for target 2.
Routine operation of development workflow 369 Linkage may negatively affect target quantification. Therefore, the displayed p-value can be used as a quality control for multiplex tests. If the selected master mix reagent contains 1 target only, no linkage can be determined. Sample ID column The sample ID of the sample or control as entered in the lane settings on the run tab.
Analyses in the development software Statistics panel The Statistics panel displays statistical information for the sample groups that contain samples that were selected for the analysis. Group column The name of the sample group as entered on the run tab or in the Settings combo box. If not all samples of a sample group are included in the analysis, the sample group name is appended with the number of included samples in brackets, e.g., "(3 out of 4)". Merged lanes are counted separately.
Routine operation of development workflow 371 Editing the default Abs Quant - All analysis By default, each project contains an Abs Quant - All analysis that includes all samples of the project. You can edit the analysis settings for the Abs Quant - All analysis, except you cannot exclude samples. If you want to perform an absolute quantification analysis on a subset of samples only, you must add a new absolute quantification analysis to the project.
Analyses in the development software 5 To display the statistics for the sample groups, choose the Statistics button. r To edit the Abs Quant - All analysis 1 In the development software, in the Navigation area, choose Analysis > > Abs Quant - All. f The Abs Quant - All tab is displayed in the work area. f The Abs Quant - All analysis is calculated. f The Results panel is displayed on the Abs Quant - All tab. f The Results panel displays 1 entry for each sample or control.
Routine operation of development workflow • • 373 From the Target drop-down list, choose the target that was used as internal control. In the Lower limit field and the Upper limit field, enter the valid concentration range for the internal control. I In the Target drop-down lists, only the targets are available for which no controls were defined on the Controls tab. For each master mix reagent, you can set 1 target as an internal control.
Analyses in the development software u Overview of development workflow without unassigned sample setup (194) r To add an absolute quantification analysis 1 In the development software, in the Navigation area, choose Analysis > > Abs Quant. f A new absolute quantification tab is displayed in the work area and listed in the Analysis menu. f The Settings combo box is displayed. 2 On the Sample selection tab, select the samples for the analysis. I The table lists all samples of the project.
Routine operation of development workflow 375 9 For each master mix reagent that contains an internal control, do the following: • From the Target drop-down list, choose the target that was used as internal control. • In the Lower limit field and the Upper limit field, enter the valid concentration range for the internal control. I In the Target drop-down lists, only the targets are available for which no controls were defined on the Controls tab.
Analyses in the development software 16 To display the calculated linkage between the targets, do the following. • Choose the Linkage button. • From the drop-down list, choose the master mix reagent. • Optionally, edit the thresholds between linked, weakly linked, and/or unlinked in the legend above the table. 17 To display the statistics for the sample groups, choose the Statistics button.
Routine operation of development workflow 377 Performing CNV analysis (386) List of tabs and settings for CNV analysis The settings provide all parameters necessary for CNV analysis. f Navigation > Analysis > > CNV > The settings are ordered on tabs in the Settings combo box. The availability of settings on a tab depends on the current settings on the other tabs. Sample selection tab The table lists all samples of the project with the sample IDs as entered in the lane settings on the run tabs.
Analyses in the development software Controls tab On the Controls tab, mark the positions of controls in the sample setups and enter the valid ranges for the controls. If you choose a merged lane, the whole set of merged lanes is selected automatically. The table on the left lists the combinations of master mix reagent and target of interest for which a sample was selected on the Sample selection tab.
Routine operation of development workflow 379 Target limits tab On the Target limits tab, optionally enter the limits of validity for targets of interest and reference targets. For targets of interest, enter the reference target copy number and the limits of the normal copy number.
Analyses in the development software • The final result is high if the calculated copy number is higher than the configured upper limit of copy number. Default values: • Lower limit of copy number = 1.8000 • Upper limit of copy number = 2.2000 List of result columns for CNV analysis A CNV tab displays the results of a CNV analysis on the Results panel, the Result overview panel, and the Statistics panel.
Routine operation of development workflow Lane column 381 The position of the sample or control in the run. Merged icon. lanes are indicated by the u About the positions of nanowell plate lanes in sample setups (153) Copy number column The calculated final copy number of the target of interest in the sample or control (final quantitative result). "N/A" is displayed if one of the following applies: • • Final (qualitative) result for the sample or control.
Analyses in the development software Ratio column The final ratio of the copy numbers of the reference target and the target of interest. If the analysis contains several reference targets, the development software takes the mean of their copy numbers for analysis. Ratio 95% CI min. column and Ratio 95% CI max.
Routine operation of development workflow Ratio 68% CI min. column and Ratio 68% CI max. column 383 The values specify the confidence interval for the 68% confidence level (based on the applied Poisson distribution and not accounting for other error sources): The probability is 68% that the ratio of the copy numbers of the reference target and the target of interest lies within the specified range.
Analyses in the development software Result overview panel The Result overview panel summarizes the results per sample or control. 14 Routine operation of development workflow Run name column Run name on the analyzer in which the sample or control was processed. The run name is used as name of the run tab in the development software. Lane column The position of the sample or control in the run. Merged icon.
Routine operation of development workflow 385 Statistics panel The Statistics panel displays statistical information for the sample groups that contain samples that were selected for the analysis. Group column The name of the sample group as entered on the run tab or in the Settings combo box. If not all samples of a sample group are included in the analysis, the sample group name is appended with the number of included samples in brackets, e.g., "(3 out of 4)". Merged lanes are counted separately.
Analyses in the development software Performing CNV analysis Perform CNV analysis to determine the differences of the number of copies of genomic segments between samples and reference standards.
Routine operation of development workflow 387 9 For each nanowell plate lane (i.e., position on a nanowell plate) that contains a control, do the following: • From the table, choose the combination of master mix reagent and target of interest. • If the same combination is used in several runs, from the Run: drop-down list, choose the run. • In the graphical representation of the sample setup, choose the nanowell plate lane that contains a control. • For a negative control, choose the Negative option.
Analyses in the development software f The CNV analysis is calculated. f The Results panel is displayed on the CNV tab. 14 Save the project. 15 To display a summary of the results, choose the Result overview button. 16 To display the bar charts as described in Displaying the bar charts (400), do the following: • At the top right of the Result overview panel, choose the button. • Optionally, adjust the display of the bar charts.
Routine operation of development workflow 389 If the reference target is detected but the variant target is not detected (i.e., there are positive-negative nanowells), the sequence of the variant target is changed. This is the so-called variant sequence. i To facilitate the clustering for indel analysis, use the 2D scatter plot type.
Analyses in the development software Analysis setup tab On the Analysis setup tab, create the analysis setups: • • • Choose the combinations of master mix reagent, variant target, and reference target. Enter the minimum percentage of the variant sequence. Optionally, enter the limits of validity. MMx drop-down list Lists the master mix reagents for which a sample was included in the analysis on the Sample selection tab.
Routine operation of development workflow 391 Controls tab On the Controls tab, mark the positions of controls in the sample setups and enter the valid ranges for the controls. If you choose a merged lane, the whole set of merged lanes is selected automatically. The table on the left lists the combinations of master mix reagent, variant target, and reference target for which a sample was included in the analysis on the Sample selection tab.
Analyses in the development software Default value for negative controls: • Upper limit = 0.0000 cp/µl List of result columns for indel analysis An indel tab displays the results of an indel analysis on the Results panel, the Result overview panel, and the Statistics panel. f Navigation > Analysis > > Indel The panels only display results for samples that were selected on the Sample selection tab in the Settings combo box. Merged lanes are analyzed together.
Routine operation of development workflow Reference column 393 The tested reference target as selected on the Analysis setup tab. u Analysis setup tab (390) MMx column The used master mix reagent as entered in the lane settings on the run tab. u List of columns on the Sample setup table view card (323) Lane column The position of the sample or control in the run. Merged icon.
Analyses in the development software Critical flags that invalidate the final result are displayed in bold. u List of flags (489) Sample type column Color-coding and icon for the control type. u About color-coding of controls (148) Merged lanes column Name of the set of merged lanes as displayed in the lane settings on the run tab.
Routine operation of development workflow 395 The number of valid nanowells is the total of the positive and the negative nanowells. u List of columns on the Clustering data card (339) Dilution factor column Dilution factor as entered in the lane settings on the run tab. u List of columns on the Sample setup table view card (323) Run name column Run name on the analyzer in which the sample or control was processed. Variant [%] 68% CI min. column and Variant [%] 68% CI max.
Analyses in the development software Raw values are regardless of applied limits. For samples, raw values are also regardless of the corresponding control results. Result overview panel The Result overview panel summarizes the results per sample or control for the selected master mix reagent. 14 Routine operation of development workflow Run name column Run name on the analyzer in which the sample or control was processed. The run name is used as name of the run tab in the development software.
Routine operation of development workflow 397 Statistics panel The Statistics panel displays statistical information for the sample groups that contain samples that were selected for the analysis. Group column The name of the sample group as entered on the run tab or in the Settings combo box. u Working with sample groups in the development software (328) Variant column The tested variant target as selected on the Analysis setup tab.
Analyses in the development software Performing indel analysis Perform indel analysis to determine the presence (insertion) or absence (deletion) of bases in a genomic sequence.
Routine operation of development workflow • 399 Optionally, clear the Limit of validity (for the total concentration of the variant and the wild type) check box. 9 For each nanowell plate lane (i.e., position on a nanowell plate) that contains a control, do the following: • From the table, choose the combination of master mix reagent, variant, and reference. • If the same combination is used in several runs, from the Run: drop-down list, choose the run.
Analyses in the development software r To edit an indel analysis 1 In the development software, in the Navigation area, choose the indel analysis from the Analysis menu. f The indel tab is displayed in the work area. 2 To display the Settings combo box, choose the button. 3 To include and/or exclude samples from the analysis, do the following: • Choose the Sample selection tab. • Select the samples you want to include in the analysis. • Choose the Update analysis button.
Routine operation of development workflow 401 4 To change the maximum value for the concentration axes, do the following: • To change the maximum value, enter the value in the Range field. Press Enter. • To return to the default value, choose the Reset button. I The Reset button is only displayed after you entered a different value. 5 To change the scale of the concentration axes, do the following: • To display a logarithmic scale, choose Scale > Log.. • To display a linear scale, choose Scale > Lin..
Unassigned sample setups in the development software Unassigned sample setups in the development software You can use unassigned sample setups in your project to plan development runs. It is not required to use unassigned sample setups in your project. You can directly add the same information later to the raw data file (run) of the development run.
Routine operation of development workflow • • • • Dilution factor of sample Name of master mix reagent ID of master mix reagent or master reagent Expiry date of master mix reagent or master reagent • • • Lot number of master mix reagent or master reagent Target and dye settings Notes and sample preparation notes 403 By default, the targets are named as the dyes. The following applies to lane settings: • Changes to a master mix reagent, e.g.
Unassigned sample setups in the development software To use the planned configuration of the detection formats for the development run, you must configure the run profile on the analyzer accordingly. u Editing run profiles on the Edit run profile panel in the analyzer software (303) About merged lanes Merged lanes emulate the partitioning of a larger sample volume into a higher number of nanowells. The system treats the nanowells of a set of merged lanes as if they belong to 1 nanowell plate lane.
Routine operation of development workflow 405 Working with unassigned sample setups in the development software To facilitate the use of unassigned sample setups, you can create, duplicate, rename, and delete unassigned sample setups. If you create a project, an unassigned sample setup with 1 universal nanowell plate is added automatically. u For adding information to unassigned sample setups (i.e.
Unassigned sample setups in the development software r To delete an unassigned sample setup in the development software 1 In the development software, in the Navigation area, choose the unassigned sample setup from the Unassigned sample setup menu. 2 Choose > Delete. 3 In the Warning dialog box, choose the Confirm button. f The sample setup tab is closed. f The unassigned sample setup is deleted from the Unassigned sample setup menu. 4 Save the project.
Routine operation of development workflow 407 u Working with raw data files and runs in the development software (317) r To add run settings to an unassigned sample setup in the development software 1 In the development software, in the Navigation area, choose the unassigned sample setup from the Unassigned sample setup menu. 2 On the sample setup tab, choose the Run settings button. f The Run settings card is displayed on the sample setup tab.
Unassigned sample setups in the development software 5 To edit the detection formats, do the following: • To disable a channel, choose the Disabled button. • To enable a channel, select the Enabled check box. • For each enabled channel, choose the dye from the Dye drop-down list. I Ensure that you disable empty channels. Only the enabled dyes can be assigned in the lane settings.
Routine operation of development workflow 409 6 To add a new master mix reagent to the project and assign it to the selected tiles or rows, do the following: • Choose the MMx field. • Enter the name of the master mix reagent. • Press Enter. f The master mix reagent is displayed on the selected tiles or in the selected rows. f By default, in plate view, all tiles with the same master mix reagent are displayed with the same color.
Unassigned sample setups in the development software I Only the dyes for channels that were enabled in the run settings are displayed. At least 1 target must be enabled for each master mix reagent. Disabled targets are excluded from clustering and analysis later in the development workflow. Ensure that you disable empty channels. 11 To map the targets to the dyes, rename the targets: • Choose the Target field. • Enter the name of the target. • Press Enter.
Routine operation of development workflow 411 3 Navigate to a folder. Enter a name for the report and choose the Save button. f The sample setup report is saved as PDF file. f If a program for viewing PDF files is installed on your computer, the PDF is displayed. 4 Print the sample setup report as a guide for pipetting.
Analysis packages in the development software Analysis packages in the development software Analysis packages provide all parameters necessary to plan and to perform diagnostic runs and to generate diagnostic results as part of diagnostic workflows. An analysis package is based upon a development workflow: In an analysis package, you can only include tests from analyses that are part of the project.
Routine operation of development workflow f Navigation > Analysis package > analysis package i > Create Ensure that you enter the information correctly. You cannot change it later. Field to enter the name that identifies the analysis package in the development software, the analyzer software, and the web application. The name is automatically appended with the version number "(V0.0)". i Ensure that you enter a unique and meaningful name for the analysis package.
Analysis packages in the development software Edit panel On the Edit panel, you choose the tests for the analysis package and enter the issuer name of the analysis package. 14 Routine operation of development workflow f Navigation > Analysis package > analysis package > Edit Creator field > Create Field to enter the creator of the analysis package. In the analyzer software, the creator is displayed on the Manage analysis packages panel.
Routine operation of development workflow 415 The General settings panel comprises the following cards: • General settings • History General settings card Number of merged lanes drop-down list Drop-down list to choose the number of nanowell plate lanes to be merged in the sample setup (1 to 8). The number applies to both samples and controls in the sample setup.
Analysis packages in the development software Default value = Export raw data Report label field Free text field to enter the text used on the analysis package report. u To create an analysis package report (433) History card On the History card, you can document the change history of the analysis package. Comment field Free text field. 14 Routine operation of development workflow For example, enter a change description whenever you create a new version of an analysis package.
Routine operation of development workflow 417 The values are pre-entered from the analyses that are used to create the analysis package. The Test definition panel comprises the following cards: • Test list • Test details • Test settings • • • Result names Controls Internal controls Test list card Card that lists all tests of the analysis package, i.e., the tests that you chose on the Edit panel for the analysis package.
Analysis packages in the development software Lower limit of detection [copies/µL] field A limit of detection > 0 accounts for noise in the data, i.e., if there are positive nanowells even if the nanowell plate lane contains no target molecules. The initial result and the final result for a target are negative if the calculated raw concentration of the target is below the limit of detection. The lower limit of detection must be lower than the lower limit of quantification (if enabled).
Routine operation of development workflow 419 Controls card Card that lists the controls defined for the test and their settings. You can edit and delete the pre-defined controls, and add new controls. The controls that are defined here are automatically added to the diagnostic sample setup. Controls table Lists the controls that were defined in the analyses that are used to create the analysis package. To add a control, choose the New button.
Analysis packages in the development software To exclude the use of an internal control, choose the None option. Lower limit field and Upper limit field The fields define the valid concentration range for the internal control. The lower limit must be lower than the upper limit. Precision = 4 decimal places Test definition panel for CNV tests On the Test definition panel, you set the parameters that apply to the individual tests of the analysis package.
Routine operation of development workflow • • • • Test list Test details Test settings Controls • Result names 421 Test list card Card that lists all tests of the analysis package, i.e., the tests that you chose on the Edit panel for the analysis package. To display the other test-specific cards, choose a test from the table on the Test list card. Card that lists the defined reference targets and the target of interest and that allows you to enter limits of validity.
Analysis packages in the development software The lower limit of validity must be lower than the upper limit of validity. Precision = 4 decimal places Test settings card Card to enter the reference target copy number and the limits of normal copy number, and to configure the display of final quantitative results 14 Routine operation of development workflow Reference target copy number field The expected copy number of the reference target.
Routine operation of development workflow 423 Controls card Card that lists the controls defined for the test and their settings. You can edit and delete the pre-defined controls, and add new controls. The controls that are defined here are automatically added to the diagnostic sample setup. Controls table Lists the controls that were defined in the analyses that are used to create the analysis package. To add a control, choose the New button.
Analysis packages in the development software Test definition panel for indel tests On the Test definition panel, you set the parameters that apply to the individual tests of the analysis package. 14 Routine operation of development workflow f Navigation > Analysis package > analysis package > Test definition > Create The required parameters depend on the test type (absolute quantification, CNV, indel). The values are pre-entered from the analyses that are used to create the analysis package.
Routine operation of development workflow 425 Test details card Card that lists the name of the master mix reagent, the name of the variant target, and the name of the reference target. The Test details card is read-only. Test settings card Min. variant [%] field Defines the minimum percentage of the variant sequence that must be present in the sample for it to be variant positive.
Analysis packages in the development software Result names card Card to enter the names that are displayed for valid final qualitative results. Default values: • "Variant Positive" • "Variant Negative" Controls card Card that lists the controls defined for the test and their settings. You can edit and delete the pre-defined controls, and add new controls. 14 Routine operation of development workflow The controls that are defined here are automatically added to the diagnostic sample setup.
Routine operation of development workflow 427 MMx settings panel On the MMx settings panel, you set the dilution factors and the clustering settings for each test. f Navigation > Analysis package > analysis package > MMx settings > Create The MMx settings panel comprises the following cards: • MMx overview Clustering settings of "{0}" MMx overview card Card that lists the settings for the master mix reagents for each test of the analysis package.
Analysis packages in the development software Card for clustering settings of master mix reagent The Clustering settings of "{0}" card lists the clustering settings for the master mix reagent of the analysis package that is selected on the MMx overview card. 14 Routine operation of development workflow The placeholder {0} is replaced with the name of the master mix reagent, e.g., Clustering settings of "MMX1".
Routine operation of development workflow 429 Working with analysis packages You can create, update, export, and delete analysis packages, and create analysis package reports. An analysis package has a .dpcrAp file extension. When creating an analysis package, you must follow the order of the breadcrumb (Edit > General settings > Test definition > MMx settings) that is displayed above the cards. i Do not change previous steps in the project while you create or update an analysis package.
Analysis packages in the development software 3 In the Create analysis package dialog box, do the following: • In the Analysis package name field, enter a name for the analysis package. • From the Plate type drop-down list, choose the nanowell plate type. • Choose the Confirm button. I Ensure that you choose the correct plate type. You cannot change the plate type later. f The analysis package is created. f The tab of the analysis package is displayed in the work area.
Routine operation of development workflow 431 I Enter a change description on the History card whenever you create a new version of an analysis package. 8 In the breadcrumb, choose the Test definition button. 9 On the Test list card, choose a test. f The cards for the test details and settings are displayed.
Analysis packages in the development software 16 In the Increment version number dialog box, do one of the following: • To update the version number to "1.0", choose the Major button. • To update the version number to "0.1", choose the Minor button. • Choose the Update button. I You cannot save changes to an analysis package without updating the version. f The version of the analysis package is updated in the Analysis package menu. 17 Save the project.
Routine operation of development workflow 433 I You cannot go back to an earlier version of an analysis package. f The version of the analysis package is updated in the Analysis package menu. 9 Save the project. r To create an analysis package report 1 In the development software, open the project as described in To open a project in the development software (296). 2 In the Navigation area, choose the analysis package from the Analysis package menu. Choose > Generate report. 3 Navigate to a folder.
Analysis packages in the development software • Analyses in the development software (358) 14 Routine operation of development workflow • Unassigned sample setups in the development software (402) Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Table of contents 435 After routine operation 15 In this chapter 437 Logging off from the web application............................ 438 Logging off from the analyzer software ........................ 439 Shutting down the analyzer ............................................... 440 Closing the development software.................................. 442 15 After routine operation Shutting down the partitioning engine..........................
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After routine operation 437 Shutting down the partitioning engine Shut down the partitioning engine if you do not work with it for any length of time, e.g., over night. i For routine shutdown of the partitioning engine, do not simply press the power switch. Instead, follow the shutdown procedure and only press the power switch when prompted to do so. Only press the power switch outside of the shutdown procedure if immediate shutdown is required, e.g., in case of system failure or emergency shutdown.
Logging off from the web application Logging off from the web application Log off from the web application after use. Save all changes before logoff. i If you close the browser window or browser tab directly, you lose all unsaved changes. If configured in the password settings, the current user is logged off automatically after the inactivity time has elapsed. u Password settings (599) r To log off from the web application 1 In the global information area, choose the logon indicator.
After routine operation 439 Logging off from the analyzer software Log off from the analyzer software if you leave the analyzer unattended for any length of time. If configured in the password settings, the current user is logged off automatically after the inactivity time has elapsed. j u Password settings (599) m Logged on to the analyzer software r To log off from the analyzer software 1 In the global information area, choose the Logoff button.
Shutting down the analyzer Shutting down the analyzer Shut down the analyzer if you do not work with it for any length of time, e.g., over night. The button to shut down the analyzer is only available in the analyzer software if the nanowell plate stack drawer is closed and the analyzer is in Analyzer not initialized status, Analyzer ready status, or Analyzer paused status. i For routine shutdown of the analyzer, do not simply press the power button.
After routine operation 441 3 To shut down the analyzer, in the Shutdown dialog box, choose the Confirm button. 4 Wait until the touch screen turns dark. 15 After routine operation 5 On the right side of the analyzer, press the power button. Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Closing the development software Closing the development software Close the development software after use. Save all changes before closing. r To close the development software 1 To close the development software, do one of the following: > • In the Navigation area, choose File > Close. • In the top right corner of the software window, choose the button. f The Close dialog box is displayed.
Table of contents 443 Non-routine operation 16 In this chapter 445 Deleting sample setups in the web application ..................................................................... 445 Non-routine operation in the analyzer software ........ 447 Managing screenshots in the analyzer software .......................................................................... 447 Audit trails in the analyzer software .................... 449 About audit trails in the analyzer software....................
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Non-routine operation 445 Non-routine operation in the web application Deleting sample setups in the web application You can delete sample setups in the web application before the run is started on the analyzer. In the web application, the batch tiles of not yet processed sample setups are displayed in the Sample setups column on the dashboard. The batch tiles are in Incomplete setup status, Pending partitioning status, Ready to start run status, or Ready to start run (loaded) status.
Non-routine operation in the web application 3 Choose the Confirm button. f The sample setup is deleted. 16 Non-routine operation f The corresponding batch tile is deleted from the dashboard. f The orders of the deleted sample setup are not allocated again and are displayed again on the Orders screen in assignment mode. Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Non-routine operation 447 Non-routine operation in the analyzer software In this section Managing screenshots in the analyzer software (447) Audit trails in the analyzer software (449) Aborting a run on the analyzer (450) Restarting the analyzer (451) Managing screenshots in the analyzer software On the Manage screenshots panel in the analyzer software, you view, export, and delete the screenshots that were taken of the analyzer software.
Non-routine operation in the analyzer software r To export screenshots 1 Optionally, to export to an external storage device, connect the external storage device to the analyzer. 2 In the analyzer software, choose Administration > Manage screenshots. f The Manage screenshots panel is displayed. f The table lists all screenshots that are currently stored on the analyzer. 3 Optionally, sort, search, or filter the table. 4 To display a preview of a screenshot, choose the screenshot.
Non-routine operation 449 6 Choose the Confirm button. f The screenshots are deleted from the analyzer. Audit trails in the analyzer software System and user actions are logged as audit trails.
Non-routine operation in the analyzer software After archiving is completed successfully, the archived audit trails are deleted from the analyzer. Creating audit trails reports in the analyzer software You can create audit trails reports from the audit trails. d j m Optionally, external storage device, e.g.
Non-routine operation 451 r To abort a run on the analyzer 1 On the Monitoring panel in the analyzer software, choose the Abort run button. f The Confirmation dialog box is displayed. 2 Choose the Confirm button. f The run is aborted. f All results are invalid. 3 Wait until Awaiting plate removal is displayed on the Monitoring panel. 4 Unload the analyzer as described in Unloading the analyzer (227).
Displaying system information Displaying system information You can access the system information in the partitioning engine software, the analyzer software, and the development software. d m To download the license information from the partitioning engine: External storage device, e.g., USB flash drive r To display the system information in the partitioning engine software 1 In the partitioning engine software, in the global > Information.
Non-routine operation 453 3 In the top right corner, choose the button. f The About dialog box is displayed. f The About tab displays general information about the analyzer and the analyzer software. 4 To display application information about the analyzer software, choose the Application tab. 5 To display license information, choose the Legal notice tab. 6 To display information about the intended use, choose the Intended use tab. 7 To close the About dialog box, choose the button.
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Maintenance 17 Maintenance ................................................................................................. 457 Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Table of contents 457 Maintenance Maintenance schedule ........................................................ 459 Replacing the partitioning fluid bottle and/or the liquid waste bottle on the partitioning engine............ 460 Data maintenance on the analyzer ................................. 466 Cleaning up not allocated orders ......................... 466 Performing manual archiving ................................. 467 Performing a manual backup.................................
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Maintenance 459 Maintenance schedule The table lists all maintenance actions and their schedule. Maintenance action Frequency Procedure Replacing the partitioning fluid bottle and/or the liquid waste bottle. When the partitioning fluid bottle is empty or expired, or the waste bottle is full. u Replacing the partitioning fluid bottle and/or the liquid waste bottle on the partitioning engine (460) Cleaning up not allocated orders. On demand or before performing manual archiving.
Replacing the partitioning fluid bottle and/or the liquid waste bottle on the partitioning engine Replacing the partitioning fluid bottle and/ or the liquid waste bottle on the partitioning engine When the partitioning fluid bottle is empty or expired, or when the liquid waste bottle is full, replace the partitioning fluid bottle and/or the liquid waste bottle. CAUTION! Sharp aspiration needle The aspiration needle in the partitioning engine is sharp.
Maintenance 461 If the partitioning fluid bottle is empty, always replace both the liquid waste bottle and the empty partitioning fluid bottle. If the partitioning fluid is expired, consider the fill levels of the partitioning fluid bottle and the liquid waste bottle for the replacement of the liquid waste bottle. If the liquid waste bottle is full, replace the liquid waste bottle. i Follow laboratory best practices and change your lab gloves following any handling of waste materials.
Replacing the partitioning fluid bottle and/or the liquid waste bottle on the partitioning engine 2 Lift the aspiration and dispensing arm completely until the aspiration needle is clear of the bottle opening and the aspiration and dispensing arm locks into place in the upper position. 3 Unload the liquid waste bottle. Close the liquid waste bottle with a screw cap. Dispose of the full liquid waste bottle according to local regulations. I Do not empty and reuse the liquid waste bottle.
Maintenance 463 8 Close the fluids door until it engages with an audible click. 9 Prime the partitioning engine on demand as described in Priming the partitioning engine (232): • In the global information area of the partitioning engine software, choose > Prime Instrument. • Wait until priming is complete. r To replace the partitioning fluid bottle 1 To open the fluids door on the right side of the partitioning engine, do the following: • Push the front edge inside until the fluids door disengages.
Replacing the partitioning fluid bottle and/or the liquid waste bottle on the partitioning engine 7 Lower the aspiration and dispensing arm completely. 8 Close the fluids door until it engages with an audible click. 9 Prime the partitioning engine on demand as described in Priming the partitioning engine (232): • In the global information area of the partitioning engine software, choose > Prime Instrument. • Wait until priming is complete.
Maintenance 465 4 Unscrew the screw cap of a liquid waste bottle. Keep the screw cap for later use. 5 Load a liquid waste bottle in the fluids door with the label facing to the front. 6 Lower the aspiration and dispensing arm completely. 7 Close the fluids door until it engages with an audible click.
Data maintenance on the analyzer Data maintenance on the analyzer Data maintenance comprises the cleanup of not allocated orders, archiving, and backup. Archiving and backup are maintenance actions that can be scheduled to be performed automatically at a predefined time. If necessary, e.g., if automatic execution is not configured or fails, perform archiving and backup manually.
Maintenance 467 f The Archiving panel is displayed. 2 Optionally, to change how far back not allocated orders are deleted, do the following: • In the Archive data older than (in days) field, change the value. • Choose the Save button. I The time period also applies to automatic and manual archiving. 3 Choose the Clean up not allocated orders button. f The Clean up not allocated orders dialog box is displayed. 4 Choose the Confirm button.
Data maintenance on the analyzer CAUTION! Unprotected archive files Insecure transfer or storage of archive files may allow for data manipulation, which may cause incorrect, invalid, or delayed results, and/or unauthorized access to personal information. r Ensure that archive files are transferred securely, are stored in a secure location, and are protected from any unauthorized access and disaster.
Maintenance 469 3 Optionally, to change how far back the data is cleaned up and archived, do the following: • In the Archive data older than (in days) field, change the value. • Choose the Save button. I The value also applies to automatic archiving. 4 Optionally, to clean up not allocated orders before archiving, choose the Cleanup not allocated orders button. 5 Choose the Manual archiving button. f The Manual archiving dialog box is displayed. 6 Optionally, to change the export path, choose the button.
Data maintenance on the analyzer CAUTION! Unprotected backup files Insecure transfer or storage of backup files may allow for data manipulation, which may cause incorrect, invalid, or delayed results, and/or unauthorized access to personal information. r Ensure that backup files are transferred securely, are stored in a secure location, and are protected from any unauthorized access and disaster.
Maintenance 471 4 Optionally, to change the export path, choose the button. I The folder configured for automatic backups is automatically pre-entered in the Export path field. f The Select folder dialog box is displayed. 5 In the folder browser, navigate to a folder. 6 Choose the Confirm button. 7 In the Manual backup dialog box, choose the Backup button. f The backup is saved as ZIP file in the folder. 17 Maintenance 8 Optionally, disconnect the external storage device.
Cleaning and decontamination Cleaning and decontamination Do not perform any cleaning or decontamination that is not described in this publication. For cleaning and/or decontamination, always consider the following: • Use only the allowed cleaning and/or decontamination solutions. Refer to the individual cleaning and decontamination procedures for the specified cleaning and decontamination solutions. • • • • • • • • • Do not use technical or denatured ethanol or isopropanol.
Maintenance • • 473 70% isopropanol p.a. DNA AWAY™ Surface Decontaminant (Molecular BioProducts, Inc.) i Refer to the individual cleaning and decontamination procedures for the cleaning and decontamination solutions specified for them. Cleaning the partitioning engine Regularly clean the outside and the nanowell plate drawer of the partitioning engine.
Cleaning and decontamination r To clean the outside of the partitioning engine 1 Moisten a lint-free cloth with 70% ethanol p.a. and clean the housing of the partitioning engine. 2 Moisten a lint-free cloth with 70% ethanol p.a. and clean the touch-screen monitor of the partitioning engine. Cleaning the nanowell plate drawer of the partitioning engine Regularly clean the nanowell plate drawer of the partitioning engine. WARNING! Risk of fire and burns Alcohol is a flammable substance.
Maintenance 475 CAUTION! Moving drawer The nanowell plate drawer of the partitioning engine opens and closes during operation. An opening drawer may strike you. A closing drawer may pinch your fingers. r Keep away from the nanowell plate drawer during operation. r Do not try to close the nanowell plate drawer manually by pushing against it. r Leave sufficient free space around the partitioning engine to allow for unobstructed movement of the nanowell plate drawer.
Cleaning and decontamination 6 Moisten a lint-free cloth with deionized water and wipe the nanowell plate drawer. I Do not use excessive force while wiping. 7 Wait until the nanowell plate drawer is dry. 8 To close the nanowell plate drawer, on the Plate Setup panel in the partitioning engine software, choose the Close button. Cleaning the analyzer Regularly clean the outside and the nanowell plate stack drawer of the analyzer.
Maintenance j 477 m Analyzer is unloaded m Analyzer is shut down u Shutting down the analyzer (440) r To clean the outside of the analyzer 1 Moisten a lint-free cloth with 70% ethanol p.a. and clean the housing of the analyzer. 2 Moisten a lint-free cloth with 70% ethanol p.a. and clean the touch-screen monitor of the analyzer. Cleaning the nanowell plate stack drawer of the analyzer Regularly clean the nanowell plate stack drawer of the analyzer.
Cleaning and decontamination c Half-yearly d m Powder-free lab gloves m Eye protection m Personal protective equipment m Lint-free cloths m DNA AWAY™ Surface Decontaminant (Molecular BioProducts, Inc.) m Deionized or distilled water r To clean the nanowell plate stack drawer of the analyzer 1 To open the nanowell plate stack drawer, in the global information area of the analyzer software, choose the button. f The nanowell plate stack drawer opens.
Maintenance Decontaminating the nanowell plate drawer of the partitioning engine 479 If the nanowell plate drawer of the partitioning engine may be contaminated, e.g., in case of accidental contact with sample material, decontaminate it by performing the cleaning procedure for the nanowell plate drawer.
Cleaning and decontamination CAUTION! Sharp aspiration needle The aspiration needle in the partitioning engine is sharp. Contact with the aspiration needle may result in personal injury. r Carefully follow the instructions in this publication for replacing the bottles on the partitioning engine and for decontaminating the aspiration needle. r When replacing the bottles on the partitioning engine or when decontaminating the aspiration needle, pay extra attention to the aspiration needle.
Maintenance 481 5 Wipe the aspiration needle with the moistened cloth. 6 Wait until the isopropanol has evaporated and the aspiration needle is dry. 7 Unscrew the screw cap of the new partitioning fluid bottle. Keep the screw cap for later use. 8 Place the new partitioning fluid bottle in the fluids door with the label facing to the front. 9 Lower the aspiration and dispensing arm completely. 10 Close the fluids door until it engages with an audible click.
About preventive maintenance About preventive maintenance On the Preventive maintenance panel, you view the preventive maintenance settings. You need administrator user role to view the preventive maintenance settings. i Preventive maintenance settings Preventive maintenance is performed by your Roche Service representative.
Maintenance 483 When preventive maintenance is completed, the counter is reset, and the next due date is recalculated and displayed on the Preventive maintenance panel. If the preventive maintenance is not performed before the due date, the preventive maintenance becomes overdue. Warning Message code 286.000.00014 Message title Preventive maintenance Category Software Severity Warning Message detail Preventive maintenance is overdue. Diagnostic run cannot be started.
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Troubleshooting 18 Flags ................................................................................................................. 487 19 Troubleshooting the partitioning engine............................................ 497 20 Troubleshooting the analyzer ................................................................. 507 21 Troubleshooting in the development software................................. 529 22 Troubleshooting in the web application .............................................
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Table of contents 487 Flags 18 In this chapter 489 Displaying the flag callouts................................................ 494 18 Flags List of flags ............................................................................... Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Flags 489 List of flags Flags are assigned to samples and controls and inform you about issues or user actions that have occurred during the workflow. Flags are listed in the web application, the analyzer software, and/or the development software, depending on the workflow. For additional information about a flag, you can display a flag callout in the software components of the system.
List of flags Flag code IP003 Severity Informational Description Actions No nanowell columns detected within the Restart the analyzer. If the flag occurs repeatedly, contact your Roche Service expected overlap area during stitching representative. u Restarting the analyzer (451) IP004 Critical Data integrity check failed Restart the analyzer. If the flag occurs repeatedly, contact your Roche Service representative.
Flags Flag code Severity Description 491 Actions RA017 Critical Reference target concentration is above upper limit of validity. RA018 Critical Reference target concentration is below upper limit of validity. RA019 Critical Wild type control concentration is too high. RA020 Critical Wild type control concentration is too low. RA021 Critical Percentage of variant control is too high. RA022 Critical Percentage of variant control is too low.
List of flags 18 Flags Flag code Severity Description Actions RD001 Critical Verification of input data failed. If the flag occurs repeatedly, contact your Roche Service representative. RD002 Critical Merging verification failed. If the flag occurs repeatedly, contact your Roche Service representative. RD004 Informational An unexpected cluster is present. RD005 Critical Lane has no valid nanowells. RD006 Critical Lane has no negative nanowells.
Flags Flag code Severity Description 493 Actions S004 Critical System: Run aborted by operator before images were captured. S005 Informational System: Run failed. S006 Critical System: Run failed before images were captured. S007 Informational System: Preventive maintenance is overdue.
Displaying the flag callouts Displaying the flag callouts In the web application, the analyzer software, and the development software, you can display flag callouts from the flags. In the web application and the development software, flags are displayed together with results. In the analyzer software, partitioning flags are displayed together with the sample setups of diagnostic runs. A flag callout always contains the flag severity and the flag description.
Flags 495 2 Mouse over the flag indicator. f The flag callout is displayed. r To display the flag callouts in the development software 1 In the development software, in the Navigation area, choose an analysis from the Analysis menu. f The analysis tab is displayed in the work area. 2 Choose the Results button. 3 Mouse over an entry in the Flags column. 18 Flags f The flag callout is displayed. Roche Diagnostics Digital LightCycler® System · Software version 1.
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Table of contents 497 Troubleshooting the partitioning engine List of messages on the partitioning engine ............... 499 Displaying the event viewer in the partitioning engine software ...................................................................... 503 Copying the logs from the partitioning engine to an external storage device ................................................. 504 Initializing the partitioning engine...................................
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Troubleshooting the partitioning engine 499 List of messages on the partitioning engine Messages alert you to events that prevent normal operation of the partitioning engine. In the partitioning engine software, messages are displayed in the global information area. u About the global information area of the partitioning engine software (83) Message Bottle compartment is empty Actions Load a partitioning fluid bottle and a liquid waste bottle.
List of messages on the partitioning engine Message Oil bottle signature is wrong Actions Replace the partitioning fluid bottle. u Replacing the partitioning fluid bottle and/or the liquid waste bottle on the partitioning engine (460) Oil expiry date is elapsed Replace the partitioning fluid bottle. u Replacing the partitioning fluid bottle and/or the liquid waste bottle on the partitioning engine (460) Oil fill state is not available • Shut down the partitioning engine.
Troubleshooting the partitioning engine Message Please exchange supply bottle 501 Actions • Unload the bottle from the position of the partitioning fluid bottle. • If the loaded bottle was a liquid waste bottle, decontaminate the aspiration needle. • Load a partitioning fluid bottle.
List of messages on the partitioning engine Message Waste bottle is missing Actions Load a liquid waste bottle. u Replacing the partitioning fluid bottle and/or the liquid waste bottle on the partitioning engine (460) Waste bottle is not available Load a liquid waste bottle. u Replacing the partitioning fluid bottle and/or the liquid waste bottle on the partitioning engine (460) Waste fill state is not available • Shut down the partitioning engine. • Wait for 5 seconds.
Troubleshooting the partitioning engine 503 Displaying the event viewer in the partitioning engine software The partitioning engine logs events in the event viewer with event severity and event code. r To display the event viewer in the partitioning engine software > Event 2 To close the event viewer, choose the Close button. Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
Copying the logs from the partitioning engine to an external storage device Copying the logs from the partitioning engine to an external storage device The logs from the partitioning engine contain relevant data required by Roche for troubleshooting purposes. If you encounter a problem with the partitioning engine and contact your Roche Service representative, you may be asked to provide the logs. Roche reviews the logs upon your request only. d m External storage device, e.g.
Troubleshooting the partitioning engine 505 Initializing the partitioning engine When an error occurred on the partitioning engine, you must initialize it. You can only continue to work with the partitioning engine after initialization. During startup of the partitioning engine, initialization is done automatically. j m Error on the partitioning engine r To initialize the partitioning engine 1 In the global information area, choose the button.
Restarting an unresponsive partitioning engine Restarting an unresponsive partitioning engine If the partitioning engine and/or the partitioning engine software are unresponsive, you must restart the partitioning engine. Always confirm that the partitioning engine and/or the partitioning engine are unresponsive before you restart the partitioning engine: • Ensure the partitioning engine is not busy and therefore not responding.
Table of contents 507 Troubleshooting the analyzer Messages in the analyzer software................................. 509 About messages in the analyzer software......... 509 Displaying and confirming messages in the analyzer software ........................................................ 511 Problem reports on the analyzer ...................................... 512 About problem reports.............................................. 512 Exporting a basic problem report .......................
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Troubleshooting the analyzer 509 Messages in the analyzer software Messages inform and alert you. Depending on the severity of the message and your system configuration, an additional callout and an acoustic signal may be displayed to alert you to messages.
Messages in the analyzer software – Triggered by errors. Working with the analyzer is not possible anymore. Immediate action is required to resolve the error. – Error messages always need confirmation. • Warning messages: – Triggered by warnings. Working with the analyzer is possible for the moment. No immediate action is required, but it may be necessary to resolve the warning soon. – Some warning messages need confirmation. • Information messages: – Triggered by normal operation.
Troubleshooting the analyzer 511 Displaying and confirming messages in the analyzer software You must confirm some messages. You can either confirm each message separately or all displayed messages at once. c When there are messages that need confirmation r To display and confirm messages in the analyzer software 1 In the global information area of the analyzer software, choose the message indicator. f The messages panel is displayed.
Problem reports on the analyzer Problem reports on the analyzer On the Problem report panel, you export basic problem reports, create custom problem reports, and/or create logs reports. You can access the Problem report panel with any user role.
Troubleshooting the analyzer 513 Basic and custom problem reports always belong to a specific run and contain system and run information from the time the run finished. Logs reports are problem reports that cover a specified time period and contain system and run information from that period.
Problem reports on the analyzer By default, the files of basic and custom problem reports are named: PR_SN_RunName_TypeOfReport.7z. You cannot change the name of a basic problem report. By default, an advanced, extended, or complete problem report has the same name (except the problem report type) as the basic problem report it is created from. You can change the name when creating the custom problem report. The files of logs reports are named: PR_SN_Logs_YYYYMMDD_YYYYMMDD.
Troubleshooting the analyzer 515 4 From the table, choose a problem report. 5 Choose the Export button. f The Select folder dialog box is displayed. 6 In the folder browser, navigate to a folder. 7 Choose the Confirm button. f A progress indicator is displayed. 8 Wait until the export of the problem report is finished. I If you cancel the export, all files that are already exported to the folder are deleted again. f The basic problem report is exported as a 7z file to the folder.
Problem reports on the analyzer 4 From the table, choose a problem report. 5 Choose the Create custom report button. f The Create custom report combo box is displayed. 6 Optionally, change the name for the problem report. I The name must not contain the following characters: ?*<>/\:"|’ 7 Choose the type of the custom problem report: • Advanced • Extended • Complete f The estimated file size of the problem report is displayed in the combo box. 8 To change the export path, choose the button.
Troubleshooting the analyzer j 517 m Enough memory in the network share or on the external storage device r To create a logs report 1 Optionally, to save to an external storage device, connect the external storage device to the analyzer. 2 In the analyzer software, choose Administration > Problem report. f The Problem report panel is displayed. 3 Choose the Create logs report button. f The Create logs report combo box is displayed. 4 Optionally, change the name for the logs report.
Initializing a paused analyzer Initializing a paused analyzer If the analyzer is paused, you must initialize the analyzer before you can continue working. i j Whenever an alarm callout or error callout is displayed, take a screenshot of the callout. m Initialize button displayed in the global information area m Analyzer in Analyzer paused status r To initialize a paused analyzer 1 In the global information area, choose the Initialize button. f The analyzer is initialized.
Troubleshooting the analyzer 519 Restarting an unresponsive analyzer If the analyzer and/or the analyzer software are unresponsive, you must restart the analyzer. Always confirm that the analyzer and/or the analyzer software are unresponsive before you restart the analyzer: • Ensure the analyzer is not busy and therefore not responding. • • If a message is displayed, follow the message instructions. Try to shut down the analyzer following the normal shutdown procedure.
Nanowell plate loading errors on the analyzer Nanowell plate loading errors on the analyzer On the Plates panel in the analyzer software, the statuses of the loaded nanowell plates indicate if there is a nanowell plate loading error. Before you can start the run on the analyzer, you must resolve all nanowell plate loading errors so that all loaded nanowell plates are in Valid status.
Troubleshooting the analyzer Status on Plates panel Invalid barcode Cause 521 Actions The nanowell plate ID does not meet the barcode criteria defined on the system. Unload the nanowell plate. For a development run, either start the run without the affected nanowell plate or replace it with a freshly pipetted and partitioned nanowell plate. For a diagnostic run, invalidate the nanowell plate in the web application. Then, start the run without the invalidated nanowell plate.
Nanowell plate loading errors on the analyzer CAUTION! Incorrect manual entering of nanowell plate ID Incorrect manual entering of a nanowell plate ID may cause incorrect results due to incorrect assignment between order and result. r If you scan or enter a nanowell plate ID manually, ensure that you scan or enter the nanowell plate ID correctly.
Troubleshooting the analyzer j 523 m Nanowell plate status: Barcode scan failed r To resolve a nanowell plate ID reading error with nanowell plate ID available (without opening of the nanowell plate stack drawer) 1 Ensure that there are nanowell plate ID reading errors: • To open the nanowell plate stack drawer, choose the Open drawer button. • Check the placement of the nanowell plates in the nanowell plate stack drawer. • To close the nanowell plate stack drawer, choose the Close drawer button.
Nanowell plate loading errors on the analyzer 6 CAUTION! Risk of incorrect, invalid, or delayed results. Ensure that you enter the correct nanowell plate ID. On the numeric keyboard, enter the nanowell plate ID. 7 Choose the Enter button. 8 On the Plates panel, choose the Accept changes button. f The nanowell plate status is updated. 20 Troubleshooting the analyzer f The nanowell plate ID reading error is resolved.
Troubleshooting the analyzer 525 2 Optionally, if there is more than 1 nanowell plate ID reading error, do the following: • To open the nanowell plate stack drawer, choose the Open drawer button. • Unload the affected nanowell plates except 1. • Discard the unloaded nanowell plates according to local regulations. For a diagnostic run, invalidate the unloaded nanowell plates in the sample setup in the web application. • To close the nanowell plate stack drawer, choose the Close drawer button.
Nanowell plate loading errors on the analyzer 9 CAUTION! Risk of incorrect, invalid, or delayed results. Ensure that you enter the correct nanowell plate ID. Scan or enter the nanowell plate ID of the affected nanowell plate. 10 On the numeric keyboard, choose the Enter button. 11 Reload the nanowell plate stack in the nanowell plate stack drawer. 12 To close the nanowell plate stack drawer, choose the Close drawer button. f The nanowell plate status is updated.
Troubleshooting the analyzer 527 Resolving an alarm of the analyzer If an alarm occurrs on the analyzer, you cannot work with the analyzer until the issue is resolved. i j Whenever an alarm callout or error callout is displayed, take a screenshot of the callout. m Alarm callout displayed with Category = Analyzer, Severity = Alarm, Ignore button, and Initialize button m Analyzer in Error status r To resolve an alarm of the analyzer 1 To take a screenshot of the alarm callout, choose the button.
Resolving an alarm of the analyzer software Resolving an alarm of the analyzer software If an alarm occurs in the analyzer software, you cannot work with the analyzer until the issue is resolved. i j Whenever an alarm callout or error callout is displayed, take a screenshot of the callout. m Alarm callout displayed with Category = Software, Severity = Alarm, and Shut down button. r To resolve an alarm of the analyzer software 1 To take a screenshot of the alarm callout, choose the button.
Table of contents 529 Troubleshooting in the development software 21 In this chapter 531 21 Troubleshooting in the development software Locating the log files in the development software.. Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Troubleshooting in the development software 531 Locating the log files in the development software The log files contain relevant data required by Roche for troubleshooting purposes. If you encounter a problem with the development software and contact your Roche Service representative, you may be asked to provide the log files. Roche reviews the log files upon your request only. j m Optionally, external storage device, e.g.
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Table of contents 533 Troubleshooting in the web application 22 In this chapter 535 Sending results again in the web application............. 538 22 Troubleshooting in the web application Invalidating nanowell plate lanes and/or nanowell plates in the web application ............................................ Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Troubleshooting in the web application 535 Invalidating nanowell plate lanes and/or nanowell plates in the web application If nanowell plate lanes and/or nanowell plates of a diagnostic sample setup are compromised, invalidate the nanowell plate lanes and/or the nanowell plates in the web application before you start the diagnostic run.
Invalidating nanowell plate lanes and/or nanowell plates in the web application CAUTION! Missing measurements or invalidated controls Invalidating a nanowell plate lane that is required for result calculation or contains a control may cause invalid or delayed results. r Take extra care to avoid wrongly invalidating a nanowell plate lane that is required for result calculation or that contains a control.
Troubleshooting in the web application 537 r To invalidate a nanowell plate in the web application 1 In the web application, in the Sample setups column on the dashboard, choose a batch tile. f The Sample setup screen is displayed. 2 To invalidate a nanowell plate, choose the column header twice. f The Plate: combo box is displayed. 3 Select the Invalid plate check box. 4 Choose the Confirm button. f On the Sample setup screen, the nanowell plate is grayed out. 5 Choose the Confirm button.
Sending results again in the web application Sending results again in the web application In the web application, you can send again results of completed batches that are already in Sent status. You cannot send again results of completed batches that are still in Send queued status or that were generated with an analysis package in In validation status.
Troubleshooting in the web application 539 22 Troubleshooting in the web application 6 Enter your password and choose the Send again button. f The result status changes to Send queued or Sent, respectively, marked with an icon or an icon in the Status column (depending on LIS connection status). f Your user name replaces the previous entry in the Send by column. Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Configuration 23 User management in the analyzer software ..................................... 543 24 Administration of the analyzer software............................................. 555 25 Settings in the development software................................................. 611 Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Table of contents 543 User management in the analyzer software 23 In this chapter 545 About user management ......................................... 545 List of user settings.................................................... 547 Managing users........................................................... 549 23 User management in the analyzer software User management .................................................................
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User management in the analyzer software 545 User management On the User management panel, you manage user accounts. The User management panel consists of the following elements: • Table of users • Detail panel displaying the user settings A A Table B To access the User management panel, you need administrator user role. B Detail panel In this section About user management (545) Managing users (549) About user management User management is performed in the analyzer software.
User management User roles Diagnostic approver Diagnostic operator 23 User management in the analyzer software Development operator Permitted actions in the analyzer software • Change own password • Manage problem reports • Manage screenshots Permitted actions in the web application • View orders, sample setups, run information, and results • Send results • Export raw data files • Perform diagnostic runs • Add, edit, and import orders • Change own password • • Manage problem
User management in the analyzer software i About passwords 547 To ensure full system access in case of a lost administrator password, create a second user with administrator user role directly after installation of the system. Passwords must comply with the global password policy configured in the analyzer software in Administration > Password settings. u Password settings (599) List of user settings User management requires the configuration of the user settings.
User management • • Case-sensitive 4 to 20 characters Additionally, the password must conform to the global password policy configured in Administration > Password settings. u Password settings (599) Administrator Diagnostic operator Check box to assign diagnostic operator user role. Diagnostic approver Check box to assign diagnostic approver user role. Development operator 23 User management in the analyzer software Check box to assign administrator user role.
User management in the analyzer software 549 You cannot retire the default administrator account "Admin FN". Default value = not retired Password never expires Check box to prevent the mandatory change of a user’s password after the expiry period that is configured in the global password policy (Administration > Password settings). You can only apply this setting to each user individually. You cannot apply this option globally to all users.
User management CAUTION! Weak passwords Weak passwords may allow unauthorized access to the system, data manipulation or loss, or unauthorized access to personal information, which may cause incorrect, invalid, or delayed results. r Use strong passwords. r Do not share passwords. r Do not write down passwords. r Do not share user accounts. You cannot delete users. To deny system access temporarily, lock a user. To deny system access permanently, retire a user.
User management in the analyzer software 551 3 In the Enter user details dialog box, enter the required information: • Full name • User name • Password • Diagnostic operator and/or Development operator I Ensure that you enter the correct user name. You cannot change it later. You must assign an operator user role in this step. For administrator user role or diagnostic approver user role, you must change the user role later in the detail panel.
User management 5 To assign or to remove a user role, select or clear the corresponding check box: • Administrator • Diagnostic operator • Diagnostic approver • Development operator 6 To allow or deny system access, do one of the following: • To prevent a user temporarily from logging on, select the Locked: check box. • To allow a user to log on again, clear the Locked: check box. • To prevent a user permanently from logging on, select the Retired: check box.
User management in the analyzer software 553 5 In the Change password dialog box, enter the new password twice. Choose the Confirm button. 6 Choose the Save button. r To lock or unlock a user 1 Choose Administration > User management. f The User management panel is displayed. 2 Optionally, sort, search, or filter the table. 4 In the detail panel, do one of the following: • To lock a user, select the Locked: check box. • To unlock a user, clear the Locked: check box. 5 Choose the Save button.
User management 3 From the table, choose a user. 4 In the detail panel, select the Retired: check box. I It is possible to unretire a user. However, to prevent a user temporarily from logging on, use the Locked: check box instead. 5 Choose the Save button. I By default, the table on the User management panel lists the active users only. To display the retired users, from the filter drop-down list, choose the All option.
Table of contents 555 Administration of the analyzer software Archiving ................................................................................... 557 About archiving ........................................................... 557 Scheduling automatic archiving............................ 560 Audio settings ......................................................................... 563 Backup .......................................................................................
Table of contents Configuring automatic export of raw data files.............................................................. 603 Diagnostic results settings ...................................... 604 About the diagnostic results settings ...... 605 Configuring diagnostic results settings... 605 User Assistance and language settings ........................ 607 About language packages and User Assistance packages .................................................
Administration of the analyzer software 557 Archiving On the Archiving panel, you schedule automatic archiving, perform manual archiving, and clean up not allocated orders. To access the Archiving panel, you need administrator user role. In this section About archiving (557) Scheduling automatic archiving (560) Archiving allows you to store auditable data and to free up disk space on the analyzer. Archive regularly to maintain system performance.
Archiving • About automatic archiving Perform a function that accesses data that is affected by archiving, e.g., create a result report for results that are applicable for archiving. Automatic archiving allows you to free up disk space on the analyzer regularly without manual intervention. Scheduling automatic archiving helps to prevent unscheduled downtime of the system because of insufficient disk space.
Administration of the analyzer software 559 Archiving is displayed as overdue on the Archiving panel if the next due date is in the past because one of the following applies: • The next due date that is calculated when saving the archive settings is already in the past. • A scheduled automatic archiving failed. For example, automatic archiving fails if the analyzer is shut down at the scheduled execution time, or if the export folder is unavailable or has not enough memory.
Archiving For cleaning up not allocated orders, the Archive data older than (in days) setting of automatic archiving also applies. For example, if you automatically archive data older than 30 days, only not allocated orders that are older than 30 days are deleted. Clean up not allocated orders regularly. Clean up not allocated orders before you perform manual archiving.
Administration of the analyzer software 561 CAUTION! Unprotected archive files Insecure transfer or storage of archive files may allow for data manipulation, which may cause incorrect, invalid, or delayed results, and/or unauthorized access to personal information. r Ensure that archive files are transferred securely, are stored in a secure location, and are protected from any unauthorized access and disaster.
Archiving 7 To configure the export path to the archive folder, do the following: button. • Choose the • In the folder browser, navigate to a folder. • Choose the Confirm button. 8 In the Archiving panel, choose the Save button. I If you configured automatic archiving to an external storage device, ensure that the external storage device is connected at the scheduled execution time. Automatic archiving fails if the configured export path is unavailable. f Automatic archiving is performed as scheduled.
Administration of the analyzer software 563 Audio settings On the Audio settings panel, you configure if the analyzer plays an acoustic signal at the end of a run and/ or when a message occurs. To access the Audio settings panel, you need administrator user role. By default, both acoustic signals are enabled. u Messages in the analyzer software (509) j m Administrator user role 1 In the analyzer software, choose Administration > Audio settings. f The Audio settings panel is displayed.
Backup Backup On the Backup panel, you schedule automatic backups and perform manual backups. To access the Backup panel, you need administrator user role. In this section About backups (564) Scheduling automatic backups (566) 24 Administration of the analyzer software About backups A backup saves the current system status and allows you to restore your system. Back up your system regularly to minimize data loss. Contact your Roche Service representative if a system restore becomes necessary.
Administration of the analyzer software 565 As a backup can take a long time, schedule automatic backups for a time when the system is not needed, e.g., during the night. The following table lists the Backup settings: Backup setting Enable automatic backup Possible values • Enabled • Disabled Default value Disabled Repeat every (in days) 1-30 days 7 days Start time: Anytime 2:00 a.m.
Backup About manual backups A manual backup allows you to save the system status on demand. If the automatic backup fails, perform a manual backup. u Performing a manual backup (469) About backup content The following data is included in the backup file: • Full database (e.g., orders and results) • • • • Analysis packages Analyzer-specific configurations Settings on the Administration panel (e.g., users and connection settings) Analyzer metadata (e.g.
Administration of the analyzer software 567 CAUTION! Unprotected backup files Insecure transfer or storage of backup files may allow for data manipulation, which may cause incorrect, invalid, or delayed results, and/or unauthorized access to personal information. r Ensure that backup files are transferred securely, are stored in a secure location, and are protected from any unauthorized access and disaster.
Backup I If you configured automatic backups to an external storage device, ensure that the external storage device is connected at the scheduled execution time. Automatic backups fail if the configured export path is unavailable. f Automatic backups are performed as scheduled. 24 Administration of the analyzer software f The Next backup due at: field lists the next planned backup and the status of the backup. Roche Diagnostics Digital LightCycler® System · Software version 1.
Administration of the analyzer software 569 Connection settings On the Connection settings panel, you connect the system to an LIS and/or AVENIO Connect, enable access via EDI, and/or enter the external IP address for NAT. To access the Connection settings panel, you need administrator user role. About connection indicators When you connect the system to an LIS and/or to AVENIO Connect, separate connection indicators are added to the global information area of the analyzer software.
Connection settings • ASTM protocol Default value = HL7 (MLLP2) IP address Field to enter the IP address of the LIS. For the IP address, the following rule applies: • Must conform to the format of IPv4 addresses. Default value = 127.0.0.1 Port Field to enter the port of the LIS. For the port, the following rule applies: • Must be an integer number.
Administration of the analyzer software Export path for raw data 571 Field to enter the export path for the raw data files of AVENIO Connect runs. To display the folder browser, choose the button. EDI group box Server name Field to enter the name of the EDI server. For the server name, the following rules apply: • 1 to 25 characters • Forbidden characters: ?*<>\/:"| Default value = "EDI Server" Port Field for the preconfigured port for the EDI server, i.e., 50052.
Connection settings • Must conform to the format of IPv4 addresses. Configuring connection settings On the Connection settings panel, you configure the connections to an LIS and/or AVENIO Connect, enable access via EDI, and/or enter the external IP address for NAT. For network-specific information, contact your local IT administrator. 24 Administration of the analyzer software i If you connect the system to both an LIS and to AVENIO Connect, the IP addresses and ports must be different.
Administration of the analyzer software 573 r To connect the system to AVENIO Connect 1 In the analyzer software, choose Administration > Connection settings. f The Connection settings panel is displayed. 2 To connect the system to AVENIO Connect, select the AVENIO Connect check box. 3 From the Communication protocol drop-down list, choose the protocol. I For network-specific information, contact your local IT administrator. 4 In the IP address field, and in the Port field, enter the required information.
Connection settings 2 To enter the external IP address, select the External IP address or NAT address check box. 3 In the field, enter the IP address as configured on the router. 4 Choose the Save button. 5 Restart the system. r To disconnect the system 1 In the analyzer software, choose Administration > Connection settings. f The Connection settings panel is displayed. 2 To disconnect the system from an LIS, clear the LIS check box.
Administration of the analyzer software 575 Laboratory information settings in the analyzer software On the Laboratory information panel, you configure the name, address, and logo of your laboratory. If configured, the laboratory information is included in all reports generated in the analyzer software and the web application.
Laboratory information settings in the analyzer software 3 In the Laboratory name field, enter the name of your laboratory. 4 To add a logo, choose the button. f The Select company logo dialog box is displayed. 5 To choose the logo file, do the following: • From the File type drop-down list, choose the file type. • In the folder browser, navigate to the folder of the logo file. • In the file browser, choose the logo file. • Choose the Confirm button.
Administration of the analyzer software 577 LIS mapping table On the LIS mapping table panel, you edit LIS test names. The LIS mapping table lists each test of an analysis package separately. The LIS mapping table does not apply to development workflows. To access the LIS mapping table panel, you need administrator user role.
LIS mapping table I If enabling an analysis package results in conflicting LIS test names, you must immediately change the LIS test names from the Manage analysis packages panel. f The LIS mapping table panel is displayed. f The table lists each test of an analysis package and the mapped LIS test name. 2 Optionally, sort, search, or filter the table. 3 To display the tests with conflicting LIS test names only, from the drop-down list, choose the Conflicts option. 4 From the table, choose a test.
Administration of the analyzer software 579 Manage analysis packages On the Manage analysis packages panel, you manage the analysis packages for diagnostic runs. To access the Manage analysis packages panel, you need administrator user role. In this section About analysis packages (579) Managing analysis packages (586) Analysis packages provide all parameters necessary to plan and to perform diagnostic runs and to generate diagnostic results. You use analysis packages in diagnostic workflows only.
Manage analysis packages – Test names – Targets and dyes – Names and dilution factors of master mix reagents – Limits of detection, quantification, and/or validity – Result names for final qualitative results – Display of final quantitative results – Control types, names, and valid ranges – Analysis settings – Clustering settings 24 Administration of the analyzer software About issuers of analysis packages About analysis package files Analysis packages can have the following issuers: • For IVD wor
Administration of the analyzer software 581 Before you can enable an analysis package in Disabled status, you must revalidate it first to change its status to In validation.
Manage analysis packages – The versions of the analysis package are differentiated by the version and version GUID. – The analysis package is imported. • All 4 identifiers match: – The analysis package already exists. – The import is aborted. – A corresponding warning message is displayed.
Administration of the analyzer software 583 The system behavior depends on the outcome of the checks. If all old versions are in In validation status or Disabled status, the new version is enabled directly. • • If an old version in In validation status is assigned to orders in the web application, these orders remain unchanged. They are not updated to the new, enabled version of the analysis package. Analysis packages in Disabled status cannot be assigned to orders.
Manage analysis packages Enabling new version of analysis package in the analyzer software Status of old version and assignment to orders are checked Check Old version in Enabled status? Consequences for versions of analysis package Consequences for orders No • New version enabled • No change for old version • No change • Old version in In validation status remains assigned to orders No • New version enabled • Old version disabled • No change No • Enabling of new version aborted • No change
Administration of the analyzer software i 585 You cannot delete LIS orders. If you do not want to update the LIS orders, you must perform the diagnostic runs. Orders that are already processed, i.e., results in the web application, are not updated to the new version of the analysis package. However, the status of the analysis package they were processed with is displayed as Disabled on the Results of screen in the web application.
Manage analysis packages Managing analysis packages On the Manage analysis packages panel, you import, enable, disable, revalidate, and export analysis packages, and access the LIS mapping table panel. You cannot delete an analysis package. Once imported, you can only disable it. To map the test names in the enabled analysis packages to the LIS test names, you can access the LIS mapping table panel directly from the Manage analysis packages panel.
Administration of the analyzer software 587 f The analysis package is in In validation status. f You can perform diagnostic runs with an analysis package in In validation status, but the results are complete immediately after the diagnostic run finishes and cannot be released or sent. 7 Optionally, disconnect the external storage device. r To enable a new analysis package 1 In the analyzer software, choose Administration > Manage analysis packages. f The Manage analysis packages panel is displayed.
Manage analysis packages 2 Do the following: • To check for other versions of the analysis package that you want to enable, sort and/or filter the table accordingly. • If no other version of the analysis package exists in the analyzer software, continue with To enable a new analysis package (587).
Administration of the analyzer software 589 6 If required, to confirm the deletion of the sample setups and/or the update of the orders, in the Change package status dialog box, choose the Confirm button. f The analysis package is set to Enabled status and the previously enabled version is set to Disabled status. f In the web application, the sample setups are deleted and the orders are updated, indicated on the Orders screen.
Manage analysis packages 8 Optionally, disconnect the external storage device. r To disable an analysis package 1 In the analyzer software, choose Administration > Manage analysis packages. f The Manage analysis packages panel is displayed. 2 Optionally, sort, search, or filter the table. 3 From the table, choose an analysis package in Enabled status or in In validation status. I You cannot disable an analysis package that is assigned to orders in the web application.
Administration of the analyzer software 591 Network share settings On the Network share settings panel, you configure the paths to network shares, i.e., folders in the network, that you can then access in the folder browsers in the analyzer software. Configuring network shares enables the navigation to import or export folders in folder browsers and facilitates the consistent use of folders, e.g., for archive files or backup files. The Roche-provided firewall must allow access to network shares.
Network share settings Available: • Network share is accessible. • All network paths that include the network share are accessible. Partial access: • Network share is accessible. • At least 1 of the network paths that include the network share is not accessible. No access: • Network share is not accessible. Pending: • Network share is not tested yet. Directly after you access the Network share settings panel, all network shares are in Pending status.
Administration of the analyzer software 593 Use an analyzer-specific account on the network server. UNC path Field to enter the UNC path. The UNC path must conform to the following formats: • \\server-name\path • \\IP-address\path Example: \\server\Analyzer\Backup If you include folders in the UNC path, ensure that these folders exist in the network. Display name Name that is listed in folder browsers for the network share.
Network share settings r To create a network share 1 In the analyzer software, choose Administration > Network share settings. f The Network share settings panel is displayed. 2 Choose the Create button. f An empty row for a new network share setting in Pending status is added to the Network share settings table. 24 Administration of the analyzer software f The fields on the right of the Network share settings table are enabled for that network share setting.
Administration of the analyzer software 595 3 To change the information in a field, do the following: • Choose the field. • Edit the field content. • Press Enter. 4 Choose the Test button. 5 If the test of the network share setting is successful (i.e., the network share is accessible), choose the Save button. I If you save the network share setting without testing it, the test is performed automatically. The result of the test is then displayed in the Accessible column.
Partitioning engine connection Partitioning engine connection On the Partitioning engine connection panel, you assign partitioning engines to the analyzer. To access the Partitioning engine connection panel, you need administrator user role. 24 Administration of the analyzer software About partitioning engine connection An analyzer only processes nanowell plates that were partitioned on an assigned partitioning engine. Therefore, you must at least assign 1 partitioning engine to each analyzer.
Administration of the analyzer software 597 However, a partitioning engine can be assigned to 1 analyzer only at a time. To assign a partitioning engine to a different analyzer, you must deassign it first. In a configuration with multiple partitioning engines and multiple analyzers, ensure that you assign each partitioning engine only to the analyzer it will be used with. Do not assign a partitioning engine to different analyzers.
Partitioning engine connection 2 To assign a partitioning engine to the analyzer, do the following: • In the Available in network group box, choose the partitioning engine. • Choose the button. f The partitioning engine is assigned to the analyzer you are currently working on and listed in the Assigned partitioning engines group box. f The partitioning engine cannot be assigned to other analyzers anymore.
Administration of the analyzer software 599 Password settings On the Password settings panel, you configure the global password policy all passwords must conform to. To access the Password settings panel, you need administrator user role. In this section List of password settings (599) Configuring password settings (601) To define the global password policy, you can set the following requirements for all passwords. f Administration > Password settings By default, all password settings are enabled.
Password settings You can only select the Password never expires check box for each user individually. You cannot select this option globally for all users. Default value = 90 days Password policy check box Check box to enable the following list of password requirements. You can only enable all or disable all password requirements. To disable a single password requirement, enter "0" in the corresponding field (if allowed).
Administration of the analyzer software 601 If a user tries to log on and reaches the maximum number of failed logon attempts, the user is locked automatically. Default value = 3 attempts Configuring password settings On the Password settings panel, you enable and disable password settings, and enter their values. If you change the password settings, the new settings only apply to passwords that are created later.
Result settings Result settings On the Result settings panel, you configure automatic export of raw data files and the diagnostic results settings. To access the Result settings panel, you need administrator user role.
Administration of the analyzer software 603 For a diagnostic run, the export of the raw data file is only possible if the following conditions are met: • All results of the diagnostic run must be complete, i.e., released and sent. The run must be listed on the Completed batches screen. • The export of the raw data file must be enabled in the analysis packages used for the diagnostic run.
Result settings 3 To configure automatic export of raw data files of development runs, in the Development raw data group box, do the following: • Select the Auto-export of research raw data check box. • Next to the Export path field, choose the button. • In the folder browser, navigate to a folder. • Choose the Confirm button.
Administration of the analyzer software 605 About the diagnostic results settings The diagnostic results settings spare you the need to release and send diagnostic results manually in the web application, and ensure that control results are included. By default, the automatic release and sending of diagnostic results are disabled, and the sending of control results is enabled.
Result settings If you enable any of the diagnostic results settings, they only apply to diagnostic results generated later. The system does not catch up on releasing and/or sending results or control results that were generated previously. j m Administrator user role r To configure diagnostic results settings 1 In the analyzer software, choose Administration > Result settings. f The Result settings panel is displayed.
Administration of the analyzer software 607 User Assistance and language settings On the User Assistance and language settings panel, you configure the language of the user interface and the User Assistance for the analyzer software and the web application. To access the User Assistance and language settings panel, you need administrator user role. i In the development software, the language of the user interface and the User Assistance is determined by the Windows language settings.
User Assistance and language settings i When you choose a different language package, or when you import a new version of the currently active language package, you must restart the analyzer for the change to take effect. u Restarting the analyzer (451) About User Assistance packages A User Assistance package contains the translation of the User Assistance publication that is accessible from the analyzer software and the web application.
Administration of the analyzer software 609 2 In the analyzer software, choose Administration > User Assistance and language settings. f The User Assistance and language settings panel is displayed. 3 Choose the Import language package button. f The Import language package dialog box is displayed. 4 In the folder browser, navigate to the folder of the language package. 5 In the file browser, choose the language package. 6 Choose the Import button.
User Assistance and language settings Changing the system language On the User Assistance and language settings panel, you change the language of the analyzer software, the web application, and the User Assistance. If you change the language, the change is applied to all users. It is not possible to set individual users’ languages.
Table of contents 611 Settings in the development software 25 In this chapter 613 25 Settings in the development software Laboratory information settings in the development software.......................................................... Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Settings in the development software 613 Laboratory information settings in the development software You can configure the name, address, and logo of your laboratory to be displayed on reports. If configured, the laboratory information is included in all reports created in the development software.
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Analytical principles 26 Analytical principles ................................................................................... 617 Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Table of contents 617 Analytical principles 26 In this chapter 619 About tests and analyses.................................................... 621 26 Analytical principles About digital PCR................................................................... Roche Diagnostics Digital LightCycler® System · Software version 1.0 · User Assistance · Publication version 1.
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Analytical principles 619 About digital PCR Digital PCR allows for absolute quantification of a target nucleic acid sequence without a standard curve. Digital PCR consists of the following steps: Sample Partitioning The system partitions the sample into a large number of nanowells. This distributes the target molecules and results in nanowells that contain the target and other nanowells that do not contain the target. The partitioned sample is run through an endpoint PCR amplification and detection.
About digital PCR • • Inhibitors are diluted relative to the target nucleic acid sequence, resulting in less inhibition. No dependence on Cq values or PCR efficiency, resulting in less influence of inhibitions. 26 Analytical principles The advantages result in higher precision, lower limit of detection, and better multiplexing performance. As no standards are required, there are lower reagents costs. Roche Diagnostics Digital LightCycler® System · Software version 1.
Analytical principles 621 About tests and analyses The system can apply 3 different analyses to determine results: absolute quantification, CNV, and indel. About absolute quantification tests and analyses An absolute quantification (Abs Quant) test detects the fluorescence of a known target nucleic acid sequence.
About tests and analyses About indel tests and analyses Insertion-deletion (indel) is the occurrence of unknown mutations in a genomic sequence that are caused by the presence (insertion) or absence (deletion) of nucleotides. Such mutations are found by simultaneously testing for a variant target and a reference target. The variant target spans the mutation site, the reference target spans an adjacent but stable site.
Glossary 1D scatter plot copy number variation Scatter plot that shows a one-dimensional point set visualization. Genomic disorder that results in an abnormal number of copies of one or more genes, such as duplication, deletion, translocation, and inversion. 2D scatter plot Scatter plot that shows a two-dimensional point set visualization. 3D scatter plot Scatter plot that shows a three-dimensional point set visualization.
fluids door liquid waste bottle Door that gives access to the fluids on the system. Bottle for the collection of liquid waste that is generated by the instrument. fluorescence Brief visible electromagnetic radiation signal that is emitted as a result of absorption of radiation (photons) by an atom, molecule, or ion. fluorescent dye Fluorescent chemical compound that absorbs and reemits light upon light excitation.
nanowell plate stack drawer thermal cycler Drawer that is used to load and unload nanowell plate stacks onto and from the instrument. Component of an instrument used to repetitively heat and cool a set of reactions to promote DNA denaturation, hybridization, and amplification in PCR. Network Address Translation Internet Protocol translation process that allows a network with private addresses to access information on the internet.
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Index A Abbreviations, 12 Abs Quant - All analysis – displaying, 371 – editing, 372 Absolute quantification – color-coding, 149 – principles, 621 Absolute quantification analyses – about, 359 – adding, 374 – Controls, 360 – controls valid ranges, 361 – development software, 359 – editing, 376 – editing Abs Quant - All, 371 – Internal controls, 361 – limits of detection, 362 – limits of quantification, 362 – Linkage panel, 368 – negative controls, 360 – panels, 363 – performing, 373 – positive controls,
– about import, 581 – settings, 412 – clustering settings, 428 – status, 580 – comments, 416 – Test definition, absolute quantification, 416 – Create analysis package, 412 – Test definition, CNV, 420 – creating, 429 – Test definition, indel, 424 – creating reports, 433 – test list, 417, 421, 424 – creator, 414 – tests, absolute quantification, 416 – deleting, 433 – tests, CNV, 420 – development software, 412 – tests, indel, 424 – dilution factors, 427 – thresholds, 428 – disabling,
– components, 74 – nanowell plate stack drawer, 74 – components inside, 76 – paused, 518 – configuring audio settings, 563 – power button, 75 – configuring automatic raw data export, 603 – power inlet, 76 – configuring AVENIO CONNECT connection, 573 – power switch, 75 – configuring diagnostic results settings, 605 – resolving alarms, 527 – configuring EDI connection, 573 – restarting, 451 – configuring laboratory information, 575 – scheduling automatic archiving, 560 – configuring LIS c
– connecting partitioning engines, 596 – run profiles, 298 – connection indicators, 109 – scheduling automatic archiving, 560 – cooling program, 120 – scheduling automatic backups, 566 – creating audit trails reports, 450 – searching tables, 143 – creating custom problem reports, 515 – sorting tables, 143 – creating logs reports, 516 – status indicator, 109 – deleting screenshots, 448 – tabs, 111 – detection formats, 120 – User Assistance, 108 – disconnecting, 574 – virtual keyboard, 1
– Plates, 112 – Preventive maintenance, 482 – Problem report, 512 – Result settings, 602 – Sample setup, 115 – User Assistance and language settings, 607 – User management, 545 Archiving – about, 557 – automatic, 558 – clean-up not allocated orders, 559 – data, 560 – files, 560 – manual, 467, 559 – performing manual, 468 – scheduling automatic, 561 Aspiration needle – decontaminating, 480 – sharp, 27 Assignment mode – web application, 95 Assignment mode disabled – web application, 96 Audio settings – a
– partitioning engine outside, 474 – specificity, 344 – solutions, 472 – Standard, 343 Clustering Clustering data card – about, 338 – development software, 339 – adjusting, 342 Clustering data table – adjusting Automatic, 348 – development software, 132 – adjusting Automatic - External seed data, 349 Clustering method indicator – adjusting Automatic (individual), 348 – development software, 132 – adjusting Manual, 350 Clustering settings – adjusting thresholds, 350 – development soft
– Sample selection, 377 Components – samples, 377 – analyzer inside, 76 – settings, 377 – system, 61 – Statistics panel, 385 Conditions, operating, 22 – tabs, 377 Configuration, computer, 28 – Target limits, 379 Configuring plate view – targets of interest, 377 – development software, 139 CNV tests Configuring table view – control names, 423 – development software, 140 – control types, 423 Connection indicator – controls, 423 – partitioning engine software, 84 – controls valid ran
Conventions used in this publication – analysis settings, 136 – abbreviations, 12 – analysis tabs, 134 – product names, 9 – assigning sample setups, 321 Copyright, 3 – bar charts, 135 Cross-reactivity, 344 – breadcrumb on analysis package tabs, 138 D – button for analysis settings, 136 – button for clustering settings, 133 Dashboard – changing display of scatter plots, 341 – web application, 91 – closing, 442 Data security, 32, 36 – clustering, 338 Decontamination – Clustering data c
– performing indel analyses, 398 – Copy number mean, 385 – plate view, 138 – Copy number relative confidence, 383 – projects, 294 – Copy number SD, 385 – raw data files, 309 – Dilution factor, 323, 366, 395 – run tabs, 130 – Dyes, 324 – runs, 309 – Final result, 364, 381, 393 – Sample setup table view card, 323 – Flags, 324, 341, 364, 381, 393 – sample setup tabs, 136 – for combinations of target of interest and master mix reagent, 384 – scatter plots, 132 – searching tables, 143 – sort
– Reference, 393 – adjusting clustering, 342 – Relative confidence, 366 – adjusting manual clustering, 350 – Run, 367, 369 – analyses, 358 – Run name, 366, 382, 384, 395, 396 – analysis packages, 412 – Sample ID, 323, 339, 363, 367, 369, 380, 384, 392, 396 – assigning sample setups, 321 – Sample preparation notes, 324 – Sample type, 365, 381, 394 – Target, 363, 370 – Target names, 324 – TOI, 380, 385 – Total copies, 365 – Total valid nanowells, 340, 365, 394 – Variant, 392, 397 – Variant [%],
– working with analysis packages, 429 Digital PCR – working with raw data files, 317 – principles, 619 – working with run profiles, 299 Display options – working with sample groups, 328 – development software, 132 – working with unassigned sample setups, 405 Disposal, 41 Diagnostic results Drawers, moving, 27 – automatic release, 605 Dyes, 165 – automatic sending, 605 – settings development, 311 – controls, 605 Diagnostic results settings E – about, 604, 605 Edges, rough, 26 – confi
File browsers – analyzer software, 124 File extensions – analysis packages, 429 – projects, 294 – raw data files, 312 G Global information area – analyzer software, 106 – partitioning engine software, 83 – web application, 89 – seed data files, 345 H Filter Hand-held barcode readers, 77 – defining custom, 145 Heatmap – deleting custom, 146 – development software, 132 Filtering High resolution nanowell plates, 160 – custom, 145 High sensitivity nanowell plates, 160 – deleting custom, 146
– sample groups, 389 – location partitioning engine, 39 – Sample selection, 389 – safety, 38 – samples, 389 Laboratory information – settings, 389 – analyzer software, 575 – Statistics panel, 397 – configuring development software, 613 – tabs, 389 – configuring, analyzer software, 575 – variant controls, 391 – development software, 613 – variant targets, 390 LAN port – wild type controls, 391 – analyzer, 76 Indel tests – partitioning engine, 73 – control names, 426 Lane settings –
– absolute quantification tests, 418 – ranges, 362, 418 Limits of validity – about, 379, 390, 421, 425 – CNV analyses, 379 – CNV tests, 421 – indel analyses, 390 – indel tests, 425 – ranges, 379, 390, 421, 425 Linkage, 368 Linkage panel – absolute quantification, 368 Liquid waste bottle – about, 160 – replacing, 464 LIS – sending results again, 538 LIS connection – configuring, 572 – indicator web application, 90 – list of settings, 569 – overview, 67 – supported characters, 185 LIS mapping table – abo
Messages Nanowell plates – about, 509 – about, 159 – archiving, 510 – characteristics, 159 – callouts, 510 – color-coding, 148 – codes, 509 – delayed processing, 30 – confirming, analyzer software, 511 – high resolution, 160 – displaying, analyzer software, 511 – high sensitivity, 160 – partitioning engine, 499 – improper handling, 28 – partitioning engine software, 84 – invalidating, 537 – severity, 509 – loading analyzer, 225 – status in analyzer software, 122 – partitioning, 221
Orders – intializing, 505 – about, 169, 250 – LAN port, 73 – cleaning up not allocated, 466 – List of messages, 499 – creating, 252 – logs, 504 – creating manually, 251 – nanowell plate drawer, 72 – deleting, 252 – partitioning, 221 – diagnostic workflows, 169, 250 – power inlet, 73 – editing, 252 – power switch, 72 – editing not allocated, 253 – priming, 232 – importing lists, 251 – radio equipment specifications, 185 – lists, 250 – replacing bottles, 460 – web application, 250
Partitioning fluid Power button – about, 163 – analyzer, 75 – characteristics, 163 Power inlet – expiry date, 163 – analyzer, 76 – onboard stability, 163 – partitioning engine, 73 Partitioning fluid bottle Power interruption, 22 – about, 163 Power switch – replacing, 463 – analyzer, 75 – RFID tags, 163 – partitioning engine, 72 Parts, 21 Preparation – moving, 26 – master mix reagents, 163 Password settings – reaction mixtures, 163 – about, 599 Prerequisites – configuring, 601
– data, 294 – target and dye settings, 311 – development software, 294 – working with, development software, 317 – file extension, 294 Reaction mixtures – opening, 296 – preparation, 163 – saving, 296 Reference target copy numbers – working with, 295 – CNV analyses, 379 Q – CNV tests, 422 – ranges, 379, 422 Quick references Releasing results, 265 – development workflows, no unassigned sample setup, 200 Replacing – development workflows, with unassigned sample setup, 208 – partitionin
– deleting notes, 263 – deleting analyzer software, 302 – development workflows, 174 – duplicating analyzer software, 301 – diagnostic workflows, 174 – editing analyzer software, 304 – editing notes, 263 – exporting analyzer software, 302 – failed sending, 538 – exporting development software, 320 – final, 173 – importing analyzer software, 302 – final in web application, 103 – opening analyzer software, 300 – missing measurements, 30 – renaming analyzer software, 300 – releasing, 265
– assignment of partitioning engine, 31 – unsupported characters, 31 – circuit breakers, fuses, 36 – waste, 33 – computer configuration, 28 – weak passwords, 32 – consumables, 21 Sample groups – contaminated partitioning engine, 29 – about, 328 – data security, 32, 36 – adding samples, 330 – disposal, 41 – creating, 329 – electric shock, 25 – deleting, 333 – electromagnetic compatibility, 23 – renaming, 332 – electromagnetic fields, 24 – updating, 331 – export files, 33, 36 – with
Scatter plots Statistics panel – changing display, 341 – absolute quantification, 370 – development software, 132 – CNV, 385 Screens – indel, 397 – web application, 94 Status Searching – analyzer, 109 – tables, 144 – batch in web application, 93 Seed data – messages in analyzer software, 122 – about, 345 – nanowell plates in analyzer software, 114 – compatibility, 347 – results in web application, 102 – exporting, 356 – run profiles, 299 Sending results, 267 Status indicator Sen
– general specifications, 181 Tabs – labels, 38 – analyzer software, 111 – maintenance overview, 177 – development software, 129 – maintenance schedule, 459 Targets – manage analysis packages, 579 – settings development, 311 – merged lanes, 62 Touch screen monitor – messages, 509 – analyzer, 74 – overview, 61 – partitioning engine, 71 – password settings, 599 Trademarks, 4 – preventive maintenance, 482 Transducers, 23 – problem reports, 512 Transport, 21 – reagents, 186 – result s
User Assistance packages – editing sample setups, 258 – about, 608 – entering run information, 261 – importing, 609 – exporting raw data files (diagnostic), 315 User management – filtering tables, 143 – about, 545 – final results, 103 – list of settings, 547 – global information area, 89 User roles, 545 – hand-held barcode reader, 77 Users – icons for analysis packages, 94 – about, 545, 546 – invalidating lanes, 535 – about passwords, 547 – invalidating plates, 535 – changing passwo
Work area – analyzer software, 110 – development software, 127 – partitioning engine software, 85 Workflows – development, 63 – diagnostic, 63 – loading analyzer, 225 – overview, 63 – overview, development, no unassigned sample setup, 194 – overview, development, with unassigned sample setup, 195 – overview, diagnostic, 193 – partitioning, 221 – performing development, no unassigned sample setup, 275 – performing development, with unassigned sample setup, 283 – performing diagnostic, 243 – quick refere
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