Optigene Genie HT User Manual

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User Manual

v1.01

(Instrument Software Version v4.00)

IFU_EN_GEN-HT Version 1.01

July2020

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Page 1 User Manual v1.01 (Instrument Software Version v4.00) IFU_EN_GEN-HT Version 1.01 July2020...
Page 2 In no event shall OptiGene Ltd. be liable for incidental, multiple, or consequential damages in connection with or arising from use of this document. Genie® HT and its design is a registered trademark of OptiGene Ltd. or its subsidiaries in the UK and other countries. IFU_EN_GEN-HT Version 1.01...
Page 3: Table Of Contents
Table of Contents Replay ..........27 Install ..........27 SAFETY NOTICES ........3 Users..........28 Language ........... 29 SUPPORT ..........11 Report..........29 USB Devices ........30 TROUBLESHOOTING AND MAINTENANCE Wireless* ........... 30 ............... 11 NETWORK CONNECTION* ....30 Self-Test ..........30 How to obtain support ......
Page 4: Safety Notices
Notices Using the instrument in a manner not specified by OptiGene may result in personal injury or damage to the instrument and the protection provided by the equipment may be impaired.
Page 5 OptiGene Limited recommends that every two years the instrument's performance is checked for degradation. This can be done by requesting and purchasing ready-made strips from OptiGene that will perform an amplification and anneal run on the instrument which can then be assessed to check for optical or thermal performance issues.
Page 6 Disconnection Method Genie® HT is disconnected by removal of incoming mains power source to the unit. Following disconnection the unit should be left for a period of at least 5 minutes before any internal assemblies are removed or examined. When in use the heating block and heated lid are hot, so allow to cool before touching the surfaces.
Page 7 Keep away from sunlight Handle with care Keep dry This way up Biohazard WEEE: waste electrical and electronic equipment should not be disposed of in your dustbin or wheelie bin. OptiGene Limited must be consulted regarding end-of-life disposal. IFU_EN_GEN-HT Version 1.01 July2020...
Page 8 A continuous programme of development is maintained at OptiGene to satisfy the evolving demands of its customers and the wider market, in both instrumentation and enzymes and assays.
Page 9 In particular, Genie® HT can perform rapid detection of SARS-CoV-2 virus (COVID-19) within nasopharyngeal and oropharyngeal swabs, using the CE-IVD registered OptiGene COVID-19_Direct and COV-19_RNA RT-LAMP kits. General Precautions for Molecular Diagnostic usage ...
Page 10 Dispose of used strips as contaminated laboratory waste Storage and Handling The Genie HT is a heavy instrument and weighs 18kg. Lift from the front and back of the instrument, never from the lids. Keep the lids closed when not in use to prevent the ingress of dust or contaminants to the optics.
Page 11 (also known as “RoHS2”). REACh Statement OptiGene Limited also declares that no products sold by the company are known to contain any of the substances of very high concern (SVHC) as intentionally added components with regards to the European Regulation No. 1907/2006 (Registration, Evaluation, Authorisation &...
Page 12: Support
When directed to do so, contact OptiGene Ltd. to schedule maintenance or calibration of a Genie® HT instrument. OptiGene Limited suggests that every two years the instrument's performance is checked for degradation. This can be done by requesting ready-made strips from OptiGene that will perform an amplification and anneal run on the instrument which can then be assessed to check for optical or thermal performance issues.
Page 13: Box Contents
USB memory stick containing this manual as a ‘.PDF’ file UNPACKING THE INSTRUMENT The Genie HT is a heavy instrument and weighs 18kg. Lift from the front and back of the instrument out of the box. NEVER LIFT THE INSTRUMENT FROM THE LIDS Please retain packaging for future use.
Page 14 3. Remove the triangular foam piece from on top of the screen. Carefully lift the instrument from the box lifting from the front and back of the machine. A second person may be required. 4. Place the instrument on a flat stable surface. IFU_EN_GEN-HT Version 1.01 July2020...
Page 15: Site Preparation
Chapter Chapter SITE PREPARATION HOW TO SET UP GENIE® HT Genie® HT has been designed to be used in a laboratory. When it is being used, the instrument should be placed on a level and stable surface and the surfaces surrounding the instrument must be clear of obstructions at all times.
Page 16: Connections
CONNECTIONS Genie® HT is ready to use straight out of the box with only a single power connection. It can be operated standalone and does not require a computer to be connected. Genie® HT can be connected to multiple peripherals (barcode scanner, printer, USB pendrive) via the front USB A sockets and connected to a computer via the rear USB B socket or to a network via the rear RJ45 socket.
Page 17: Opening & Closing The Lids
RJ45 TO USB (DIAGNOSTIC USB (TO PC) NETWORK PORT) OPENING & CLOSING THE LIDS Gently lift the lids upwards. Close the lids by lowering gently. Care must be taken to ensure that objects are not obstructing the lids when trying to close it and under no circumstances should the lids be forced open or closed.
Page 18 Note: If this button is pressed during a run, Genie® HT will not enter standby. When in standby, normal operation can be resumed by pressing anywhere on the screen. IFU_EN_GEN-HT Version 1.01 July2020...
Page 19: User Interface
Chapter Chapter USER INTERFACE Genie® HT uses a touchscreen for viewing and inputting data. Touch the screen gently and press the appropriate keys when required. The touch screen can be operated while wearing protective gloves or by using the stylus included with the instrument.
Page 20: Genie® Ht Login Screen
GENIE® HT LOGIN SCREEN If users are set up on the instrument and a log in is required, the next screen will be a login screen. Log in using your user login and password. HOME SCREEN The next screen will be the home screen. This gives an overview of the status and temperature of all of the blocks, and their current position in their runs.
Page 21: Blocks
When a block is enabled it will be shown as a black box with a colour indicator to show its number and status. If a block is disabled or not installed, then the block will show as grey. If this has happened unexpectedly please contact OptiGene. IFU_EN_GEN-HT Version 1.01...
Page 22: Block Status
BLOCK STATUS The block status will be shown using one of three colours. Each block has an LED indicator next to its lid which also corresponds to these colours, allowing the user to glance at the instrument and know the status of the blocks: Green: The block is at a free to use and is below 40˚C.
Page 23 TIP! By opening a lid or by pressing a block will result in the block automatically being selected. Selected blocks will look like this, and be highlighted and show the status. Unselected blocks will look like this and the status symbol will be grey. Blocks that are already in use will be unable to be selected and will show like this.
Page 24 Once all the blocks are selected the next step is to select a test. Buttons can be assigned (in the Settings menu) to profiles and are shown on the left. Alternatively, touch ‘Other…’ to create a new profile, or open another saved profile. The numbers of blocks selected are listed, along with the reminder to close the lids.
Page 25: Settings
SETTINGS Pressing the spanner icon in the taskbar will load the Settings. USER Changes to the logged in user’s name and password can be changed here. Type the new password, and then confirm this by typing it in again and press the tick in the menu to confirm or the cross to cancel and return to the settings page.
Page 26: Graph Options
The background colour and the default colours of the lines on graphs can be changed here. Click the background button or a graph number and then drag the cursor on the colour chart to select a colour. The small table of coloured boxes on the right show the colour that is currently set, the default colour and the previous colours that have been...
Page 27: Tests
TESTS Set up the quick start buttons on the test selection screen. Up to 8 profiles can be stored as a quick start button. Touching ‘…’ will allow the user to browse the saved profiles on the instrument and assign that profile to the corresponding quick start button on the test selection screen.
Page 28: Video
VIDEO Pressing the ‘Video’ button will start a pre-loaded demo video. Additional features will be added to this in the future. When the video is playing, there are several gestures which control the playback: 1 finger tap: Pause / resume 1 finger swipe up/down: Increase / decrease volume 2 finger swipe left/right: Skip -/+ 30s 3 finger swipe down: Stop &...
Page 29: Users
USERS On the Users screen, users can be added or removed with different levels of access. Default access: This sets the default access when the instrument is turned on. By default the instrument will be in Admin mode. In this mode all features are fully available.
Page 30: Language
calling and can change the buttons Administrator: The user will have full unrestricted access to all the instruments settings and can add users and set language. LANGUAGE Default language: This sets the default language of the instrument. REPORT These options can be used to adjust reports of runs.
Page 31: Usb Devices
This will run a diagnostics on the instrument to see if there are any problems and report back if there is. If the instrument reports a problem, please contact OptiGene Limited for assistance. It is advised to run the Self-Test at the start of each session.
Page 32: Copy & Paste
COPY & PASTE Users are able to copy and paste in any text box which can save time in entering well names or run names. To copy: In a text box, if text is not highlighted, highlight the text by holding down on the text box until a pop-up appears, and select ‘Select All’...
Page 33 To paste: Touch the text box you wish to paste into, and then hold down on the box until a pop-up appears and select ‘Paste’. IFU_EN_GEN-HT Version 1.01 July2020...
Page 34: Profiles
PROFILES PROFILE SCREEN OVERVIEW This screen shows the overview of the profile. To start the run, press the play icon. If multiple blocks are selected when starting a run, the same profile will be used on all selected blocks, including all well names and result calling.
Page 35 The graph shows the temperature profile of the run. Touch the graph to adjust the profile by touching the appropriate temperature or time box. The notes section will change to show the temperatures and times of the different phases of the run. Pressing the graph again will toggle the notes back.
Page 36 Pressing the save icon will save the profile. Name the profile, press the tick button and it will be saved within the ‘PROFILE’ directory in the on-board memory allowing it to be loaded for future runs. Press the cross to cancel. If the profile is saved at this point the well names, abbreviations and all result calling will also be saved as...
Page 37: Active
ACTIVE Once a run is started, the software will go back to the ‘Home’ screen. To view the graphs of a block, touch the block. The ‘Temperature’ graph screen will be shown initially. The other screens can be accessed using the tabs. PROFILE This shows the temperature profile that is running.
Page 38: Amplification
ADVANCE Advances to the next phase of the run (Preheat to Amplification or Amplification to Anneal). STOP The ‘Stop’ button will abort a run in progress. A confirmation pop up box will prompt ‘Yes’ or ‘No’. AMPLIFICATION This shows the fluorescence data that is being acquired during the amplification phase of the experiment.
Page 39: Results
MULTIPLE CHANNEL OPTIONS Genie® HT uses two different channels depending on the profile being run. These buttons allow either the first or second channel to be selected. The graphs will update by pressing the relevant button on the ‘Amplification’ and ‘Anneal’ pages. SELECTION OF GRAPHS Pressing the well name on either the ‘Amplification’...
Page 40 REPORT GENERATION Pressing the button shown on the results page will generate an A4 PDF report. This will be a single page report showing the amplification graph, the anneal graph and the results table. These reports will be saved into a ‘Reports’ directory on the internal storage.
Page 41 is put into the CSV. An example of a generated CSV file opening in Microsoft Excel. Any graph can have its data exported to a CSV file also by clicking on Export data in the Graph Options menu. PRINT RESULTS TABLE Pressing the button shown on the results table will print the table onto a label if the correct printer is attached to the Genie®...
Page 42: Additional Options
ADDITIONAL OPTIONS Touching the button shown on the amplification or anneal plots will show a drop down menu with some additional options. BY WELL Selecting ‘By well’ will show all fluorescence plots by well rather than by fluorescence channel. This allows comparison of both channels at the same time.
Page 43 SHOW PLOT Selecting ‘Show plot’ will produce a second menu to select which plot to display on the screen depending on which signal processing step is wanting to be viewed. These are explained below and further in Chapter 6. Raw unprocessed fluorescence Spike The data after spike removal Step...
Page 44: View
VIEW To view previous runs press the folder icon on the status bar. This will display a file browser window. All Genie® HT runs are saved in the ‘LOG’ folder. To open, click on ‘LOG’ and then tick icon, or double press on the folder name. Each run is stored in a folder by date order: Year/Month/Day.
Page 45 Each run is stored in a folder by date order: Year/Month/Day. The default filename for the each run is the instrument serial number followed by a sequential number. Select a file, then touch the tick button to load the file. To copy a file, touch the copy icon, shown with the blue arrow.
Page 46 ZOOMING FUNCTION Zooming is available on temperature, fluorescence and anneal graphs. To zoom in on the area of interest, touch the plot area and drag to the right and/or down. To zoom out, touch on the plot area and drag to the left and/or up. A double press on the screen will zoom out to the full extent of the graphs.
Page 47: Genie Result Calling
Chapter Chapter GENIE RESULT CALLING OVERVIEW Genie® instruments can generate results according to detected amplification times, anneal peaks and other features. Due to the varying requirements of differing applications, setting up the parameters is highly flexible. Analysis is based on targets, where each target has its own set of parameters and possible results.
Page 48: Result Calling Interface
RESULT CALLING INTERFACE Pressing this button on the profile screen will allow the user to change the parameters for result calling for the profile. All the parameters are stored within the profile and the run file. This screen shows an overview of the ‘Detection targets’, showing the number of regions of interest, the number of results, and which targets are assigned to...
Page 49: Target Parameters
TARGET PARAMETERS This screen shows the Target parameters. The explanation of the different options is below. Name The name of the target is displayed in the results table and various reports. Type The target type determines the purpose of the target: Sample A normal sample for analysis Pos control...
Page 50 Excessive step removal will cause flat areas and shifted amplification. The step removal threshold is target-dependant and is affected by noise:signal ratio of the assay. Slope Slope correction adjusts for drift by examining the initial fluorescence and removing the slope from subsequent fluorescence data after a given time period (Time). Slope correction occurs after spike and step removal.
Page 51: Regions Of Interest
REGIONS OF INTEREST This screen shows an overview of all the regions of interest for the selected target. The type of region, as well as which phase of the assay and plot is summarised as well as the more specific details in the box below. The regions can be edited and deleted from this screen.
Page 52 Slope The data after slope correction Normalised The data after normalisation Limited The data after limiting (value set in the Target parameter screen) Ratio The ratio (dF/F) of adjacent points (after step removal). This plot is smoothed with an averaging filter. Derivative The gradient of the data (generated with a differentiating filter) 2nd Derivative...
Page 53 FEATURES Feature type: Any Positive if: Any point on the graph is within the window. Negative if: All points in X range are outside Y range. Complete when: X position passes the window or a point in range is found Point identified: The first point that falls in the window (without interpolation) Additional parameters:...
Page 54 Feature type: Average Positive if: The average of all points in X range falls within Y range Negative if: The average of all points in X range falls outside Y range Invalid if: There are no points in X range Complete when: X position passes window Point identified:...
Page 55 Feature type: Threshold All thresholds required or prohibited by a result are considered together. A threshold that is prohibited has its Y range inverted. If peaks (or dips) are required, each peak is checked against all required thresholds. Positive if: There is a point/peak where all thresholds that are in X range are also in Y range or there is a peak where no thresholds are in X range.
Page 56 Feature type: Reference This is an advanced calling feature to allow results from one well to affect others. Positive if: The referenced target result is positive Negative if: The referenced target result is negative Invalid if: The referenced target result is invalid Complete when: The referenced target produces a result Point identified:...
Page 57: Result Definitions
Relative regions allow features to be aligned to other features. Example 1: Find the first peak ratio after normalised fluorescence has passed a threshold. 1. Create an 'any' region, testing normalised fluorescence 2. Create a 'peak' region, testing smoothed ratio; X range 0-0, relative to region 1 Example 2: Test the fluorescence at a peak ratio location.
Page 58: Overall Result
Text This is the result message seen by the user on the results table and recorded in reports. Colour/ on These are the foreground and background colour of the displayed result. Result The type of the result None: An unused result that will block later results until determined. Provisional: An intermediate result that will be shown until/unless overridden.
Page 59 This screen shows the defined overall results. Result definitions are tested in order. The first matching result is displayed. This order can be changed using the up and down arrow buttons. The Compare feature is explained below. OVERALL RESULT DEFINITIONS The result definition set up screen.
Page 60 An overall result is displayed at the top of the results table, as shown in the screenshot. IFU_EN_GEN-HT Version 1.01 July2020...
Page 61 WELL COMPARE Values calculated for wells can be compared and included in the overall result. The compare set up screen. The explanation of the different parameters is below. Name The compare name appears in the results set-up. Phase Select the phase to compare (e.g. isothermal or anneal) Plot Select which data step to compare (e.g.
Page 62: Connecting To External Devices
Chapter CONNECTING TO EXTERNAL DEVICES Genie® HT is a standalone instrument; however, it can be connected to external devices for software updates, data upload and further analysis. Files can be transferred to a PC running Microsoft Windows (XP, Vista,7, 10) via the USB connection on the back of the instrument or via WiFi to a phone/mobile device with a network connection or via a pendrive to the USB socket on the rear of the instrument.
Page 63 Open the USB drive in ‘My Computer’. Run the file ‘GenieInstall.msi’. Follow the onscreen instructions. *A prompt may appear requesting installation of .NET Framework 4.0. This must be installed prior to installation. Follow the link to the Microsoft download page. http://www.microsoft.com/en- gb/download/details.aspx?id=17718 Choose a location for the installed program.
Page 64: Wireless Connection
The installer will copy all necessary files to the computer. Once the installation is complete, exit by clicking ‘Close’. A Genie® instrument can now be connected to the computer. When connected via USB and switched on, the Genie® instrument will appear as a USB drive and files can be viewed from Genie®...
Page 65: Genie® Ht Software Updates
 To download the latest firmware, visit the OptiGene website (http://www.optigene.co.uk). Click on ‘Support’ and click on the appropriate link on the right hand side of the page and download the ‘.zip’ file.  Open the ‘.zip’ file and extract the contents to a new folder. The contents of the folder will include the latest firmware as two ‘.mot’...
Page 66 Now on Genie® HT touch Settings, and then touch ‘Install’. Genie® HT will prompt for a file to use for the update. Touch on the file, and touch the tick button. The Genie® HT will then install the updated software and restart the instrument.
Page 67: Genie® Ht Technical Specification
Chapter Chapter GENIE® HT TECHNICAL SPECIFICATION Sample Number 12 x 8 wells Sample Volume 10 µl to 150 µl 10.1” High-brightness LCD with multi-touch projective capacitive touch panel (1280 x Touchscreen 800) Heater technology Ceramic substrate with resistive coating Cooling method Forced convection Temperature sensor High-precision thermistor...
Page 68 In no event shall OptiGene Ltd. be liable for incidental, multiple, or consequential damages in connection with or arising from use of this document. Genie® HT and its design is a registered trademark of OptiGene Ltd. or its subsidiaries in the UK and other countries.