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Optigene Genie HT User Manual Download Page 49

 

IFU_EN_GEN-HT Version 1.01 

 

July2020 

48

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

 

A positive control that is expected to amplify. 

Neg control

 

A negative control that should not amplify. 

Reference

 

Some other secondary target 

Chan

 

The fluorescence channel / colour to examine.  All regions for a target use the same 
channel. 

Quenching

 

Indicates that amplification causes a decrease in signal.  Ratios and derivatives are 
inverted for quenching. 

Spike removal

  Enable/disable spike removal.  Spike removal identifies single-point spikes in 

fluorescence and replaces them with the average of the two adjacent points. 
 
Spike removal analyses the data to remove rogue spikes from the fluorescence data.  
Spikes can be caused by particles or bubbles in the well and by external environmental 
factors.

 

 

Spike threshold

  Spike detection finds points in fluorescence that are proportionately higher or lower 

than the points on either side.  The threshold should exclude normal noise in the 
signal.  Peak noise in the unsmoothed ratio plot with spike and step removal turned off 
gives a good indication of the minimum threshold. 

The spike removal threshold is target-dependant and is affected by noise:signal ratio of 
the assay. 

Step removal

 

Enable step removal.  Step removal identifies sudden steps in fluorescence and 
subtracts the step height from all subsequent fluorescence values.  Steps can be 
caused by particles, bubbles, drips and settling of well contents. Step removal occurs 
after spike removal. 

Step threshold

   Step detection is approximately based on detecting single point spikes in the ratio 

(unsmoothed, with step removal turned off) exceeding the threshold on both sides.  
Set the threshold to clearly exceed the peak-to-peak noise.

 

Summary of Contents for Genie HT

Page 1: ...IFU_EN_GEN HT Version 1 01 July2020 User Manual v1 01 Instrument Software Version v4 00 ...

Page 2: ...tion in this document is subject to change without notice OptiGene Ltd assumes no responsibility for any errors that may appear in this document This document is believed to be complete and accurate at the time of publication 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...

Page 3: ...er 24 Colours 24 Graph Options 25 Tests 26 Date and Time 26 Screenshot 26 Video 27 Replay 27 Install 27 Users 28 Language 29 Report 29 USB Devices 30 Wireless 30 NETWORK CONNECTION 30 Self Test 30 Copy Paste 31 Profiles 33 Profile Screen Overview 33 Active 36 Profile 36 Temperature 36 Amplification 37 Anneal 37 Results 38 Additional Options 41 View 43 GENIE RESULT CALLING 46 Overview 46 Result Cal...

Page 4: ...owever to avoid any risk to the safety of the equipment operator or anybody in the vicinity of the equipment please read this chapter before unpacking and using the instrument If there is any doubt as to the correct use of the equipment contact the vendor Notices Using the instrument in a manner not specified by OptiGene may result in personal injury or damage to the instrument and the protection ...

Page 5: ...m the instrument Do not touch the instrument or any fluid flowing from it while it is connected to the mains supply Always follow local health and safety guidelines The instrument is not intended for use with flammable substances It is not advised to open the lids whilst the instrument is running as it could cause measurement errors leading to incorrect results It is advised to run the Self Test f...

Page 6: ...adhere with local health and safety and COSHH regulations If in doubt consult the person responsible for the equipment in the laboratory Cleaning Method The Genie HT can be disinfected using the following procedure which can be used as a safety measure if this equipment is routinely exposed to bio hazardous materials and it is recommended that it should be performed prior to moving or shipping the...

Page 7: ...ate of Manufacture Use by date Consult electronic instructions for use Store at temperature range 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 ...

Page 8: ...n both instrumentation and enzymes and assays The Genie platform OptiGene Genie instruments are essentially highly sophisticated temperature controlled fluorimeters They are almost exclusively applied to running molecular diagnostic assays employing isothermal amplification of DNA and RNA enabling sensitive detection of bacteria and viruses at a molecular level by fluorescence measurement Genie HT...

Page 9: ...ated block technology of the Genie platform incorporating integrated optics and photodetectors dedicated controller and data acquisition electronics The user interface is via a 10 1 projective capacitive touch panel connectivity is via USB 2 x USB A and 1 x USB B ports and RJ45 ethernet Intended Use The Genie HT is specifically designed to run any isothermal amplification method that employs targe...

Page 10: ...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 Handle the instrument and its accessories with care and wear appropriate personal protective equipment when preparing and handling Genie strips See the specific instructions for the preparation and use of the Genie strips supplied with the assay...

Page 11: ...erature 0 C 40 C Storage Temperature 20 C 70 C Approvals CE Dimensions 635mm L X 434mm W X 153mm H Weight 18kg 40lbs Connections 1 x USB B 2 x USB A 1 x Power in 1 x RJ45 Network connection 1 x USB A diagnostic port Environmental protection IP20 Wireless Connections Bluetooth WiFi Power supply Input 100 240V AC 50 60Hz RoHS Compliance OptiGene Limited declares that to the best of our knowledge all...

Page 12: ...one 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 SUPPORTED CONSUMABLES IMPORTANT Genie HT uses a proprietary tube strip that maximises optical and thermal efficiencies Other tubes and strips will not fit IMPORTANT Forcing non supported consumables will ...

Page 13: ...e box NEVER LIFT THE INSTRUMENT FROM THE LIDS Please retain packaging for future use If repacking the instrument for transport make sure to safely dispose of any used strips in any of the blocks prior to packing Allow 10 minutes to unpack and set up the instrument Choose a location with sufficient space to be able to see the screen and load strips into the instrument 1 Cut the tape on the flaps on...

Page 14: ...0 13 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 ...

Page 15: ...rfaces surrounding the instrument must be clear of obstructions at all times Care must be taken not to unduly restrict the air at the outlet vents at the sides Restricting airflow may impede operation and could affect performance Electrical points should be close to the instrument to avoid injury from trailing wires It is recommended that the instrument is kept away from sinks and other wet areas ...

Page 16: ...rals 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 Located at the rear is the on off power switch and power cable connector Connect the power cable into the back of the instrument and when the switch is in the on position Genie HT will power up and progress through its checks DUAL USB ...

Page 17: ...NSERTING TUBES IMPORTANT Genie HT uses a proprietary tube strip that maximises optical and thermal efficiencies Other tubes and strips will not fit IMPORTANT The shape of the tubes is such that they will only fit in one way round The locating pins on the block have corresponding holes in the strips Genie HT can be shut down using the power button in the bottom left corner At this point Genie HT ca...

Page 18: ...IFU_EN_GEN HT Version 1 01 July2020 17 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 ...

Page 19: ... screen can be operated while wearing protective gloves or by using the stylus included with the instrument IMPORTANT Do not use a pen or any other sharp implements to touch the screen GENIE HT WELCOME SCREEN When switching on the LED above the screen will be amber in colour Wait for the light to change to green then touch the screen to access the login screen or home screen Chapter Chapter ...

Page 20: ...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 The menu to the right gives access to the soft power switch starting a run accessing and viewing old log files settings and the data and time ...

Page 21: ... spanner icon BLOCKS The blocks are listed in the order they are in the unit Pressing on a block will do different things depending on what its status is ENABLED DISABLED 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 pleas...

Page 22: ...ng a lid that is red will result in the warning alarm sounding Orange The block is available to use but is still cooling down to 40 C It is advised to wait until the status goes green again before starting a new run TIP When files are open or have finished running on a block use a two finger swipe down on the block to close the file STARTING A RUN In order to start a run there are several ways to ...

Page 23: ...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 To de select a block press the block again To add more blocks to the run press on the blocks to select them or open the lids ...

Page 24: ...ew profile or open another saved profile The numbers of blocks selected are listed along with the reminder to close the lids A run cannot be started until all the lids are closed Once a test is selected the well names are shown along with the number of blocks selected and once the lids are closed a play button Pressing this will start the run Touching on the well names will allow editing of the pr...

Page 25: ...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 Pressing the log out button will log the user out COLOURS ...

Page 26: ...show the colour that is currently set the default colour and the previous colours that have been used Pressing on any of them will set the colour GRAPH OPTIONS Show grid This will enable disable the grid behind graph plots Show points of interest Enable disable any dots on the plots that have been generated by the result calling Line weight set the line weight of all plots default 1 Default fluore...

Page 27: ...lection screen To remove the buttons untick the box next to the profile name DATE AND TIME Date click in the white box for date and enter in the format DD MM YY Time click in the white box for time and enter in the format HH MM SS Press Set to save or click the back button to cancel SCREENSHOT Screenshot A small yellow moveable icon will appear on the right hand menu which when pressed will take a...

Page 28: ...g 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 exit REPLAY Replay This will replay a run file as if it were running in real time Select the file and press play INSTALL Pressing Install will allow updating of the instrument software See Chapter 7 ...

Page 29: ...is selected and the instrument is restarted This is the level that the instrument will default to on start up To create a new user click on the Add User button shown and then enter the details for the user and select an access level Press the tick to save or the cross to cancel in the menu bar The levels of access are as follows No access The user is disabled can be used to temporarily revoke acce...

Page 30: ...ese options can be used to adjust reports of runs At end At the end of a run if the boxes are ticked the Genie will automatically create a PDF report a CSV comma separated value file and print the result table to the connected printer accessory The separator of the CSV file can be set between a tab and a comma depending on what is required The CSV data can be the results table only the raw data al...

Page 31: ...ORK CONNECTION COMING SOON SELF TEST 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 Features are currently in development ...

Page 32: ...opy 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 and then hold down again and select Copy ...

Page 33: ...IFU_EN_GEN HT Version 1 01 July2020 32 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 ...

Page 34: ... The top text box is for the run name The wells are colour coded for identifying individual plots on the temperature amplification and anneal graphs These can be changed in Settings The well names can be edited by pressing on the particular well and typing using the on screen keyboard The large notes box is a text box which can be used for adding notes about the run The Channels area allows select...

Page 35: ...atures and times for the pre heat amplification and anneal phases can be adjusted The phases can be enabled or disabled using the tick box next to their name To set a thermal gradient maximum of 7 degrees across a block enter a range of temperatures in the Amplification temperature box The range of temperatures should be entered separated by a hyphen as shown below The Wait button on the pre heat ...

Page 36: ...file 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 part of the profile ...

Page 37: ...n will be shown initially The other screens can be accessed using the tabs PROFILE This shows the temperature profile that is running At the top of this screen there is a text box to edit the run name edit the well names and add notes TEMPERATURE This shows the current temperature of the block as the experiment is progressing EXTEND This adds 10 minutes to the current phase of the run ...

Page 38: ...al 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 ANNEAL This shows the fluorescence derivative data that is being acquired during the anneal phase of the experiment ...

Page 39: ...ressing the relevant button on the Amplification and Anneal pages SELECTION OF GRAPHS Pressing the well name on either the Amplification or the Anneal page cycles the state of the related curve on the graph between normal highlighted and off RESULTS This shows the results of the experiment Each sample name is shown as well as amplification time and annealing temperature and any result that has bee...

Page 40: ...s table These reports will be saved into a Reports directory on the internal storage An example of a generated report file EXPORT TO CSV Pressing the button shown on the results page will generate a CSV comma separated values file with the results in and save it in the Reports directory on the Genie instrument The formatting can be switched between tab or comma separated using the setting in Admin...

Page 41: ...el 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 instrument via the USB ports on the front of the instrument ...

Page 42: ...he 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 This can be reversed by the same process ...

Page 43: ...p removal Slope The data after slope correction Normalised The data after normalisation Log The log of the normalised data 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 The gradient of the derivative a second application of the same filter Ratio4 An...

Page 44: ...he 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 Each run is stored in a folder by date order Year Month Day ...

Page 45: ...le then touch the tick button to load the file To copy a file touch the copy icon shown with the blue arrow To paste a file touch the paste icon shown with a green arrow To delete a file touch the trash can icon shown with a red arrow When the file has opened Genie HT will display the profile that was run the temperature log amplification data anneal data and the results table Up to 12 runs can be...

Page 46: ... 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: ...he target parameters specify the fluorescence channel target type and various signal processing options Detection starts with examining regions of interest on various graphs for required features The presence or absence of features in the regions determine which result is displayed for the well The presence or absence of control targets in other wells can also be included in the determination Adva...

Page 48: ... targets showing the number of regions of interest the number of results and which targets are assigned to which well From here new targets can be added imported from other runs or profiles edited or deleted If you wish to import targets from another profile or run file touch Import and then select the file you wish to import from you can then select which target from that file you wish to import ...

Page 49: ...he data to remove rogue spikes from the fluorescence data Spikes can be caused by particles or bubbles in the well and by external environmental factors Spike threshold Spike detection finds points in fluorescence that are proportionately higher or lower than the points on either side The threshold should exclude normal noise in the signal Peak noise in the unsmoothed ratio plot with spike and ste...

Page 50: ...s in the same half strip 1 4 5 8 Strip Applies to all targets in the same strip 1 8 Running controls in a different strip is of dubious validity so is not directly supported Smoothing This setting adjusts the amount of smoothing applied to anneal derivative plots If this value is set to 0 the default smoothing settings in the instrument is used If this is set to a value between 1 and 8 the instrum...

Page 51: ...er set up quicker Alternatively touching Other will allow the user to create something custom This is the set up screen for the region The explanation of the different parameters is below Regions of interest define which features to examine to generate a result Name The region name appears in the results set up Type Selects the feature type to examine explained further below in the section titled ...

Page 52: ...value found by another region BE AWARE Compatibility of units is not checked it is possible to make nonsensical selections e g by making a time range in seconds on an amplification plot relative to an anneal temperature in C Result X Y Displays the X and or Y value found on the results table provided the region is detected and used in the result Result column Specifies which column s of the result...

Page 53: ...tive if Any point in the X range falls outside the Y range Complete when X position passes the window or a point in X range falls outside Y range Point identified The first point in X range that falls outside Y range if any Additional parameters None Uses Range check Feature type Min Positive if A minimum width in X range falls within Y range Negative if No group of points in window cover width Co...

Page 54: ...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 Y Average Y value within X range X Midpoint of X range Additional parameters None Uses Level check ...

Page 55: ...Crossing threshold with multiple conditions or regions Additional peak detection criteria e g minimum fluorescence Feature type Peak Positive if A peak is detected in X range with peak point in Y range before interpolation All required thresholds that are in X range must also be satisfied Negative if No peak detected or all peaks out of Y range or thresholds are not satisfied Complete when Peak fo...

Page 56: ... result of the target Has a valid point Uses matching Phase and Plot Has the Reference option set Additional parameters Well Well number reference In Relative location of reference well Same in the same well as the current target Adjacent in the well adjacent to the current well other well of pair Pair Well 1 or 2 in the current pair Half Well 1 4 in the current half strip Strip Well 1 8 in the cu...

Page 57: ... overview of the target results The type and how many regions required prohibited are shown The order of which the results are called is important This can be changed by selecting a result and using the up and down arrows The first matching result will be displayed in the result table New results can be added and results can be deleted from this screen Adding or editing a result will show this scr...

Page 58: ...ntrols that must be positive to satisfy this result Prohibited Select all regions and controls that must be negative to satisfy this result Unselected regions and controls have no effect on the result Regions that are both required and prohibited should be avoided this combination may be given a special meaning in the future All positive control targets whose scope includes a particular well are c...

Page 59: ... until no pending wells can affect the result e g if a prohibited well is positive the state of other wells is irrelevant Text This is the result message seen by the user and recorded in reports Colour on The foreground and background colour of the displayed result Required Select all wells and comparisons that must be positive to satisfy this result Prohibited Select all wells and comparisons tha...

Page 60: ...IFU_EN_GEN HT Version 1 01 July2020 59 An overall result is displayed at the top of the results table as shown in the screenshot ...

Page 61: ...o compare e g isothermal or anneal Plot Select which data step to compare e g normalised fluorescence Axis Select which axis to compare X or Y Well 1 2 Set which wells to compare Target The targets to compare Range The comparison is positive if the difference between well values is in the specified range Well 2 value Well 1 value A region that is set to Use as reference tests the selected phase an...

Page 62: ...E A pendrive can be plugged into the USB A sockets on the front of the unit This allows files and software updates to be transferred to and from the unit without it needing to be connected to a PC The pendrive can be accessed via any file manager screens including the software update screen allowing updates to be performed at a site without needing a computer WIRED CONNECTION Disclaimer Genie Expl...

Page 63: ...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 Confirm to start the installation ...

Page 64: ...puter 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 Explorer WIRELESS CONNECTION Currently in development ...

Page 65: ... 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 files To install the updates connect Genie HT to a computer Navigate to My Computer and open the Genie HT drive The drive is named with the instrument serial numbe...

Page 66: ...he tick button The Genie HT will then install the updated software and restart the instrument Please wait for it to finish before trying to do anything else Repeat this action for both files If the update was a firmware update Genie HT will restart when completed Genie HT will automatically delete the files if they are on the internal file system when the update has completed ...

Page 67: ...0 C Temperature accuracy 0 1 C Temperature uniformity across block 0 2 C Temperature gradient Programmable up to 8 C Optics source 470 nm 590nm dual colour LED with high quality interference filter 40 nm band pass Detection optics Photodiodes with high quality interference filters 510 560 nm band pass 620 nm long pass Operating temperature 0 C 40 C Storage Temperature 20 C 70 C Approvals CE Dimens...

Page 68: ... notice OptiGene Ltd assumes no responsibility for any errors that may appear in this document This document is believed to be complete and accurate at the time of publication 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 subsi...

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