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CheckExtractor™ - Greiner Bio

1. CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 11 3 Causes of Trouble Trouble Cause Solution Barcodes are not Direct sunlight interferes with the cor Place the CheckExtractor in an area without direct read rect action of the barcode reader sunlight If necessary re enter the barcode manually The barcodes do not fulfil the specifi Barcodes are not cations Especially the quiet zone and Make sure the barcodes fulfil the specifications See read the length of the barcode have to be 12 2 If necessary re enter the barcode manually observed Place the barcodes vertically on troughs and tube as Barcode are misaligned or misplaced shown in the corresponding figures If necessary re enter the barcode manually Carrier is not loa The Autoload cannot catch the Make sure the carrier is pushed in all the way to the ded Carrier first mechanical block CheckExtractor refuses to work at all Barcodes are not read The period of 200 days between two a A service is necessary services has been exceeded The CheckExtractor allows for the extraction method only input file Rename you input file accordingly which file names end with EXT Input file is not found Be sure that the elution plate is fully thawed spun down and open before loading it into the CheckExtractor Run stopped due to The rip racks were not filled as shown Start a run only with en
2. 5 4 1 2 Protection of method and library files Users who have been assigned as Lab Operator will only have read access to these files and will not be able to edit or delete them 5 4 1 3 Protection of output files The output files see chapter DATA MANAGEMENT will be protected by Windows access rights Users who have been assigned as Lab Operator will only have read access to these files and will not be able to edit or delete them 5 4 2 Input files For every run a worklist is required This worklist contains all necessary information about the samples to be run on the CheckExtractor and for the tracking of the samples e g with a LIMS 5 4 2 1 Input file for Extraction Method There are three common ways how the CheckExtractor creates the worklist 1 An input file is provided by the LIMS The user just loads it from the LIMS directory using the Import button The CheckExtractor converts the import file into a worklist Please contact your LIMS provider to create a input file in the form depicted below 2 An input file is manually written into an Excel file This Excel file is then loaded using the Import button The CheckExtractor converts the import file into a worklist 3 It is also possible although not recommended to create a worklist at the beginning of the run Instead of using the Import button click in the first sample field and type in the sample ID and the barc
3. CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Take care that no liquid gets inside the tip channel Whenever it is necessary to move Channels on the x Arm move them gently by pushing close to their y slide Never force them as this may lead to damage If possible switch on the instrument as this will result in a smoother motion when Channels have to be moved on the x Arm 11 Clean the stop disk and the O rings of the pipetting head outer part of the pipetting channels with a lint free cloth soaked in MICROLAB Disinfectant Spray 12 Spray the front and side cover with MICROLAB Disinfectant Spray and wipe dry Do not use highly concentrated alcoholic solutions because they turn the cover panes dull 13 Clean the Autoload protecting ribbon with a cloth soaked in MICROLAB Disinfectant Spray and wipe without exerting pressure Do not directly spray the Autoload unit or any electrical boards or connectors Use a soaked cloth in the surroundings of electrical parts 14 Clean the x guide shaft behind the upper front cover with a dry cloth at least once a month 9 5 Printing a Maintenance process status Report The maintenance process report is printed as follows 1 Go to File gt Open Report All maintenance and verification processes which are found in the default Report Path are listed 2 If necessary change the report path using the browse button 3 S
4. Instructions for Use Revision BQ 395 01 June 2015 SampleTransfer Extraction Start the sample transfer run Start the extraction run Start the PCR setup run Figure 12 GUI start screen In order to avoid false operating several error messages are part of the GUI and appear in case of an erroneous handling For explanations and recommended steps please refer to chapter TROUBLESHOOTING SampleTransfer action Start the sample transfer run Start the extraction nin Start the PCR setup run Figure 13 Software overview CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 23 5 4 Special Functions 5 4 1 User Management The onboard software of the CheckExtractor allows access to features at different levels For routine use of the CheckExtractor the user level is defined as Lab Operator All other user levels are for service purposes only and only accessible by Greiner Bio One representatives Group User Authorisation Lab Operator Operators may run any method The adjustment of the Windows user settings on the controlling PC will be within the responsibility of the system administrator Please ask your system administrator to add all user in the lab to the group Lab Operator 5 4 1 1 Protection of PCR config files Users who have been assigned as Lab Operator will only have read access to these files and will not be able to edit or delete them
5. Se al Number 2509 _Expited Date Time Processed Date Time Processed Status Mandatory D aily maintenance required 26 02 2010 17 10 00 8 02 a010 1415 0i ey mandatory completed 05 03 2010 021 5 00 25 02 2010 14 15 00 successful mandatory completed 20 07 2010 0459 00 25 02 210 14 15 00 ssful mandatory Figure 25 Maintenance and Verification Run Window Select the desired maintenance routine by clicking the specific check box and by pressing the Run Process button The CheckExtractor software will issue on screen instructions detailing all procedures required to perform the selected maintenance routine Always wear disposable gloves during maintenance Do not clean the instrument in the vicinity of open flames or devices which could create sparks Do not use hot air blowers to dry the instrument The liquids used for cleaning are flammable When cleaning CO RE gripper tool be very careful of sharp edges on the CO RE gripper s pincers This manual provides indications regarding general disposal of waste In addition any regulations specific to the country of operation must be taken into account and observed Routine Completion A maintenance routine is completed once the procedure has been fully executed and the results are within the specifications Aborting Maintenance Procedures Aborting a maintenance procedure will lead to a failed status and maintenance will need to be started again 9 4 1
6. WORKFLOW uuuuuuunn00nnnunnnnunnnnunnnnnnnnunnnnnnn nun 37 Ca Mivcc EMTS TAU LEY SUNG CONS aaa oo a ee dig 37 A ROOM SED O 37 7 3 Sealing and storage of plates a o 38 sl y sealng and storage ofthe elution plato er 38 AS orto le ER Ol ILS reaa a a a a a Dae 38 Poe AAS CIOS IG OM he PER paar 39 8 SHUTDOWN PROGEDURE se ace masse 40 8 14 Reglllar ShUldoWn era era ee een i oe a ee ee 40 82 Deeontam nallon a 40 BS USI UNE RIO O eek ee ee E a en t 40 9 MAINTENANGE E E es arcane ena 2ee 43 Deals ALOE ON ee ee ee ee set mes 43 924Maintenance lntervals TO sy rE eT te 43 93 Maternal edu ed o a ea ur ao o a aan i a en ar aa ne 43 94 Maintenance Proced resS ee Rs reeneoans 43 gA TEPPAN Maenan orem ee mee ener Rene el 44 OA ES Dance ea N 45 9 5 Printing a Maintenance process status Repott 2 u0 u00n00an0nnunannnnunnnn nun nun nnnn nun anne 48 g ome tea Mantenne e e 49 9 7 Further Maintenance and Service uu22u02200 n000n0n0n0nnnunnnunnnunnnun nun nnunnnnnnnnnnnnnnnnnnnnnnnennn 49 9 8 Finishing the Maintenance and Cleaning u u u200 n000n00n nnnnnnnnnnnnnannnnnnn nun nnnnnnnn 49 305EEGHNIGAL SUVPPO BE me een 50 AA e a O 5 0 51 o nn ee ev an en 51 I Fal i 0 ee 52 113 GAUSS Of rombo O Be NS SIS aN ce eet a ree ne 55 10 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 12 TECHNICAL SPECIFICATIONS ccccceeesecceeeeeeeenaeeeeeeaeeeeeneseeneaseeeoeasee
7. disinfectant and leave them to dry If they are heavily soiled soak these carriers afterwards in a solution of MICROLAB Detergent and Disinfectant See the product data sheet for further information Examine each carrier for scratches on the barcode and any signs of damage If damage is apparent replace with new carriers 2 Once the weekly maintenance program is resumed the Autoload will be repositioned to the right hand side of the instrument Open the front cover and wipe the deck with a cloth saturated with MICROLAB Disinfectant Spray The slide blocks must be checked and cleaned if required Close the front cover Do not directly spray at the Autoload unit or any electrical boards or connectors Use a soaked cloth in the surroundings of electrical parts 3 The next step of the maintenance procedure will reposition the Autoload to the left hand side of the instrument At this point the tip waste needs to be emptied and cleaned Dispose of tip waste with the rest of the laboratory s contaminated waste The tip waste the tip eject plate and the plastic bag should always be treated as if they are contaminated gt Remove the tip eject plate from the tip waste station and clean it Spray MICROLABTM Disinfectant Spray directly onto the surface and wipe Remove the frame that holds the plastic bag in place and discard the plastic in the laboratory s contaminated waste Pull a new plastic bag over the frame and re att
8. DIN EN ISO 9001 2000 DIN EN 18113 3 ISO 14971 1 3 Trademark The used brand names and labels are the property of the respective owner CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 1 4 Terms used in this Manual GLOSSARY OF SYMBOLS Caution Electronic equipment can be the source of electrical shocks DO NOT attempt to gain access to parts of the instrument marked with this label DO NOT attempt to repair any electrical parts DO NOT open the instrument housing Service and repair should only be carried out by authorized and qualified personnel of the manufacturer Hot Surface DO NOT touch Laser beam DO NOT stare into the beam UV light Waste Electrical and Electronic Equipment Collect separately ac cording to national laws E A CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 h checkExtractor AAA CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 1 4 1 Abbreviations NETTE Meaning meee of m peee CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 1 4 2 Name and Description of Components Overview Name Meaning Controlling PC The personal computer PC which runs the software that controls the CheckExtractor Extracted DNA in elution buffer Elution plate Barcoded PCR plate into which the extracted DNA is eluted MASTERBLOCK MASTERBLOCK Deep well pla
9. Daily Maintenance After clicking Yes the daily maintenance procedure will be started Pressing No will abort the procedure The front cover the hinged Plexiglas window that shields the instrument in front can be opened for user intervention 1 Once the maintenance procedure has been started the pipetting arm moves to the left side The operator now has access to the deck to check if cleaning is needed or not e If the deck is clean continue with the daily maintenance e If the deck needs to be cleaned the daily maintenance can be interrupted Instead of the daily maintenance carry out the weekly maintenance 2 Continuing the daily maintenance procedure will lead the user to the next maintenance task The tip waste needs to be emptied Discard tip waste with the rest of the laboratory s contaminated waste N The tip waste has to be considered as contaminated CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 3 For the next steps the maintenance needles are required Figure 26 Maintenance needles 4 The procedure continues with the tightness check of the pipetting channels The pipetting arm will travel to the right side to pick up the maintenance needles Two checks are done with the pipetting channels the over pressure and the under pressure check For the capacitive liquid level cLLD check the needles are picked up again One channel after the other is checked for
10. a version if necessary 9 8 Finishing the Maintenance and Cleaning Carriers must be completely clean and dry before re using Place the magentic separator on the holder right in front of the heater shaker HHS N For the reagent carrier Make sure that the 2 adapters for the tubes are placed in the right position 49 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 10 TECHNICAL SUPPORT If you have any questions or experience any difficulties concerning one of the products please do not hesitate to contact your local Greiner Bio One distributor or directly the technical support department support dx gbo com Greiner Bio One employs a technical service department staffed with experienced scientists with extensive practical and theoretical expertise in molecular biology and on the different oCheck products CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 90 11 TROUBLESHOOTING 11 1 Error Messages Error message Cause Solution Cannot start method xxx The maintenance process has not Start the maintenances method and Daily Weekly maintenance is required been carried out recently follow its instructions See section 10 No input file was loaded or no sample Make sure that a input file is loaded Please select at least one sample is selected and at least one sample is checked Make sure the number of selected samples is less than or equal to 96 Click
11. as the files which have been created during the extraction method So for the above example this would again be the subdirectory C MethodOutput 201 3 11 21_10 26 25 067_E1012ELF0001 24 Similar to the extraction method the file names created by the PCR setup method all start with the date and time of the run of the PCR setup method followed by the barcode of the PCR plate The file names end with one of the following endings Name Meaning GBO_PCR_General xls General information about the PCR run Excel file Information about all pipetting steps i e volumes source and target position GBO_PCR_Report xls etc Excel file The PCR setup method creates the input file for the next run of PCR setup method it is stored in this file GBO_PCRSampleList SMP xls GBO_PCR Worklist APDWLxls PCR_Worklist APDWL xIs Internal worklist nn Information about sample position and result of PCR setup 5 4 5 3 Trace files Additionally you will find trace files in the subdirectory For every run independent whether extraction method or PCR setup method a new trace file is created These trace files contain low level information about every step the CheckExtractor carried out during the run These files are stored for service purposes only They do not contain any information necessary for daily work 5 4 6 Back up For the safety of your data it is highly recommended to back up your data regularly The CheckExtractor does not car
12. be changed frequently especially during DNA extraction e Sample tubes Never touch the inside of a reaction tube cap To avoid cross contamination open only one tube at a time e Pipetting Appropriate micropipette filter tips with aerosol barriers must be used sterile free of DNase RNase and human DNA Pipette tips should always be changed between liquid transfers 2 2 2 General precautions e Upon arrival check the kit components for damage If one of the components is damaged e g buffer bottles contact your local Greiner Bio One distributor Do not use damaged kit components since their use may lead to poor kit performance e Do not use kits after the expiry date e Do not use expired reagents e Do not mix reagents from different batches e Use only reagents equipment provided with the kit and those recommended by the manufacturer e Regular calibration maintenance should be performed for the CheckExtractor see chapter MAINTENANCE and other equipment e g pipettes e Pipetting of small amounts of liquid in the microliter range is a challenge Therefore take care to pipette as accurately as possible e To avoid microbial contamination of the reagents take care when removing aliquots from reagent tubes e Unused reagents and waste material must be disposed of in accordance with federal and state guidelines 2 2 3 Working safely e Always wear a suitable lab coat disposable gloves and protective goggles e
13. of a linear barcode For the requirements of the barcode please refer to chapter BARCODES Attach this barcode to the corresponding sample tube The barcode must be aligned in axial direction i e along the length of the tube The barcode is constricted to 20 aloha numeric characters gt 6 6 2 Filling the sample drawers 6 6 2 1 Preparing the samples During the extraction method the CheckExtractor pipettes the sample from the sample tube into the MASTERBLOCK It is therefore necessary that the samples are easy to pipette Please follow the instructions in the oCheck DNA Extraction Kit CheckExtractor IFU for preparing the samples prior use Avoid the transfer of cell clots since these may plug the pipette tips 6 6 2 2 Setting up the samples in the drawer The system pipettes the samples starting with the leftmost sample drawer track 20 It takes the samples from the rear end of the drawer i e the sample deepest inside the CheckExtractor is taken first Since the scanner is placed on the right side of the sample drawer all sample barcodes must be turned to the right opening in the drawer positions Be aware that the CheckExtractor is able to process any number of samples between 1 and 96 Nevertheless the oCheck DNA Extraction kit CheckExtractor allows only 48 or 96 extractions per run So numbers other than 48 or 96 will cause loss of reagent material CheckExtractor Instructions for Us
14. plate a sealing temperature of 170 C and a sealing duration of t2 0 seconds must be set If one of these values or both are not correct please adjust the values using the A and W keys In order to adjust the sealing temperature press the SET key in the top left corner of the front of the device The currently set sealing temperature appears on the display and flashes The required temperature can then be set using the A and W keys By pressing again the last visible sealing temperature is confirmed and the currently set duration of the sealing procedure is displayed also flashing The duration can now also be adjusted using the A and W keys By pressing again the SET key the duration time is confirmed and stored on the device Wait until the device has reached a temperature of 170 C the actual temperature is constantly displayed In addition to the display this is also identifiable by a beep sound that is heard when the device is ready for use Open the device by pressing the OPERATE key The tray with insert for the PCR plate will open up automatically Remove the metal frame and put the PCR plate onto the insert of the tray Then place the sealing foil Pierce Seal REF 865 804 onto the PCR plate Make sure that the blue line is facing side up 38 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 and that all wells are well covered Place the metal f
15. setup method is set up But Either place the correct elution plate The elution plate on position 2 does an elution plate with a barcode that into the instrument or change the not have the expected barcode does not match the input file was worklist to the one that corresponds loaded to the current elution plate An error occurred while running vector The error description is The method loaded is not validated Call your Greiner Bio One representa File xxx must not be used in routine and has been corrupted in some way tive to reinstall a validated method work File not validated xxx 11 2 Error Codes All pipetting steps are monitored by the CheckExtractor You will find the results of the pipetting step of the Extraction method in the MethodOutput directory of the corresponding run The file name ends with _GBO_EXT_PipettingTracking xls Besucher eingebe i eren nn d Formatie e gt il fe B E D E E G H J K L M N SourceLabwarelD SourceLabwarePosition MainErrorCodeAsp RecoveryAsp VolumeCheck TargetLabwarelD TargetLabwarePosition MainErrorCodeDisp RecoveryDisp VolumeDisp ChannelNumber DateAndTime MaN_VB_10x45_skirted_2200_0001 0 Notchecked ReagentTrough fi 759 1 2015 05 20 11 49 13 MaN_VB_10x45_skirted_2200_0001 0 Notchecked ReagentTroughl 759 1 2015 05 20 11 49 14 ReagentTroughl ReagentTrough1 ReagentTrough1 ReagentTrough1 ReagentTrough1 9 ReagentTroughl IB Add Buffer M1 ReagentTro
16. to the final PCR MasterMix Afterwards the prepared and sealed PCR plate can be placed in the PCR cycler to perform the DNA amplification 5 2 Hardware The CheckExtractor comprises of two parts The CheckExtractor itself and the controlling PC The PC with the graphical user interface GUI guides the user through all the steps that require manual intervention when setting up a run The two devices communicate via a USB connection all necessary data and commands The CheckExtractor carries out the run and either confirms the successful completion to the PC or reports any errors CheckExtractor CheckExtractor lt gt greiner bio one Controlling PC USB Connection Liquid waste Figure 4 CheckExtractor and the controlling PC The CheckExtractor performs both pipetting operations and transport of plates placed on its work surface Pipetting refers to the transfer of small quantities of liquid from one container to another A pipetting operation is achieved by aspirating drawing liquid from a source container then transferring and dispensing dropping it into a target container CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 5 2 1 Deck The CheckExtractor internal work surface is known as the deck The deck is where all the carriers are housed These carriers hold reagent containers such as tubes microplates or other kinds of labware The deck of the CheckExtractor is
17. underlying sealing foil may partially detach from the plate However this is not a problem for taking out PCR products from the PCR plate 39 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 8 SHUTDOWN PROCEDURE 8 1 Regular Shutdown At the end of each day it is recommended to shut down the CheckExtractor N Make sure all reagents samples and plates are removed from the deck 8 2 Decontamination Following is the recommended procedure for decontaminating of the CheckExtractor e Spray the front and side cover with MICROLAB Disinfectant Spray see chapter ORDER INFORMATION e Open the front cover and spray the deck with MICROLAB Disinfectant Spray see chapter ORDER INFORMATION or wipe it clean with a soaked cloth e Remove the tip eject plate of the tip waste station and clean it e Spray MICROLAB Disinfectant Spray directly onto the surface of the tip waste station e Remove the frame that holds the plastic bag in place and discard the plastic bag in the laboratory s contaminated waste Put the tip eject plate back in place e Spray or wipe out the tipwaste drawer e Clean the tip eject sleeve outer part of the pipetting channels with a lint free cloth soaked in MICROLAB Disinfectant Spray See chapter ORDER INFORMATION e Clean all carriers with MICROLAB Disinfectant Spray see chapter ORDER INFORMATION and let them dry If they are heavily soiled soak them aft
18. 5 01 June 2015 4 WASTE DISPOSAL The CheckExtractor is a piece of electrical equipment and therefore has to be treated as such and ultimately disposed of in compliance with all local laws Electronic waste has to be collected and separated following the regulations of the electronic waste act For users in the European Union the directive 2012 19 EU contributes to sustainable production and consumption by the re use recycling and other forms of recovery waste electrical and electronic equipment WEEE This reduces the unnecessary disposal of waste and contributes to the efficient use of resources and the retrieval of valuable secondary raw materials To achieve this goal the members of the EU ensure the correct treatment of all collected WEEE and therefore WEEE is disposed of separately from other items Figure 2 WEEE YN It is necessary to dispose of WEEE separately 4 1 Reagents and samples Guanidine hydrochloride may be in some buffers and can form highly reactive compounds when combined with bleach Bleach or acidic solutions should not be added directly to the sample preparation waste Contamination of the liquid waste with residual infectious material is highly unlikely but cannot be completely excluded Thus liquid waste must be considered infectious and be handled and discarded according to local safety regulations Please carefully follow federal state and local guidelines for waste disposal Liquid waste has to be co
19. CR setup method PCR setup method method Method in which the final MasterMix is added to the eluate in which the final MasterMix is added to the eluate File in which all pipetting steps that were carried out in an extraction run are listed Volu Pipetting tracknmgiiie mes and possible errors are stored here See also Report file Carrier for the MASTERBLOCK the bottle adapter the elution plate and the PCR plate File in which all pipetting steps that were carried out during the run extraction run or Report file PCR setup run are listed Volumes and possible errors are stored here The scheme of the plate is indicated Run Control Part of the CheckExtractor s software that does the communication between the cont rolling PC and the CheckExtractor itself It therefore controls the sequence of the runs Sample carrier Carrier Sample carrier Carrer for sample tubes Sample ID Unique identifier for each sample Tip carier carrier Tip carrier Carrier for the 300 yL tips and the 1000 pL tips 75 for the 300 Carrier for the 300 uL tips and the 1000 pL tips tips and the 1000 uL tips Position or rail on the loading desk All carriers are loaded in at least one of these Track tracks The tracks are numbered Carrier for five reagent troughs CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Carrier for the tubes for the final PCR MasterMix the proteinase K and the magnetic Tube carrier bead
20. DS Be Tea AN een OA SE aT 21 rede AS Naked ee rennen 21 52 22 o A sn eaten tcc amet ua eek Gea nna tenet tes nee ona 22 22 PLEIN A A cee ee eee 22 5 3 Software Graphical User Interface occoonconncccncccnnccncocncocnconnconnconnnnnnrnnnrnnncnnrcnnncnnarannnon 22 SA Sbee F218 6 0511 on Ss ee on a nel ee Ree To nr ee e ll ohne at e RS 24 SAk ANC UU eat ean am an er a ese et ee ee 24 5 4 2 NDS e en ree tre reaper ro ea 24 A 28 34A Maa BACON o o od ee eee at 29 9 2 0 A eee ee eae ee tee ee eee eer eee nee eee hes 29 SA Sel Kell De O 30 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 o PARED SPARES ener Per aia 32 AE as A PA o e o OOO 32 6 2 Required Consumables and Equipment 22u22002n00anunnnunanunnnunnnnnnnnnnnnnnnnnnnnnnnnnnn 32 6 3 Preparation Prior to InstallatiON oocconconcccnnoccccnnoccccnconconnnoncnnncnnrnnncnnnonnnnnrnancnnrnnrnnnnnnns 33 64 Bringing imo ODE UI ascii rre 33 6 5 Installation and configuration ooocconcccncccnnocnnocanecanenanonanonnnonnnonnrnnnrnnnrnnnrnnnrnnnrnnrrnnrrnnrrnnnena 34 66 Preparation Prior to VES lic 34 A ii E E E EAT O EA N 34 6 6 2 Filling the sample drawers ispiicrcecsasceonstestcdersindspiesnszespietienienssadesiveaniaeasneapieaisenesbinrsedancisesncas 34 Rio PREDIO ELROMPI OE nE ee EEE E 35 God o A 35 e A ie Wty gee Pe mene eee pe ee eng fr en ental emer eee 36 6 6 Gro A A Dee 36 7 INSTRUCIONS FOR THE OCHECK
21. Greiner Bio One All rights reserved No part of this publication may be reproduced transmitted transcribed stored in retrieval systems or translated into any language or computer language in any form or by any means electronic mechanical magnetic optical chemical manual or otherwise without prior written permission from Greiner Bio One The information in this guide is subject to change without notice Greiner Bio One reserves the right to change its products and services at any time to incorporate the latest technological developments Although this guide has been prepared with every precaution to ensure accuracy Greiner Bio One assumes no liability for any errors or omissions nor for any damages resulting from the application or use of this information Greiner Bio One welcomes customer input on corrections and suggestions for improvement Microsoft Windows and Excel are registered trademarks of the Microsoft Corporation Microlab is a registered trademark of Hamilton Bonaduz AG The Greiner Bio One Logo the CheckExtractor Logo and oCheck are property of Greiner Bio One All other company and product names might be trademarks of the respective companies with which they are associated Patent no EP 1171240 US 7033543 Hamilton Bonaduz AG Approvals This instrument is in compliance with the following directives of the Council of the European Community and the according standards 98 97 EC 2004 108 EC ISO 13485 2007
22. The kits are for in vitro diagnostic use only and should be exclusively used by personnel trained 12 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 in in vitro diagnostic laboratory practice e Take care whilst handling biological samples containing potential human infectious material To minimise the risk of infection from potentially infectious material it is recommended to work under laminar airflow conditions until sample lysis is completed Handle and dispose all biological samples as if they were capable of transmitting infectious agents e Avoid direct contact with the biological samples as well as splashing or spraying Always wear lab coat gloves and goggles while working with human samples e Never pipette solutions by mouth e Do not eat drink smoke or apply cosmetic products in the work areas e Wash hands carefully after handling of samples and reagents 2 3 Instrument The CheckExtractor conforms to European standards with regards to interference immunity However if the CheckExtractor is subjected to electromagnetic RF fields or if static electricity is discharged directly onto the CheckExtractor its Liquid Level Detection ability may be adversely affected It is therefore recommended that the CheckExtractor is kept away from any other equipment that emits electromagnetic RF fields in the laboratory and that static electricity is minimised in its immediate environment During opera
23. Your for Health greiner bio one WAN WwW NUN ANY Your Power for Health CheckExtractor Instructions for Use For in vitro diagnostic use by professional laboratory personnel only Greiner Bio One GmbH Maybachstr 2 72636 Frickenhausen Germany Made in Germany 865 070 gt greiner bio one Revision BQ 395 01 June 2015 1 GENERAL These Instructions for Use are written for operators of the CheckExtractor using software version 1 1 or higher Due to software evolution slight changes in the dialog boxes displayed in this manual may occur When a modification is made that may have adverse effects on the system using this manual an update or amendment will become available Every effort has been made to ensure that the information contained in this manual is updated and accurate as of the date of issue or revision and it is consistent with the product described However no guarantee is given or implied that the document is error free or accurate with regard to any specifications The instrument manufacturer reserves the right to make changes to this manual without notification 1 1 Intended Use Automated System for the extraction of nucleic acids The system has been validated for the following applications e oCheck DNA Extraction Kit CheckExtractor REF 517070 e PapilloCheck for 288 analyses REF 465088 e PelvoCheck for 288 analyses REF 504288 1 2 Copyright 2015
24. a certified training course Any deviation from the procedures given here could lead to erroneous results or CheckExtractor malfunction 2 3 2 Biological Safety The CheckExtractor is designed to prepare medical samples This implies that the samples may contain infectious material especially viruses Therefore it is mandatory and the responsibility of the laboratory s manager that only trained personnel work with the CheckExtractor and the associated reagents and samples All work has to be carried out in accordance to national regulations Also the disposal of sample material reagents and used laboratory equipment like pipette tips and micro plates needs to follow national regulations It is in the responsibility of the laboratory s manager to make sure that the safety and disposal standards are fulfilled The sample to be extracted and prepared for the analysis in the CheckExtractor are potentially infectious Handle these samples with extreme care to keep you and your environment save 2 3 3 Results and Data Data loss can be a common problem when dealing with computers This may be due to technical problems or user errors Although the CheckExtractor is designed and developed in a way that reduces the risk of data loss to a minimum data loss can never be fully excluded It is therefore highly recommended that you back up your data regularly in particular if the CheckExtractor is not connected to a LIMS see cha
25. ach it Put the clean tip eject plate back in place Do not spray the maintenance needles 5 To prevent unreliable barcode reading check the laser scanner window of the barcode reader and clean it with a lint free cloth or Q tips lightly soaked in Ethanol 70 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 The laser scanner window must be completely dry and free from dust and fibres before the instrument can be reused 6 For the next steps the maintenance needles are required Figure 29 Maintenance needles 7 The procedure continues with the tightness check of the pipetting channels The pipetting arm will travel to the right hand side to pick up the maintenance needles Two checks are carried out with the pipetting channels the over pressure and the under pressure check 8 For the capacitive liquid level cLLD check the needles are picked up again 9 The end of the weekly maintenance program is displayed Weekly maintenance successfu Figure 30 Weekly Maintenance successful Window The weekly maintenance process status is saved on the instrument and a report file is created see the section 12 5 Following the weekly maintenance clean the rest of the instrument as follows 10 Clean the tip eject sleeve outer part of the pipetting channels with a lint free cloth soaked in MICROLAB Disinfectant Spray MULTILINK Figure 31 Cleaning of eject sleeve 47
26. at might appear For the PCR setup method similar data is saved in the file that ends with _GBO_PCR_Report xls 92 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Datei Start Einfugen Seitenlayout Formeln Daten berpr fen y amanenn sas Fo A 3 Kopieren Einf gen E Pe Format u Sample001 Sample002 Sample003 Sample004 Sample005 Sample006 8 Sample00 9 Sample008 WN seqElutionPlate Sample009 J 7 tiv Oy Ary 1 y E1406013001207 Gre_96_VB_PCR_2A1 E1406013001207 Gre_96_VB_PCR_2B1 E1406013001207 Gre_96_VB_PCR_2C1 E1406013001207 Gre_96_WB_PCR_2D1 E1406013001207 Gre_96_VB_PCR_2E1 E1406013001207 Gre_96_VB_PCR_2F1 E1406013001207 Gre_96_WB_PCR_2G1 E1406013001207 Gre_96_YB_PCR_2H1 E1406013001207 Gre_96_VB_PCR_2A2 Figure 34 PCR Report file Steerns nam EL a 337 Yo 000 So E1406013001183 Gre_96_VB_PCR_AI E1406013001183 Gre_96_VB_PCR_B1 E1406013001183 Gre_96_WB_PCA_C1 E1406013001183 Gre_96_VB_PCR_D1 E1406013001183 Gre_96_VB_PCR_E1 E1406013001183 Gre_96_VB_PCR_F1 E1406013001183 Gre_96_WB_PCA_ GI E1406013001183 Gre_96_WB_PCA_H1 E1406013001183 Gre_96_WB_PCR_A2 Sonde ou 5 aaa amm 5 Ok 5 Ok 5 Ok 5 Ok 5 Ok 5 Ok 5 Ok 5 Ok 5 Ok Bee Cercs Coca PTA Enee IZA EEE ooo eo eo oo oo o oo oo oo oo Disp Recovery Recovery SourceSeqName SourceLiquidID SourceBarcode SourceLabwarelD SourceLabwarePosition TargetBarcode TargetLabwarelD TargetLabwar
27. by default This can be achieved by File gt Options gt Save gt Save file in this format For detailed information please refer to your Microsoft Excel manual In the combo box named File name type in the name of the input file This name is up to you The filename is only limited by the parameters set by the Microsoft Windows operating system and must end with EXT starting with a dot and all letters in upper case 1 For example The characters lt gt must not be used 27 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 The file name of the input file for the extraction method must end with EXT An example for the file name of a input file would be ExtractionWorklist48Samples EXT xls 5 4 2 2 Input file for PCR setup method A worklist is also needed for the PCR setup method This worklist is created by the CheckExtractor at the start of the PCR setup method The worklist again is based on an input file that is again a simple Excel file In contrast to the extraction method the input file of the PCR setup method is created by the CheckExtractor itself The file name of the input file for the PCR setup method must end with SMP An example for the file name of a input file would be 2013 12 12_18 07 30 330_E13070BF000561_GBO_PCRSampleList SMP xIs At the end of every extraction run the input file for the correspo
28. ckExtractor Instructions for Use Revision BQ 395 01 June 2015 7 INSTRUCIONS FOR THE oCHECK WORKFLOW For the performance this instruction for use is designed to individually choose the applications you need or you prefer The general part of the instruction for use ends here and in the following Supplements the respective application procedures are described in detail 7 1 General instructions When implementing currently used state of the art techniques in molecular biology into a laboratory the following instructions must be considered to ensure both maximum safety for laboratory staff and high quality results Execution of molecular biology techniques such as DNA extraction amplification and detection of the amplification products require appropriately qualified personnel In addition a clean and well structured workflow is required to prevent erroneous results such as those occurring due to DNA degradation or contamination by amplification products To ensure this it is necessary to separate the areas of extraction amplification and detection as described in Chapter 8 1 2 Each area should be equipped with separate equipment consumables lab coats and gloves Never transfer lab coats gloves or equipment from one distinct area to another 7 2 Room separation It is absolutely necessary to separate the areas of DNA extraction amplification and hybridisation Sample material must not be introduced in the area for setting up
29. ding desk p 1010 mm with loading desk 12 1 2 Distances A minimum amount of space should be left on all sides of the CheckExtractor to allow for servicing operations and ventilation of the system This space should be no less than Side Distance 12 1 3 Enviromental Conditions Parameter Range Operating 20 25 C Temperature Storage 25 70 C Operating 20 80 non condensing Humidity Storage 10 90 non condensing indoor No direct sunlight or other intensive light sources Sunlight Indoor storage only Up to 2000 m above mean sea level Altitude Storage as required for air travel 12 1 4 Operating Data CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Parameter Range Maximum power consumption lt 600 VA Voltage 115 V 230 V Frequency 50 60 Hz 5 Delayed action fuse 115 V 6 3 A T6 3AL250 230 V 3 15 A T3 15A250 Installation Temperature range 15 30 C Relative humidity 15 85 no condensation Noise level lt 65 dBA regarding EN27779 Altitude Up to 2000 m above sea level Wave length 254 nm Power 3 x 30 W The CheckExtractor fulfils the requirements of directive 2004 108 EC EMC UV Lamp 12 1 5 Pipetting Specifications Volume ul Tip Size 300pul Tip Size 1000ul Accuracy Precision 12 1 6 Connectivity The CheckExtractor itself and the controlling PC are equipped with standard USB 2 0 sockets for com
30. divided into equal tracks T for loading carriers in predetermined positions This eliminates the need for precise measurement of positions The tracks are numbered from left to right starting with 1 Figure 5 shows the layout of the deck It comprises from left to right e two carriers of tip racks e one plate carrier for the PCR plate the elution plate the MASTERBLOCK and 10 mL bottles e one reagent carrier for the reagent troughs e one tube carrier for the reagent tubes e multiple sample carriers for the sample tubes e the position for the heater shaker and the magnetic separator and e the waste position Trough Carrier Heater Shaker Plate Carrier F Jar NG 3 ae a Region B Reagent Carrier Sample Carriers Figure 5 Deck layout The tip racks are divided into three tip regions A B and C e Region A 300 uL tips e Region B 1000 uL tips the CheckExtractor will only pick up a complete column of 8 tips at a time from this region e Region C 1000 uL tips the CheckExtractor pick up single tips here The positions on all carriers are numbered from the end that is far inside the CheckExtractor to the front In other words The through or plate positions are numbered in the order in which the barcode scanner sees them 5 2 2 Pipetting The CheckExtractor is equipped with eight 1000 uL pipetting channels These pipetting channels work in parallel for simultaneous transfer of l
31. e Revision BQ 395 01 June 2015 6 6 3 Preparing Elution Plates For the PCR setup method the CheckExtractor takes an elution plate with DNA material extracted previously If the extraction run was carried out right before the PCR setup the elution plate may still be on the plate carrier In this case no further steps are required Alternatively the DNA may have been extracted and stored at 4 C or in a freezer In this situation make sure that the contents of the elution plate is fully thawed and spun down Open the plate no sealing film or cover must be left on the plate Be sure that the elution plate is fully thawed spun down and open before loading it into the CheckExtractor M 6 6 4 Reagent Barcodes All reagents have to be barcoded For details please refer to the IFU of the corresponding extraction kit and oCheck kit respectively Attach the barcode labels to the reagent troughs before starting the run To do so place all needed troughs into the trough carrier Hold the trough carrier in a way that the rounded edge of the troughs faces to the left side Then place the barcode label vertically in the middle of the troughs Be sure to attach the barcodes no closer than 20 mm and 10 mm from the edges of the trough as drawn in Figure 22 Each trough corresponds to a defined reagent Attach the labels in the right order The right order is indicated on the screen when loading the reagent troughs You may also refer to th
32. e IFU of the extraction kit Figure 22 Attach the buffer barcode to the corresponding trough Make sure that the barcode is orientated vertically on the trough and is placed inside the borders indicated see Figure 22 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 6 6 5 Magnetic Separator The magnetic separator must be in place before starting the run Place the magnetic separator on the holder right in front of the heater shaker HHS Please refer to Figure 5 for the exact position of the magnetic separator 6 6 6 Liquid Waste Since liquid waste is generated during the run it is necessary to connect the CheckExtractor to the liquid waste bottle Empty the liquid waste bottle prior to a run before you connect it with the CheckExtractor Follow the local regulations for disposing liquid waste See also chapter Waste Disposal The volume of the liquid waste bottle should last for a few runs The CheckExtractor reminds you to empty the bottle if not enough volume is left for the next run Liquid waste has to be considered as potentially infectious material Dispose this material according local safety regulations Place the lid on the liquid waste bottle Be sure that the hose and the sensor cable are properly attached to the lid and the CheckExtractor If there are doubts about the connections of the hose or the sensor cable call your Greiner Bio One representative Che
33. ePosition WorklistVolumes PipettedWYolumes PipettingStatus MainErrorCodeAsp MainErrorCodeDisp Asp o 00 00 0000 Here the error codes are given in the 12th and 13th column for aspiration and dispensing respectively Description There is a wrong set of parameters or parameter ranges Steps lost on one or more hardware components or compo nent not initialized or not functioning No capacitive signal detected during carrier calibration proce dure Error Code Type No error Syntax Error Hardware Error Calibrate Error Not Executed Error Clot Error Barcode Error Insufficient Liquid Error Tip Present Error No Tip Error No Carrier Error O Execution Error h h Pressure LLD Error NO Not possible to unload the carrier due to occupied loading tray position i eb Unload Error Pressure liquid level detection in a consecutive aspiration is not allowed i gt Pressure LLD Error Dispense in jet mode with pressure liquid level detection is not allowed Cover Open Error Cover not closed or cannot be locked The pressure based aspiration dispensation control reported an error not enough liquid Wash Liquid Error Waste full or no more wash liquid available Temperature Error Incubator temperature out of range Overshot of limits during aspirate or dispense Note 20 TADM overshot On aspirate this error is returned as main error 17 On dispense this error
34. eenaeeeseneeeees 56 TN Sal AAA Ay A 56 Bel SWL ML ne ee ee 56 de DEN een ernennen ee 56 en ae ceo e E 56 12 1 4 SILBER 56 A PIE el eli een ee ee een 57 fas BoM E eE A A 5 2 12 SEN A AAA 57 BE APP er eee E ee ee eet eer eer 58 Be Barcode a A 58 1222 a e es AAA EEE ER 58 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 2 SAFETY INSTRUCTIONS AND PRECAUTIONS 2 1 General Safety Information Please make sure that you have read this user manual carefully and pay particular attention to the safety information before using the CheckExtractor The instructions and safety information in this user manual must be followed to ensure safe operation of the instrument and to maintain the instrument in a safe condition Although the CheckExtractor is developed with all care and tested throughout errors may occur due to various reasons Greiner Bio One does not guarantee the obtained results Any diagnostic result generated using the CheckExtractor should be interpreted in conjunction with other clinical or laboratory findings 2 2 Warnings and Precautions 2 2 1 Contamination prevention e Lab coats must be worn throughout the procedure and different sets of lab coats are required for each laboratory room e Lab cleanness The working place must be decontaminated with DNA AWAY or any other appropriate cleaning solution before and after work e Gloves must be worn during each step of the analysis and must
35. electa report and press the Open button The Report Viewer displays the selected report file 4 Goto File gt Print to print the report file CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 9 6 If Maintenance Fails If an error is encountered during a maintenance procedure try to resolve the problem and restart the maintenance procedure If you cannot resolve the error yourself call your local service representative 9 7 Further Maintenance and Service Because the CheckExtractor is an IVD accessory it is compulsory to keep the instrument always in optimal condition This guarantees the highest reliability of the results of the CheckExtractor It is therefore mandatory to regularly service the instrument A built in timer locks the instrument if service has not been performed on the instrument in the previous 200 days has not been serviced within the previous 200 days N Make sure to service your CheckExtractor on time The CheckExtractor will be unusable if it Please be sure to contact your local service representative on time for the next service The service includes e cleaning and lubricating the guides e checking parts that are subject to wear and tear e checking of the pipetting and liquid system checking of the functioning of the instrument checking of the positioning of all moving parts adjustment if required Installation of software and firmware updates within
36. erwards in a solution of MICROLAB Detergent and Disinfectant See the product data sheet for further information Use the UV light 8 3 Using UV Light To assist the decontamination processes the CheckExtractor is equipped with an UV light since UV light destroys DNA It therefore makes sense to decontaminate the deck by using UV light at the end of each day Make sure the CheckExtractor is unloaded after the last run The tips may stay on the deck UV light may be harmful to the reagents Therefore please remove all reagents before using the UV light To start the decontamination of the deck using UV light close the front cover with the UV cover Place it in the opening of the front cover by holding the UV cover horizontally by the handles and with the two catches towards the CheckExtractor Hook the catches under the front cover Move the lower edge of the UV cover downwards and towards the CheckExtractor until closes and seals the front of the unit UV light is harmful to your eyes and skin Never start the UV light before the front cover is tightly closed with the UV cover CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Double click the icon for the UV light which lays on the desktop A warning reminds you to close the UV cover and to wear suitable clothing Follow the in structions and press the OK button To test whether the UV light bulb works the UV light will turn on
37. ese routines must be executed at the next start up If any parts of the instrument carriers or racks have become contaminated the weekly maintenance procedure must be performed immediately 93 Materials required e Disposable latex gloves e Protective glasses e Lab coat e Paper towels e Lint free cloths or Q tips e Ethanol 70 Do not use to clean the cover e De ionized water e MICROLAB Detergent amp Disinfectant see chapter ORDER INFORMATION e MICROLAB Disinfectant Spray see chapter ORDER INFORMATION Do not use disinfecting materials which contain hypoclorite Javel water Chlorox or bleaching fluids Prepare disinfectant fluids according to manufacturers guidelines f Use cleaning disinfecting and decontaminating fluid in accordance with manufacturer s instructions 9 4 Maintenance Procedures The operator will be guided by the CheckExtractor software through the maintenance procedures To execute a maintenance procedure double click the following icon on the desk top In the Hamilton Maintenance and Verification Run window the process status information view lists all maintenance and verification processes for the connected selected instrument It is from here that all the maintenance procedures can be initiated 43 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 File NN Preen a Instrument Microlab STAR WD Global mandatory flag mandaton
38. ferent sizes of tips on the same pipetting head in the same run e Picking up a gripper and other tools e Eliminating aerosol production upon tip ejection Do not use any tip types other than the Hamilton CO RE tips Other tips may not be mounted correctly and may lead to erroneous results 5 2 3 Gripper The CO RE Gripper is the plate handling tool that is picked up by two pipetting channels during a run The CO RE Gripper transports the different plates MASTERBLOCK Collection Block and Elution plate to and from positions on the deck of the CheckExtractor E JE Ps al Figure 9 CO RE Gripper 5 2 4 Heater Shaker The Heater Shaker HHS is designed to heat and shake microplates that conform to the SBS format Loading and unloading as well as the independent heating and shaking function of the HHS is under control of the CheckExtractor software Before shaking the microplates are locked into position in the center of the HHS When the shaking process has finished the microplates are unlocked and can be easily removed from the heater shaker using the CO RE Gripper 21 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Figure 10 Heater Shaker HHS 5 2 5 Barcode Scanner The red instrument on the right side in the housing is the barcode scanner Every time the autoload loads a drawer into the CheckExtractor M the barcode scanner is moved into position adjacent to the drawer Since a
39. for approx one second During the check of the UV light Avoid exposure to UV light Exposure may cause severe eye or skin injury Wear suitable face shield gloves and protective clothing Make sure that the UV cover is placed in the correct position to completely close the instrument before switching on the UY lights Press OK to test the UV light Please confirm with Yes if the UV light is working If no press Cancel and call your Greiner Bio One representative for further instructions Check UV light result confirmation gt Have you seen the UV light flashing Yes UV light ts working Mo Retest the UV light Cancel Aborts the run Ys Cancel You will then be asked for the duration of the decontamination cycle and if any delay should be applied Insert these two times in minutes and press the OK button A decontamination time of 30 min is recommended UV light timer Please set the decontamination duration and delay timer for the UV light in minutes Decontamination duration minutes 0 E Time to wait before decontamination starts 10 minutes 41 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Before starting the UV light make sure that the pipetting arm of the CheckExtractor can move freely Doublecheck the tightness of the UV cover and your personal UV protection Then start the UV light by clicking the OK button During the UV decontaminatio
40. ge Cause Solution Not enough 1000 ul tips for less than en Load a sufficient number of tip racks There are not enough tips in region C 8 channels were loaded into the instrument The carrier which is to be loaded is Please slide the carrier carefully on either not on the loading desk or is the loading desk until your feel a not inserted correctly mechanical stop Double blind entry failed vinen ed Ba ata manualy Re enter the barcode in both fields the two entries are different The extraction plate is missing A While loading the plate carrier no Unload the carrier insert the extrac reload of the carrier is required extraction plate was detected tion plate and reload the carrier again The loaded carrier is not the carrier Make sure to load each carrier at its Wrong carrier type detected en expected specific track number Not enough buffer xx was loaded in Trough xx does not contain enough Refill the trough trough xx buffer for the run Carrier xxx not found on the loading tray Too much Buffer M1 was loaded in Since M1 is mixed with the protei Reload the trough 1 with the exact trough 1 A reload of the carrier is nase K it is compulsory to provide a amount or Nt required precise amount of M1 to the system Error while creating PCR input file PCR input file is corrupted areal Greiner Bio One represen Unable to update general file General file is corrupted e Greiner Bio One represen A PCR
41. ge of the elution plate For storage at lt 20 C the elution plate has to be closed after unloading from the CheckExtractor Close the elution plate after removal from the device by attaching a Greiner Bio One adhesive foil Silver seal 80 0 140 MM REF 676 090 Press it firmly onto the surface of the plate Store the plate at lt 20 C It is recommended to use the Greiner Bio One adhesive foil Silver seal REF 676 O90 for storage of the elution plate as it can easily be removed from the plate if the plate has to be reused for a PCR setup using the CheckExtractor But it is also possible to use the sealing procedure described for the PCR plate to close the elution plate 7 3 2 Sealing of the PCR plate After the unloading procedure of the CheckExtractor the PCR plate must be sealed before transferring it to the PCR cycler For this purpose a sealing foil Pierce Seal REF 865 804 is welded onto the PCR plate using a heat sealer Model 4S3 REF 865 802 This procedure is described in Figure 24 Turn on the heat sealer using a switch at the rear part of the housing Turn it on about 5 minutes prior to use to ensure that the required sealing temperature of 170 C can be reached Check the programmed sealing temperature and duration of the sealing procedure by pressing the SET key 1x the sealing temperature is displayed 2x the duration of the sealing procedure is displayed For the correct sealing of the
42. hapter MAINTENANCE if it was in a laboratory environment with infectious or hazardous materials The CheckExtractor must be repacked in the original shipping crate only by an authorised service technician contact your local Greiner Bio One representative There must be no containers or tips on the CheckExtractor during transportation The service technician and the laboratory share the responsibility for the installation qualification IQ and the operation qualification OQ i e verification and training The process qualification PQ is the sole responsibility of the laboratory CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Only original Greiner Bio One CheckExtractor specific parts and tools may be used with the CheckExtractor e g carriers racks CO RE tips and waste containers A breakdown of the power supply during a run may cause the loss of data If data loss is unacceptable use an independent power supply or an Uninterruptible Power Supply UPS 2 3 1 Operating the Instrument When using the CheckExtractor Good Laboratory Practices GLP must be observed Suitable protective clothing safety glasses and protective gloves must be worn particularly when dealing with a malfunction of the instrument where the risk of contamination from spilled liquids exists Any persons operating the CheckExtractor and the controlling PC which runs the CheckExtractor software must have attended
43. he item Format Cells See Figure 15 meh File Home Imt Pape Layout Formulas Data Review View Cut Ja Copy u xa u e Wir Tet General o Alignment Ti pl el E Paste Special insert Delete Clear Conterits Figure 15 Select the item to format the cells as text CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 25 3 When the item Format cells is selected a window appears Activate the first tab named Number and select in the list Category the item Text See Figure 16 740 e TANSO E rer y ee Be TE G 7 NA N nite Eat B SR men A Text format cells are treated as text even when a number is in the cell The cell is displayed exactly as entered Figure 16 Format cells as Text 4 Finish the steps by clicking the OK button In the next step rename the first and active spreadsheet It is mandatory to name this spreadsheet Samples To rename the spreadsheet double click its name in bottom left corner The name it is normally Sheet1 is highlighted Type in Samples and confirm your input by clicking in an arbitrary cell in the spreadsheet Figure 17 Figure 17 Rename the Spreadsheet into Samples The spreadsheet is now correctly formatted for your input file The first row of the input file has to contain the four entries see Figure 18 SamplelD SampleBarcode BP Desc
44. iquids and support pipetting with disposable tips The Dynamic Positioning System DPS of the CheckExtractor moves each pipetting channel independently on the y Axis as well as the z Axis Each channel uses its own high precision motors 19 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 and electronics to reach any position on the deck gt 2 T w Gd a E P y u de i 3 BE ET F Figure 6 Pipetting tips The CheckExtractor is based on the air displacement pipetting principle Air displacement means that the liquid is aspirated into and dispensed from a disposable tip or needle by the movement of a plunger Between the plunger and the liquid surface is air No system liquid of any kind is involved in the pipetting procedure Plunger Barrel Tip Figure 7 Air displacement technology The first task for the CheckExtractor Pipettor is to pick up a disposable tip Due to the unique compression induced O ring expansion CO RE technology precise tip attachment and positioning is achieved The system requires no vertical force for tip attachment or tip ejection thus eliminating mechanical stress and improving overall system reliability along with pipetting soeed and capability 20 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Figure 8 Figure 7 Co Re technology The principle of the CO RE technology has the following advantages e Allowing dif
45. is returned as main error 4 Labware Gripped Error Labware already gripped CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 k O1 Parameter Error O N Improper Aspiration Error Error Code Type Description 2 Labware Lost Error Labware lost during transport Illegal target plate position Cannot place plate plate was gripped in a wrong direction Illegal Intervention Error Cover was opened or a carrier was removed manually Undershot of limits during aspirate or dispense Note 26 TADM undershot On dispense this error is returned as main error 17 On aspirate this error is returned as main error 4 je Beer seem tere The labware to be loaded was not detected by Autoload No Labware Error modus Unexpected Labware Error The labware contains unexpected barcode may only occur on a Reload Carrier step 108 fwrong Labware Error The labware to be reloaded contains wrong barcode Barcode Mask Error The barcode read doesn t match the barcode mask defined The barcode read is not unique Previously loaded labwa 110 Barcode Not Unique Error re with same barcode was loaded without unique barcode check Barcode Already Used Error The barcode read is already loaded as unique barcode it s not possible to load the same barcode twice n2 Kit Lot Expired Error Kit Lot expired A Barcode contains character which is used as delimiter in 113 Delimiter Error result string
46. ll disposables and samples in the drawer are labelled with a barcode the barcode scanner registers all these components This allows the CheckExtractor M e Confirmation of the presence and correct positioning of all reagents e Confirmation of the number and position of all samples throughout the extraction process e Complete traceability of all the samples through the extraction process e Monitoring of the PCR and elution plates e Mapping of the sample position from plate to plate 5 2 6 UV light The CheckExtractor is equipped with a UV light This UV light helps to decontaminate the desk The UV light bulb is situated inside the housing The housing itself is UV resistant to protect the user and the environment against UV radiation Please use the UV light during shutdown see chapter SHUTDOWN PROCEDURE or maintenance 5 3 Software Graphical User Interface The Graphical User Interface GUI has been designed to guide the user through the entire process is easy to understand and self explanatory To start the GUI just a double click on the CheckExtractor icon on the desktop is necessary Figure 11 CheckExtractor icon on desktop After the double click on the desktop icon the GUI start screen appears where you can choose which program Sample Transfer optional Extraction or PCR setup the CheckExtractor should perform The GUI guides you through the information needed to start the run 22 CheckExtractor
47. mouse pointer besides the tips press the left mouse button and drag the mouse pointer Release the mouse button to toggle the marked tips e To remove all tips in the tip editor press the Remove All button e You can zoom in or out by turning the mouse wheel When the marked tips in the tip editor corresponds with the real situation click the OK button Always load full tip racks only 5 4 4 Manual Barcodes Entry In the unlikely event that a barcode is destroyed and not readable anymore it is possible to manually type in the barcode To do so position the cursor by clicking in the box where the barcode needs to be A window comes up with two entry boxes see Figure 21 Type in the barcode in the upper box and press the return key on your keyboard For confirmation type in the barcode again in the lower box While you type the barcode in the lower box the barcode in the upper box will be hidden This double blind entry makes sure that no typing errors will corrupt the database of the LIMS Load Carrier Error e e Insert Barcode Position 1 Enter barcode Confirm barcode Figure 21 Popup window for manual barcode entry 5 4 5 Data Management For each run the CheckExtractor generates different output files which contain all the information that relates to that particular run All the files from one run are stored in one individual subdirectory And all these subdirectories are stored collectively in the direc
48. mple028 4121300010053 30 sample029 4121300010054 31 sample030 4121300010055 PP int RETE TOOLE TE M4 gt M Sheeti lt Sheet2 lt Sheet3 93 Figure 18 Example for a input file When finished save the input file on the controlling PC It is necessary to save the input file in the Excel 97 2003 format i e with the extension xls Do not use the Excel 2010 format xlsx The input file needs to be saved in Excel 97 2003 format xls Do NOT save input files in the Excel 2010 format xlsx Therefore always use the Save As option in the File menu In the dialog click on the drop down menu named Save as type Choose the item Excel 97 2003 Workbook CO el ji New folder Organize v New folder FA Microsoft Excel 3X Favorites SB Libraries jE Computer G Network File name ExtractionWorklistd8SamplesEXT a OC Ab Excel Workbook Excel Macro Enabled Workbook Tags Excel Binary Workbook Title TEN ERTEILEN Subject XML Data Single File Web Page eb Page Company Excel Template Categories Excel Macro Enabled Template Comments Excel 97 2003 Template Text Tab delimited Unicode Text XML Spreadsheet 2003 Microsoft Excel 5 0 95 Workbook a Hide Folders CSV Comma delimi Formatted Text Space delimited Text Macintosh Figure 19 Save the input file in the Excel 97 2008 format Manager It might be helpful to save data in the Excel 97 2003 format
49. munication between the two devices The PC has additional USB sockets which can be used to connect external data storage devices like USB sticks for the back up of data or the importing of input files The CheckExtractor can be integrated into a LIMS via the ethernet RJ45 connector on the PC 12 1 7 Instrument Life Span The instruments have been designed for a lifespan of 6 years under the assumption that the user maintenance and preventative maintenance is performed at the appropriate intervals may lead to false results Return the instrument to your supplier after 6 years N The maximum lifespan of the CheckExtractor is limited to 6 years Working with an older instrument CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 12 2 Barcodes 12 2 1 Barcode Specifications Lancione Maximum 20 characters excluding start stop and check characters depending on the code 9 9 length see label dimensions Minimum module width X dimension including a print tolerance gt 0 1651 mm 0 0065 Maximum module width X dimension including a print tolerance lt 0 508 mm 0 02 Best reading performance with X dimension 0 254 mm 0 01 Code Density Tolerance IN CEI IN IN CI IN IN E TETTT TI CI IES CI 7D The barcode print must be of a high quality A printed barcode with an ANSI CEN ISO grade A or B is required Offset typographic intaglio and flexographic printing are suitable Mecha
50. n process the pipetting arm will move Please ensure that no collision can take place Avoid exposure to UV light Exposure may cause severe eye or skin injury Wear suitable face shield gloves and protective clothing Make sure that the UV cover is placed in the correct position te completely close the instrument before switching on the UV lights 42 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 9 MAINTENANCE 9 1 Introduction The CheckExtractor is designed to require a minimum amount of maintenance by the user However to preserve the accuracy and reliability of the instrument the following preventive maintenance procedures must be performed on a regular basis according to the maintenance schedules given below Periodic maintenance routines need to be run in order to ensure safe and reliable operation of the CheckExtractor and its accessories Since the CheckExtractor is an IVD accessory the maintenance routines are mandatory 9 2 Maintenance Intervals In order to maintain the CheckExtractor in good working condition the following maintenance intervals should be observed Daily Recommended before CheckExtractor start up or shut down Weekly Recommended at the end of the week before CheckExtractor shut down Six monthly Preventive service maintenance carried out by a service technician If the operator decides not to run either daily or weekly maintenance before shutdown th
51. nding PCR setup is stored in the output directory see chapter DATA MANAGEMENT Likewise the PCR setup method creates a input file for a subsequent PCR setup run i e if you choose to re run a elution plate the input file is already stored 5 4 3 Tip Editor During every tip loading step the tip editor window comes up see Figure 20 For each tip region A B and C see Figure 5 Deck Layout the tip editor appears separately The tips which are expected to be present on the deck are shown in brown Normally this situation is correct since the CheckExtractor tracks which tips have been used Nevertheless check the tip situation before every run to avoid an abort of the run due to insufficient tips Set the first and the last position of the tip sequence as the actual current and count position of the tip sequence respectively tano positions First last Remove Al 1 senso0uUms BT AT is gt Reset Remove All EJ fey Figure 20 Tip Editor CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 If the tip positions displayed on the screen do not correspond with the real situation on the deck you can edit the CheckExtractor software using one of the following methods e To add or remove tips click on the tip position in the tip editor The colour of the tip toggles between brown and white i e tip in place to no tip in place e To toggle more tips at once position the
52. nical dot matrix and thermo matrix printing are not suitable The surface may be treated sealed or plastic coated Print quality 12 2 2 Sample Barcodes ep tte S u L 036 871 7 AS Figure 35 Barcode dimensions Dimension Min Max caze EC S bww em S Ecodewan CO o FDstanoe mom ode totes O OOO i O O CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Figure 36 Tube barcode The label must be attached within a range of between 20 mm to 65 mm from the bottom of the tube The label must fit tightly at an angle of approximately 90 to the tube s axis The label must fit tightly over its whole length CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 99
53. nsidered as potentially infectious material Dispose this material according local safety regulations Further information can be found in the instructions for use of the Greiner Bio One oCheck DNA Extraction kit CheckExtractor and the appropriate oCheck kit CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 5 SYSTEM DESCRIPTION 5 1 System Overview greiner bio one NENNEN DENN hee Vesna e e a e e e ie E y daa A A g WN VA A NS SA ABA Valois NARA DASS ia How ph fp ae Figure 3 The CheckExtractor The CheckExtractor is a fully automated system for DNA extraction from patient samples and the subsequent preparation steps necessary for PCR based diagnostic tests Especially designed for the use with the oCheck products from Greiner Bio One e g PapilloCheck and PelvoCheck CT NG it offers a maximum in reliability a high throughput combined with a marginal hands on time The CheckExtractor is based on superior air displacement pipetting technology This increases accuracy and repeatability while providing chain of custody with pipette condition monitoring and recording The CheckExtractor is configured with one arm consisting of an 8 pipetting channel and one gripping device The auto load option provides barcode tracking of samples lab ware racks and carriers The purpose of the instrument is to perform the follo
54. ode in the respective columns The barcode can although be scanned with the handheld barcode scanner If the input file is created manually please observe the following instructions Your LIMS has to follow the instructions as well A template of the Excel file is already installed on the controlling PC Nevertheless in the case this template is missing the following instructions guide to a functional input file CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 All data is treated as text in the worklist soreadsheet in Excel so ensure all cells are formatted as text This is especially important when sample ID or barcodes start with zeroes e g 0012345 Make sure all columns in the Excel file are formatted as Text To enable this text formatting 1 Select all cells by either clicking in the topmost left corner of the spreadsheet i e the area above the row numbers and left to the column headings or press on the keyboard simultaneously the Ctrl key and the A key All cells are highlighted or coloured See Figure 14 Di gq a E bid wy F Qu i edea Sr y Bi ae PT ad aad a a ee nn TE u Te Pee aT ore a e AS Ten u Ka Copy Paste B Er ze ce Format Painter T kerm En Clipboard F F Alignment Figure 14 Select all cells 2 Click the right mouse button on the heading of the first column i e the grey area marked A A menu appears Select t
55. on the green tick to deselect the sample Please specify a user id me walle InpLL BOX JESOES teen Please fill in your user ID ID is empty Position the cursor in this box and scan the kits barcode or enter it manually Expiry day of extraction kit must be in The kit is expired Wes oie the future Enter the expiry date of the kit in this box or move the cursor in the Bar code Ref box an scan the barcode You selected more than 96 samples Please deselect some samples in More than 96 samples are selected order to start the run Please specify an extraction kit The white input box besides Bar barcode code Ref is empty Please specify an extraction kit expiry The white input box besides Expiry Date is empty Enter the lot number of the kit in this box or move the cursor in the Bar code Ref box an scan the barcode Cover not closed The front cover is still open Close the front cover The liquid waste cap switch indicates that it is not fastened on the bottle or The sensor at the liquid waste bottle the cable is not plugged in Please does not give a signal check the bottle and the cable Please specify an extraction kit lot The white box besides the tack Lot number Number is empty Check that the bottle top is closed and the cable is connected on both ends The liquid waste bottle is full and has The liquid waste does not have Please empty the liquid waste bottle
56. ough tips The number of requi missing tips in the tip editor red tips is denoted by the software Run stopped un expectedly and all The front cover was opened during Do not open the front cover before you are asked to samples are marked the run clean up the desk with an error PCR setup errone Elution plate was not correctly pre ous pared While registering the sample IDs in the Excel spreadsheet leading zero es are vanish a zen Not enough sample volume 900 ul of sample are necessary to process the sample The liquid level detection found a wrong volume or the tip touched the bottom of the sample tube Make sure all columns in the Excel file are formatted as Text Sample ID not cor rect in the worklist Sample was not extracted Be sure that the sample tube is inserted firmly and all the way down into the drawer Uncontrolled or Strong electromagnetic RF fields in unpredictable be terfere with the CheckExtractor RF haviour sources may be mobile phones Do not place the CheckExtractor close to equipment that emits electromagnetic RF fields 11 4 Assistance For further information please contact your local Greiner Bio One representative 95 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 12 TECHNICAL SPECIFICATIONS 12 1 Physical Properties 12 1 1 CheckExtractor Dimension Value Width 1124 mm Depth 795 mm without loa
57. perating the CheckExtractor For special training contact your local Greiner Bio One representative All maintenance steps have been carried out according to chapter MAINTENANCE Only Greiner Bio One Extraction kits Greiner Bio One oCheck kits and approved accessories are loaded into the Check Extractor see chapter ORDER INFORMATION Samples are put into the CheckExtractor in the defined sample tubes See chapter ORDER INFORMATION Follow the instructions of the relevant Greiner Bio One Extraction kit and Greiner Bio One oCheck kit The CheckExtractor does not include any controls Positive and negative controls must be inserted in the runs like ordinary samples CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 6 5 Installation and configuration The CheckExtractor when delivered to a customer is set up by a technician from Greiner Bio One or one of its representatives Everything that is required for a successful installation of the CheckExtractor is carried out by this technician Do not unpack and install the CheckExtractor yourself Special training is needed Unpacking and installation of the CheckExtractor by any unauthorised personnel will result in loss of warranty 6 6 Preparation Prior to Operation 6 6 1 Samples 6 6 1 1 Sample Barcode Each sample needs to be equipped with a unique identification code It is recommended to print this unique code in form
58. pter BACK UP The back up of data is in the sole responsibility of the laboratory s manager Back up your data regularly CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 3 SHIPMENT AND STORAGE The CheckExtractor when delivered to a customer is set up by a technician from Greiner Bio One or one of its representatives Everything that is required for a successful installation of the CheckExtractor is carried out by this technician Do not unpack and install the CheckExtractor yourself Special training is needed Unpacking and installation of the CheckExtractor by any unauthorised personnel will result in loss of warranty Nevertheless please check the outside of the packaging for any damage If you find any damage please contact your Greiner Bio One representative immediately The CheckExtractor is delivered on two pallets Store them closely together to have both readily available for the installation Figure 1 CheckExtractor when delivered Parameter Range Temperature range 25 C 70 C Relative humidity 10 90 no condensation indoors Indoor storage only Be aware that the CheckExtractor is delivered on two pallets with a weight of approx 260 kg The pallets have approximately the dimensions given in the following table Dimension Pallet Pallet Il Weight 220 kg 40 kg CheckExtractor Instructions for Use Revision BQ 39
59. rame on the top of the plate e Close the device by pressing again the OPERATE key The tray will then close automatically and the sealing procedure starts e After the sealing procedure the tray opens again automatically First remove the metal frame and then the sealed PCR plate After removal of the PCR plate the device can be closed by pressing the CLOSE key To avoid bending the metal frame it is recommended to keep the frame inside the device When closed the device can be turned off anytime using the power switch at the rear part of the housing Turn on the heat sealer 5 minutes prior to use Use sealing temperature of 170 C and duration of t2 0 seconds Press OPERATE to open device Remove the metal frame and put the PCR plate onto the insert of the tray Place sealing foil Pierce Seal REF 865 804 onto the PCR plate Place metal frame on top of the plate Press OPERATE Remove sealed plate press CLOSE Turn off sealer Figure 24 Sealing procedure using a heat sealer 7 3 3 Reclosing of the PCR plate After performing the hybridisation the PCR plate can be resealed and stored again at lt 20 C e Close the PCR plate by attaching a Greiner Bio One adhesive foil Silver seal REF 676 090 Press it firmly onto the surface of the plate Store the plate at lt 20 C The adhesive foil is stuck directly onto the sealing film When removing the foil it is possible that the
60. ription SampleMatrix Under these titles the information for each sample is given While the columns Description and SampleMatrix are optional the first two columns SamplelD and SampleBarcode are compulsory they have to be filled in 26 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Page Layout Formulas Dota Rewew View u AR E a V Wrap Text T Good 2 i AutoSum 4 nie Fill A Er A gt FED RR Biere Center gt yo YB 23 Conditional For check Cell Explanatory Input Linked Cell sert Delete Format Formatting as Table rre E Chpbosd ont Alignment A Number Styles _ ES PARA fe 4121300010060 C SampleBarcode Description SampleMatrix 2 sample001 4121300010022 3 sample002 4121300010023 4 sample003 4121300010024 5 sample004 4121300010026 6 sample005 4121300010027 7 sample006 4121300010028 8 sample007 4121300010029 9 sample008 4121300010030 10 sample009 4121300010031 11 sample010 4121300010032 12 sample011 4121300010033 13 sample012 4121300010035 14 sample013 4121300010036 15 sample014 4121300010037 16 sample015 4121300010038 17 sample016 4121300010039 18 sample017 4121300010041 19 sample018 4121300010042 20 sample019 4121300010043 21 sample020 4121300010044 22 sample021 4121300010045 23 sample022 4121300010046 24 sample023 4121300010047 25 sample024 4121300010048 26 sample025 4121300010049 27 sample026 4121300010050 28 sample027 4121300010052 29 sa
61. ry out data back ups It is the sole responsibility of the user or lab personnel to initialise the back up process CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 It is the sole responsibility of the user to back up all data on a regular basis Please use the functionality of the Microsoft Windows operating system or your LIMS for the back up Save all the files discussed in chapter DATA MANAGEMENT for a complete back up including the trace files l e back up the complete directory C MethodOutput 31 CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 6 PROCEDURE 6 1 Order Information Equipment Greiner Bio One Cat No Quantity CheckExtractor 865 070 Line cord USB cable Keyboard Mouse v O Hand held barcode scanner 6 2 Required Consumables and Equipment Consumables Greiner Bio One Cat No Quantity box oCheck DNA Extraction Kit for CheckExtractor for 288 analyses PapilloCheck for 288 analyses PelvoCheck CT NG for 288 analyses 1000 uL pipette tips 3840 300 uL pipette tips 5760 Sample tubes 1000 Caps for the sample tubes 1000 Reagent troughs 60 mL PCR and elution plate MICROLAB Detergent amp Disinfectant MICROLAB Disinfectant Spray gt oO bd oO OO i O O Equipment Greiner Bio One Cat No Quantity box Magnetic separator Adapter for heat sealer Plate centrifuge CheckExtractor Ins
62. s MO Unique identifier for each user Following IVD and FDA formalities it is mandatory that User ID every user who works with the CheckExtractor has to log in with its own unique user Protective cover with handles which is used during UV light decontamination Worklist List with samples to be processed CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 TABLE OF CONTENTS dl Re rar 3 14 as UL A PI o io PS een 3 o g see te see ec ns cise maeine weenie EEE SUR E 3 EI WV Shel aia iia 3 LI TELAS USCA NA CANS MISMA aan an o Ea 4 O a A A Eee 6 1 4 2 Name and Description of Components Overview ccccsccecseeeceeeeceseeceeeeseeeessusesseeeeseneees T 2 SAFETY INSTRUCTIONS AND PRECAUTIONS 22002000a200an0nanunnnnnnnnun nun ann 12 2 lo General male Uy Ihformallon ee eee eee ie eee ee eee ere epee i 12 2 2 Waminas and Precautions vr endende bene 12 A A es er are 12 2 227 Geer all ple alten Se ee 12 2A ITANONG Saray N a et NOE 12 A O O O On 13 23 1 Operating inc qi Mi o o eo ed el ep Ed 14 29322 A i Nat ee Nth Re EEE tae i ds 14 A RESULS AMG D Abel uiiee reve ser tarot N ee 14 32 SHIPMENT AND STORACE a asia 15 4 As auceh nt revanmarsuanwacncsermokeeaeesneenectecnshwaneeumweaseeaaes 16 4 1 Reagents and samples no een an 16 E A LION a 17 SO ee ee ee 17 Sal ai e ee 18 S2 A Up ee eine 18 A a Lp ANG PER DEREN E ANBIETET PERPREREURGRRE ENT AR 18 Bed DECKE ee 19 22 IDEN ER 19 AI
63. te in which the extraction steps are carried out The solution containing the oCheck PCR MasterMix mixed with the enzymes DNA po Final MasterMix lymerase and UNG a ron Peace PPOR The mix of the final MasterMix and the eluate ready for the PCR reaction mix l E o Heater shaker HHS o the deck that heats up the MASTERBLOCK and also shakes it for mixing Input fle file Inputfle Excel file with samples to be processed Liquid waste All liquid material that requires disposal Liquid waste bottle waste bottle Liquid waste bottle Container which collects the liquid waste Platform at the front of the CheckExtractor on which the carriers are placed to be Loading deck loaded Kaane separstor Plate with 24 magnets required for the separation steps The magnetic separator must 9 p be placed in the CheckExtractor on the position shown in Figure 5 Script or program which defines the steps the CheckExtractor has to carry out and the Method z amounts of liquid to pipet i E g oCheck PCR MasterMix oCheck PCR MasterMix is delivered in the oCheck assay without the enzymes DNA and final PCR MasterMix polymerase and UNG Therefore the final PCR MasterMix contains oCheck PCR Mas terMix HotStarTaq Polymerase and Uracil N Glycosylase PCR plate Barcoded PCR plate which will contain the final PCR reaction PCR setup S of the PCR including preparation of the final MasterMix and the PCR setup P
64. the final PCR MasterMix Figure 23 shows an example of how a laboratory may be separated into 3 distinct sections Figure 23 Room separation Room 1 is designated for DNA extraction with the CheckExtractor and the processing of the PCR plate The setup of the PCR reaction mix should be carried out in room 2 the preparation is optimally performed in a protected surrounding e g a PCR hood to avoid reaction contamination The prepared MasterMix is transferred back to the CheckExtractor in room 1 for performing the PCR setup In room 3 the hybridisation washing drying and the analysis of the processed oCheck chip using the CheckScanner and CheckReport Software is performed Each room is used exclusively for the application or technique indicated to prevent sample contamination The use of colour coding could be advantageous in avoiding the accidental exchange of equipment and consumables between areas CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Neither equipment nor consumables should be interchanged between the different laboratory rooms and spaces Hence duplications in equipment and consumables are a necessity and have to be taken into account 7 3 Sealing and storage of plates In this chapter the sealing of the plates is described in order to store them at lt 20 C Nevertheless it is recommended to perform the PCR immediately after the extraction 7 3 1 Sealing and stora
65. the proper functioning of the cLLD The end of the daily maintenance is displayed Daily maintenance execute successfully completed Figure 27 Daily Maintenance successful Window The daily maintenance process status is saved on the instrument and a report file is created See the section 12 5 If any parts of the instrument carriers or racks have become contaminated the weekly maintenance pro cedure must be performed 9 4 2 Weekly Maintenance The following tasks are carried out by the weekly maintenance Cleaning the deck and carriers Checking the condition of the carriers Empting and cleaning of the tip waste Checking the tightness of the pipetting channel Verifying the functioning of the cLLD Cleaning of the pipetting head stop disk O ring tip eject sleeve Cleaning of the covers Autoload protecting ribbon After initialisation of the instrument the operator will be asked to execute the weekly maintenance CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Weekly maintenance deck and tip waste Do you want to execute the weekly maintenance for deck and waste es Figure 28 Weekly Maintenance Window When the instrument is initialised the weekly maintenance program advises the user to unload the deck manually This step is carried out automatically by the Autoload 1 Clean all carriers and with the MICROLAB Disinfectant spray or a cloth that is soaked with
66. tion the CheckExtractor must be shielded from direct sunlight and intense artificial light The instrument should be positioned in the laboratory such that personnel have access to the front and sides of the instrument for operation maintenance opening and removal of protective covers To calculate how much room is needed consider the dimensions of the instrument See chapter TECHNICAL SPECIFICATIONS and sufficient room for a person to move and work comfortably around it Do not expose the CheckExtractor to direct sunlight Periodic maintenance daily maintenance weekly maintenance six monthly maintenance is a mandatory part of the work routine Discard used tips and do not reuse them Do not empty the tip waste during arun Do not try to open the front cover during a run as it may cause the run to abort This will cause the loss of sample material and reagents since a new run has to be started Never lift a fully installed instrument to transport it from one place to another It must be re installed in the new work location by an authorized service technician only The instrument weights more than 150 kg Necessary precautions should be taken when transporting the instrument Only certified technicians are authorized to perform mechanical maintenance on the CheckExtractor For repair or shipment all mechanical parts must be put in their rest positions A CheckExtractor sent away for repair must also be decontaminated see c
67. to be emptied before the run can enough volume left to take the liquid Be aware that the liquid waste is po start waste for the next run tentially infectious material see 5 2 l Make sure the barcode is undamaged A barcode is expected at the given l s l and clean and faces to the right Barcode Error position of the carrier but cannot be hand side If necessary re enter the read barcode manually B re th r fulfils the requi A barcode is expected at the given oe or ae 2 l rements given in 14 2 especially the Barcode Error position of the carrier but cannot be 3 mm of the quiet zone If necessary read re enter the barcode manually Make sure the reagents are at the The CheckExtractor finds a reagent indicated positions in the correct car Barcode Error Ha barcode at a wrong position rier If necessary re enter the barcode manually Either load all the samples which are Some samples defined in the input defined in the input file or change file are not present the input file to reflect the samples loaded Tubes with the following barcodes are missing but have been defined in the worklist Tubes with the following barcodes Samples have been loaded into have been loaded but have not been the instrument which are not in the defined in the worklist worklist Please remove these samples or change the input file CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 Error messa
68. tory C MethodOutput 5 4 5 1 Extraction method The subdirectories in this folder are named with the date and time of the run Additionally the barcode of the elution plate is added CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 For example 2013 11 21_10 26 25 067_E1012ELF0001 24 is a subdirectory of a run started on the 21st of November 2013 at 10 26 25 067 The eluate can be found in the elution plate E1012ELF000124 The directory contains files whose names begin with the same information as the directory they are contained within e date time and elution plate barcode Each file will then have a different suffix based on the type of file and the information it relates to The file names end with one of the following endings Name Meaning GBO_EXT_General xls General information about the extraction run Excel file Information about all pipetting steps e volumes source and target position GBO_EXT_Pipetting Tracking xls etc Excel file GBO_EXT_Samples xls Description of the pipetted samples Excel file GBO_PCRSampleList SMPxls The extraction run already creates the input file for the PCR setup method it is stored in this file GBO_EXT_ConsolidatedReport pdf Information about sample position and result of extraction 5 4 5 2 PCR Setup Method For each run of the PCR setup method the CheckExtractor creates output files These files are stored in the same subdirectory
69. tructions for Use Revision BQ 395 01 June 2015 6 3 Preparation Prior to Installation Before the CheckExtractor is delivered make sure you consider the physical and operational properties of the instrument See chapter TECHNICAL SPECIFICATIONS and the requirements listed here Choose a place for the CheckExtractor in the lab according to these specifications Do not expose the CheckExtractor to direct sunlight Place the CheckExtractor on a table or bench that is suitable to bear its weight 150 kg Do not place the CheckExtractor close to equipment that emits electromagnetic FF fields Since the CheckExtractor will be connected to a power line make sure that an earthed electrical socket is within 1 5 m of the installation site Be sure to have a magnetic separator on hand when the CheckExtractor is set up See chapter ORDER INFORMATION The CheckExtractor requires a minimum width of 800 mm to pass through any opening So any doors that the unit will pass through on delivery and installation will require this dimension 6 4 Bringing into Operation Liquid waste will arise during a run Therefore the CheckExtractor is equipped with a liquid waste bottle This bottle is connected to the liquid waste via a hose As no pump is fitted to the hose the liquid waste bottle has to be placed underneath the CheckExtractor see Figure 4 Prior to each run make sure that e Only trained personnel are o
70. ugh1 Add Buffer M1 ReagentTrough1 Add Buffer M1 ReagentTroughl A Add Buffer M1 ReagentTrough1 Add Buffer M1 ReagentTrough1 a Add Buffer M1 ReagentTroughl Add Buffer M1 ReagentTrough1 2 Add Buffer M1 ReagentTrough1 H Add Buffer M1 ReagentTrough1 Figure 33 Pipetting Tracking file oo 145 1 2015 05 20 11 50 36 145 2 2015 05 20 11 50 36 145 3 2015 05 20 11 50 36 145 4 2015 05 20 11 50 36 145 5 2015 05 20 11 50 36 145 6 2015 05 20 11 50 36 145 2015 05 20 11 50 36 145 8 2015 05 20 11 50 36 145 1 2015 05 20 11 50 37 145 2 2015 05 20 11 50 37 3 2015 05 20 11 50 37 4 2015 05 20 11 50 37 145 5 2015 05 20 11 50 37 145 6 2015 05 20 11 50 37 145 2015 05 20 11 50 37 0 Notchecked ProcessingPlateHhs 0 Notchecked ProcessingPlateHhs 0 Notchecked ProcessingPlateHhs 0 Notchecked ProcessingPlateHhs 0 Notchecked ProcessingPlateHhs 0 Notchecked ProcessingPlateHhs 0 Notchecked ProcessingPlateHhs 0 Notchecked ProcessingPlateHhs 0 Notchecked ProcessingPlateHhs 0 Notchecked ProcessingPlateHhs 0 Notchecked ProcessingPlateHhs 0 Notchecked PracessingPlateHhs 0 Notchecked ProcessingPlateHhs 0 Notchecked ProcessingPlateHhs 0 Notchecked ProcessingPlateHhs OS ISO SS a ot nt St a ooooooooooooooooo ooooooooooooooo0 If an error occurs open this file In the 1st column the pipetting step is shown In the 4th and 9th column error codes are given for aspiration and dispensing respectively The following table lists all error codes th
71. wing tasks e Sample transfer from primary tubes in a collection block optional can be purchased separately on request e Deoxyribonucleic acids DNA extraction from clinical samples with GBO reagents e PCR setup of a microplate in association with GBO reagents The three tasks are executed independently sample transfer or extraction or PCR setup The CheckExtractor is designed to process up to 96 samples per run and optimised for 48 and 96 samples respectively to process in parallel Please refer to the IFU of the corresponding Greiner Bio One Extraction kit or Greiner Bio One oCheck kit for further details relating to e recommended number of samples e sample volume e run time for the extraction and the PCR setup CheckExtractor Instructions for Use Revision BQ 395 01 June 2015 5 1 1 Extraction The CheckExtractor is designed for the extraction of viral bacterial and human genomic DNA from samples of human origin by professionals By using the oCheck DNA Extraction Kit CheckExtractor REF 517 070 a chemical lysis supported by heat treatment is performed By using the magnetic bead technology the DNA is bound and fixated After well defined washing steps to remove cell debris and proteins the purified DNA is eluted from the beads in a suitable solution for the following PCR setup 5 1 2 PCR Setup After a successful extraction the CheckExtractor prepares the PCR reaction mix by adding the DNA eluate

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CheckExtractor™ - Greiner Bio