Home

Affy Molecular Diagnostic Software Guide

Contents

1. Invalid Command Communication error In the current Worklist screen detected on the alert pane follow the Note where in recommended resolution You protocol error may need to occurred Identify if chip is filled Contact Affymetrix for service Temperature Timeout Temperature does not Temperature has not Call Affymetrix technical reach specified reached required level in support for service temperature expected time if ambient temperature is within operating specifications 15 to 30 degrees C Valve Motion Error In the current Worklist screen on the alert pane follow the recommended resolution If problem persists contact Affymetrix for service Valve Not Homed In the current Worklist screen on the alert pane follow the recommended resolution If problem persists contact Affymetrix for service Valve Out of Position In the current Worklist screen on the alert pane follow the recommended resolution If problem persists contact Affymetrix for service Meaning of Error Messages The following lists some of the common error messages and what they mean Table A 3 AMDS may display these as alerts To resolve these alerts follow the recommended resolution in the current Worklist screen on the alert pane Table A 3 Error Messages Appendix A GeneChip Fluidics Station FS450Dx 92 Error Message Meaning Follow the recommended resolution in the current Worklist screen on the al
2. LOAD VIAL 1 Prompt for loading vial 1 LOAD VIAL 2 Prompt for loading vial 2 LOAD VIAL 3 Prompt for loading vial 3 Filling with A Empty fill with wash A mix by drain and fill repeat leave cell full Filling with B Empty fill with wash B mix by drain and fill repeat leave cell full Draw 1st Stain Empty draw sample to both sensors Draw 2nd Stain Empty draw sample to both sensors Draw 3rd Stain Empty draw sample to both sensors Table A 5 LDC Messages Continued Appendix A GeneChip Fluidics Station FS450Dx 95 Message Meaning EJECT CARTRIDGE Prompt for removal of cartridge ENGAGE WASHBLOCK Prompt for engagement of washblock DO CLEAN CYCLE Begin cleaning cycle REMOVE STAIN VIALS Prompt to remove stain vials if present LOAD 3 EMPTY VIALS Prompt to load vials Purging with water Purge with 5mL water to clean line Washing needle 1 Performing wash needle 1 procedure Purging with air Purge with air Washing needle 2 Performing wash needle 2 procedure Washing needle 3 Performing wash needle 3 procedure Washing Lines Wash tube from valve to waste Prime Lines Equilibrate tube from valve to waste with wash A REMOVE ALL VIALS Prompt to remove vials LOAD SAMPLE VIAL IN LOC 1 Prompt for loading sample vial in location 1 Flushing with WashA Flushing with wash
3. 0 000 000 e aes 83 Replacing the Peristaltic Tubing Procedure 0 0 eee 84 Fluidics Station Troubleshooting and Assistance 0 auauua anaran eee 86 Troubleshooting Decision Tree 2 cece eus s pe yan 86 Problems and Sol tions a virus ees CoG aE khac RE RE BEI eas 89 Meaning of Error Messages n n aana aaaea g1 Other Problems and Solutions 0 0 00 ccc e 93 When to Contact Affymetrix 2 0 ns 94 Fluidics Station LCD Messages 0 2 00 eee eee 94 The FS450Dx Instrument Specifications 2 e 96 Regulatory Compliance 2 ce eee eee 97 RegulatO to wie eet ew wine sor PDAS c ot eee weed ON ia a we e e Rec t 8 98 China RoHS Restriction of Hazardous Substances Compliance 2000 99 SJMIT3 642000 erinesid ET LAS eS PITE bod riae tute na ae pesar ch 100 GeneChip Scanner 3000Dx with AutoLoaderDx 0055 101 INTFODUCTION x ei OE CREDO PPM od Medie I exui Bebe 101 Sate Operation cr eoo P wy ytd iets Barbe de es E Ee Es 102 When to Contact Affymetrix 0 0 0 ern 102 Eg eC ETT 102 Electrical Sat ele a sararan ra ard a OE Nec atro a ARR aide ele RR e pee e du s 103 Workstation AutoLoader Connections 0 0000 cc ee 104 Scanner Indicator Lights and On Off Button 0 0 00 ee 105 SCANNING AthayS sacs da que dne tem eds fue adr GR a eae hen RR eee a 108 Using Tough Spots to Prevent Leaks 0 0 e 108 Loading Arrays into the Carousel 0 0 paiia i 109 Loadin
4. 4 Click Station Setup The Fluidics Station Setup widow displays Figure A 12 on page 77 Appendix A GeneChip Fluidics Station FS450Dx 77 Figure A 12 The Fluidics Station Setup screen Fluidics Station Setup gt al 4 Prime Fluidics Station Shut Down Station Close Setup Screen wave Buffer Infi lelp About PmmaQesenHo vio PmmguHGUrame2022 o PiiingforHumansnpcov22 i Select Assay O OO E E a ES a MUN 2 1 a O O E c e pNaPimed 00 amp lt 5 In the Fluidics Station Setup screen select o The Station n The Assay to be primed from the drop down 6 Highlight the stations to be primed This step enables the Prime Station button on the toolbar 7 Click Prime Station The status field displays the priming message Figure A 12 on page 77 8 Follow the instructions in the LCD screen on the fluidics station as the prime protocol progresses The LCD screen on the fluidics station and the fluidics station dialog box indicate the status of the prime and when AMDS has completed the priming protocol After you have primed the fluidics station you are ready to hybridize or wash and stain a sample Fluidics StationDx Care and Maintenance This section provides instructions on caring for and maintaining the instrument and on troubleshooting if problems arise Ins
5. 2 Click Show Navigation Figure 1 2 on page 10 on the Help toolbar The entire help system displays including navigation buttons a navigation tree and a help topic 3 Click on the navigation buttons to locate your desired help topic You can a Click through the Contents list Select a topic from the Index Search for a topic Select a topic from your Favorites list Chapter 1 Welcome to AMDS 10 Figure 1 2 Show Navigation Button on Help Screen Toolbar Back Forward Main HelpPage Close Terminology T hese are key terms related to the Affymetrix GeneChip System 3000Dx v 2 Test Request a unique record of an assay performed on a particular specimen Repeated runs of the same specimen would be represented by multiple test requests Each test request is associated with a specific array cartridge Assay Software Module or ASM the software package that enables processing of a particular assay on a GCS3000Dx v2 system Each ASM is supplied by Affymetrix or authorized partners in the form of a CD Assay the procedure that processes the specimen to produce the result This would include the lab work and processing through the GCS3000Dx v2 workflow In this manual the term assay typically refers to the Assay Software Module Array the microarray a glass substrate with oligonucleotide probes A plastic cartridge surrounds and protects the array and forms the array cartridge Figure 1 3 on page
6. Chapter 4 Test Request Processing 43 Non Active Worklist Viewing Non Active Test Requests You can view test requests on the Non Active Worklist when You have canceled them before test request processing is complete After you approve test requests and before they have been archived and purged Once you archive and purge a test request you can only view it from CD DVD or network location where you created the archive For more information see Archiving and Purging Test Requests on page 57 After you approve test requests and before you archive them you can view test requests on the Non Active Worklist Figure 4 15 on page 43 to display non active test requests The system moves test requests to the Non Active Worklist when they have completed processing in AMDS e g when the results have been viewed and approved or when you cancel them To view test requests on the Non Active Worklist 1 Click the Non Active Worklist button Figure 4 15 on page 43 on the Administrator pane Figure 4 15 Non Active Worklist Button Non Active Worklist AMDS Administrative Features AMDS supports the following administrative features Viewing logs Managing assays Managing users Managing the system To access these features click on the corresponding buttons in the Administrator pane Figure 5 1 on page 44 If a button is disabled you do not have access to that feature Your user privileges are define
7. System Maintainer A user with a System Maintainer role can access all the System Management screens and perform tasks like archiving test requests maintaining the instruments and general system configuration This user cannot perform any of the processing steps for a test request and cannot view any patient data When assigning the System Maintainer role to a user we recommend not assigning them access to any assay software modules Laboratory Supervisor A user with a Laboratory Supervisor role can perform all of the tasks associated with the Technologist role and all of the tasks associated with the System Maintainer role Adding a User Before adding a user you should review the different AMDS user roles in About User Roles on page 50 Ifthere are no assays installed on the system you do not have the option of granting assay access to a user Guests and system maintainers should not be granted access to assays To add a user 1 In the User Management toolbar click Add User The Add User screen displays Figure 5 7 on page 51 2 Establish the following characteristics of the new user Select the Active box to make the user currently active or deselect the Active box to create a user without granting immediate access to the system Enter a user ID Enter the user s first and last name Optional Enter a comment Create and confirm a password The password must have a minimum of 8 characters 1 uppercase and 1 lower
8. The error generally occurs if there insufficient quantities of fluids are provided or if the wrong fluids are provided You can Determine the source of the problems on the station LCD Follow the resolution procedure in the alert details Clear the alert and continue the fluidics run If you continue to see this error it may indicate a system failure Call Affymetrix technical support See the section Fluidics Station Troubleshooting and Assistance on page 86 Troubleshooting the Scanner There are several autoloader errors you can correct Autofocus Error This error generally occurs if the array cartridge glass substrate is smudged or dirty usually from a thumb print Clean the array clear the alert and retry Barcode Could Not Be Read Retrieve the array and process using the manual scan procedure See Scanning Arrays in Manual Mode on page 41 GeneChip Fluidics Station FS450Dx Introduction Figure A 1 Affymetrix GeneChip Fluidics Station 450 This section introduces the Affymetrix GeneChip Fluidics Station 450Dx aka the fluidics station and its components gives an overview of how the fluidics station works and covers the safe use of the fluidics station The fluidics station is part of the GCS3000DX v 2 that includes the GeneChip 3000Dx Scanner with AutoLoaderDx NOTE Throughout this manual the images of the fluidics station are pictures of the RUO version of the produc
9. Affymetrix recommends the use of dedicated bottles for bleach and DI water You can obtain additional bottles from Affymetrix Part Number Description 400118 Media Bottle SQ 500mL 400119 Media Bottle SQ 1000mL The Bleach Cycle 1 Disengage the washblock for each module by pressing down on the cartridge lever Remove any array cartridge Figure A 13 on page 78 Figure A 13 Disengaged washblocks showing cartridge levers in the down position remove any cartridges Remove cartridges if any Washblocks disengaged with cartridge lever down 2 Prepare 500 mL of 0 525 sodium hypochlorite solution using deionized water Shake well For example follow these directions to make 500 mL of bleach Appendix A GeneChip Fluidics Station FS450Dx 79 In a 1 liter plastic or glass graduated cylinder combine 43 75 mL of commercial bleach such as Clorox bleach which is 6 sodium hypochlorite with 456 25 mL of DI H O mix well Pour the solution into a 500 mL plastic bottle and place the plastic bottle on the fluidics station Lu IMPORTANT The shelf life of this solution is 24 hours After this period you must prepare a fresh solution NOTE Each fluidics station with four modules requires 500 mL of the 0 52596 sodium hypochlorite solution 3 Place on the fluidics station an empty one liter waste bottle a 500 mL bottle of bleach solution and a one liter bottl
10. Clicking in various regions of the screen with the cursor will cause the associated help topic to display in the lower half of the center panel Chapter 1 Welcome to AMDS 9 Figure 1 1 Online Help Button and Cursor Display All v Display All v Accessing Context Sensitive Help Context sensitive help provides both general information about the user interface as well as detailed information about specific tasks General User Interface Help After you click Help the cursor will turn into a question mark Use this question mark to click on a pane in the left or right interface panels to get general information about Workflow Pane Administrator Pane User Details Pane a Device Status Pane Alerts and Alert Details Panes A help topic related to your selection displays Task Oriented Help Getting help for a specific task is slightly different For example 1 Onthe Workflow pane or Administrator pane click on the button related to activity you need help with a If you clicked on a Workflow button the related worklist displays in the center panel a If you clicked on an Administrator pane button the related administration screen displays 2 Click Help 3 Click on the center panel A help topic related to your selection displays Accessing the Complete Help System To view the complete help system 1 Click Help and then click anywhere on the AMDS interface Context Sensitive Help displays
11. Device Status and Alert Icons Chapter 6 AMDS Troubleshooting On the Device Status pane check the device status icon to check device status These are the Device Status icons Green check mark the device is ready White circle with green arrow the device is running properly Yellow triangle check the Alert and Alert Details panes Red circle with slash the device is not connected Red circle with white x the device is turned off or attempting to connect Viewing Alerts and Alert Details 62 The Alerts pane Figure 6 2 on page 63 provides a short description of an error and the Alerts Details pane Figure 6 3 on page 63 provides a full description and suggests corrective action Click on the alert in the Alerts Pane and view the corresponding alerts details on the Alerts Details pane Then follow the procedures described in Resolving Alerts on page 64 Chapter 6 AMDS Troubleshooting 63 Figure 6 2 Alerts Pane All Figure 6 3 Alert Details Alert Details Specimen ID Assay Name Workflow Step Date Time 2011 02 12 17 29 Details The hard drive health has degraded There has been loss of hard drive redundancy and you should take the necessary precautions while waiting for the hard drive health to be restored Recommended Resolution Please contact your Dell service representative Individual Test Request Errors Th
12. workstation and the scanner Perform this function if you are experiencing problems connecting to the scanner 1 On the System region of the User Performed Services screen click Restart Scanner to restart the scanner For complete instructions related to the scanner see GeneChip Scanner 3000Dx with AutoLoaderDx on page 101 Viewing RAID Storage Status Depending on your AMDS workstation model you may have a RAID Storage Console button on the User Performed Service System region If your system displays this button you can click on it to view the RAID Matrix volumes and check the health of your hard drive Consult your RAID console documentation for more information If your system does not display this button check the hard drive status on the Device Status pane In either case if the hard drive status is not optimal contact Affymetrix support Managing the Printer On the Printer region of the User Performed Services screen Figure 5 12 on page 56 you can View the printer name View the number of jobs in queue Change the printer s online offline status o Taking the printer offline disables the print button on screens where it is available Bringing the printer online enables the print button o To take the printer offline for printer maintenance etc and stop printing jobs in queue select Offline o To bring the printer online select Online a Purge all print jobs Click Purge All to remove all the jo
13. 1 Click the System Management button Figure 5 1 on page 44 on the Administrator pane 2 From the System Management menu Figure 5 8 on page 52 select one of the following a User Performed Services User Performed Service Log Archive Test Requests a General Configuration The selected screen displays Figure 5 8 The System Management Menu System Management Configuration Station v Managing Instrument Settings on the User Performed Service Screen This screen provides controls to manage the following a Fluidics stations System hard drive Scanner RAID settings not applicable to all systems Printer Firewall Chapter 5 AMDS Administrative Features 53 Figure 5 9 User Performed Service Screen System Management User Performed Service Fluidics Station Configuration Time Elapsed Since Bleach Interval Alert Limit d Station v Bleach Interval Warning Limit d Last Bleach E d 5 m Change Tubing Warning Limit d Last Change Tubing d Change Tubing Alert Limit d Procedure Bleach v Perform System Configuration HDD Space Available 923 GB HDD Space Warning Limit 11 Export File Size 0 MB Clear 7823 GB HDD Space Alert Limit 8 25 744 GB Restart Scanner Printer Firewall Printer Name AMDSPrinter Last Backup 2011 02 11 15 16 Online Offline Number ofJobs in Queue 8 Purge Al
14. 10 We often use the term array to refer to the array cartridge For convenience we also refer to the GeneChip Fluidics Station 450Dx as the fluidics station or as the F S450Dx and the GeneChip Scanner 3000Dx with AutoLoaderDxe as the scanner or GCS 3000Dx Figure 1 3 Affymetrix GeneChip Array Cartridges P N 520019 Lot SAMPLES Exp Date 00 00 00 For Research Use Only WES I 52001900000000000000SAMPLES41931 CytoScan HD Array GeneChip S AX Affymetrix Text Alerts T ext alerts will draw your attention to a particular piece of information There are five types of text alerts Note Tip Important Caution and Warning Chapter 1 Welcome to AMDS 11 NOTE Notes present information pertaining to the text or procedure being outlined fl TIP Information presented in Tips provide helpful advice or shortcuts for completing a task IMPORTANT Important notes alert you to information important to the understanding or implication of the procedure or text MA CAUTION Caution notes advise you that the consequence s of an action may be irreversible and or result in lost data n WARNING Warnings alert you to situations where physical harm to person or damage to hardware is possible Technical Support Please consult your user manual online help and especially their troubleshooting sections before contacting Affymetrix technical support If
15. 50 60 Hz Working Environment Temperature 59 F 85 F 15 C 30 C Humidity 10 90 Non condensing Clearance 2 in 5 cm onside back 12 5 in on top Pollution Degree 2 Installation Category Il Altitude lt 2000m Electrical Supply Provide voltage frequency or power rating per unit label Main Supply Voltage Are not to exceed 10 of the nominal supply Fluctuations voltage Regulatory Compliance Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 120 CE Mark Declaration of Conformity We Affymetrix Inc 3420 Central Expressway Santa Clara CA 95051 Declare under sole responsibility that the Affymetrix GeneChip Scanner model GCS3000Dx v 2 and its accessory Autoloader Dx conforms to the relevant provisions of the following standard s of safety and compliance and or other normative documents EU In Vitro Diagnostic Medical Devices Directive 98 79 EC Annex III CE Declaration ISO 13485 2003 Medical Devices Quality managements systems requirements for regulatory purposes Electromagnetic Compatibility EMC Directive 2004 108 EC EN 61326 1 2006 EN 55011 2007 Amendment A2 2007 Class A EN 61000 4 2 1995 Amendment 2 2001 EN 61000 4 3 2006 Amendment 1 2008 EN 61000 4 4 2004 EN 61000 4 5 2006 EN 61000 4 6 2007 EN 61000 4 8 1993 Amendment 1 2001 EN 61000 4 11 2004 EN 61000 3 2 2006 Class A EN 61000 3 3 1995 Amendment 2 2006 EU Low Voltage Directive 20
16. 96 operating temperature 96 other problems and solutions 93 peristaltic tubing replacement 83 pollution degree 96 power input 96 power requirements 96 precautions 66 problems and solutions 89 regulatory 98 rinse cycle 81 running a protocol 71 setting up 38 shutting down 75 starting 70 troubleshooting 86 using 39 69 weight 96 Fluidics station protocols 70 G GeneChip 3000Dx AutoLoaderDx 101 Hard Disk Space 113 Home procedure 70 Homing valves 70 Hybridizing 35 I Indicator lights AutoLoaderDx 106 Install assay 47 Instrument related errors resolving 61 Instrument troubleshooting 64 Intended use 8 L Laser safety 102 Leaks preventing 108 Logging off 26 Logs viewing 44 Missing fluid error 89 Molecular Diagnostic System administrative features 44 Normal operational scanning mode 40 Oo Operational and data input errors resolving 64 P Peristaltic tubing change 53 Peristaltic tubing replacement 83 Printer management 55 Probe array handling 29 Problems and Solutions fluidics station 86 Processing test requests 35 Protocol bleach 78 running on a fluidics station 71 Protocols fluidics station 70 Index 130 Resolving alerts 64 Rinse cycle 81 S Scanner AutoLoaderDx 101 Scanning arrays 108 normal operational mode 40 Select 48 Shutting down 26 Specifications AutoLoaderDx 118 FS450Dx 96 Specimen ID adding additional information 33 Starting the fluidics s
17. All Deselect All Cancel Deactivating an Assay You can deactivate an assay if you no longer use this assay and do not want it to appear as a selection in the AMDS application There is no mechanism to uninstall an assay 1 Select an assay from the Assay Management screen Figure 5 3 on page 47 2 Click Deactivate on the Assay Management toolbar Once you deactivate an assay you can still complete the workflow for any active test requests for this assay The assay will no longer be available for entering new test requests Repairing or Reactivating an Assay To repair or reactivate an assay reinstall the assay as if it were a new install See Installing Assays on page 47 Installing a Certificate NOTE You must be logged in as a Laboratory Supervisor or System Maintainer to install a certificate Some assays may require the transfer of data to a remote system during the analysis phase of the workflow This transfer requires the installation of a server certificate to enable AMDS to trust the server through https protocols As a security measure AMDS requires that you or the Affymetrix field service technician install a SSL server certificate installed on your local workstation in order for your workstation to communicate with the remote server This is required for the transfer of the Gene Profiling cGMP v1 1 Assay test request data to the data transfer server You should have the certificate installed before
18. Error Messages Message Meaning HEATER_LOW Warning The warming chamber temperature is low Refer to the troubleshooting guide COLD_CHAMBER_LOW Warning The cold chamber temperature is low Refer to the troubleshooting guide COOL_HOTSIDE_HIGH COLD_CHAMBER_HIGH Warning The cooler hot side temperature is high Refer to the troubleshooting guide Note Before calling technical support check around the ventilation vents to ensure that nothing is blocking them Warning The cold chamber temperature is high Refer to the troubleshooting guide Note Before calling technical support check the scanner door to ensure that it is not open HEATER_HIGH Warning The warming chamber temperature is high Refer to the troubleshooting guide Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 117 Manually Removing a Lodged Array Cartridge In the event that a array becomes lodged in the array transport mechanism follow the procedure outlined below 1 Turn the scanner off and remove the power cord from the back of the unit 2 Open the AutoLoaderDx door on top of the unit 3 Remove the carousel from the system Keep the arrays in carousel and at the proper temperature while recovering the array still in the AutoLoaderDx 4 Remove the hole plug which is just in front of the array slot in the base piece of insulation In the photo to the right the scr
19. Firewall Last Backup 2011 02 11 15 16 Viewing User Performed Service Logs NOTE Do not confuse the View Service Log function with the View System and Audit logs that are described in the section Viewing Logs on page 44 A User Performed Service Log entry will be created for most of the actions you perform on the User Performed Services screen You can open and view the service logs for user performed services Chapter 5 AMDS Administrative Features 57 To view and filter user performed service logs 1 From the System Management menu select User Performed Service Logs See Changing System Management Screens on page 52 The User Performed Service Logs screen displays 2 You can filter the log by Date Time Procedure User Device Description 3 Click Remove Filter to view all log entries You can also print the user performed service log Figure 5 14 View User Performed Service Log System Management Total 1 User Performed Service Log Bleach script update Affymetrix Service Technician Fluidics Maintenance Script Successfully updated bleach script to Bleachv3 450 bin Archiving and Purging Test Requests AMDS allows for test requests to be archived and subsequently purged in order to conserve space on the hard drive Test requests can be archived multiple times before they are purged NOTE Once test requests are purged there is no way to restore the archived t
20. Metal Parts External Metal Parts Labels Packaging Shipping Materials Internal Lasers Optics amp Sensors Adhesives Internal Power Supplies Motors and Pumps O O O O O O X Indicates that the toxic or hazardous substance contained is above the limit of 1000 ppm for lead and above 100 ppm for cadmium O Indicates that the toxic or hazardous substance contained is below the limit of 1000 ppm for lead mercury hexavalent chromium polybrominated biphenyls and polybrominated diphenyl ethers and below 100 ppm for cadmium Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 127 SJ T11364 2006 libn S miss BRICK HOPES mA Tae REEF RRS SB Pb R Hg ta Ca Aii 18 MAS d 2i m PBB i PBDE 3E EET N jx ie a See STEN MERRBERSID ET CREDIS i DEBERE AL PASTA PETA BY ae BAR MRE Ht eR IS ESA E ate ea M LECAERIE Ht ab QoS E D lip A ea aS NE IR m IE a 5 d 2 Bou 3 n n r B j 2 YE j 2 rT Aon i z T FEE Reh eae er ru LUE a E EN E MESSER Y Tit lt P HAIRS BTR EBERT Dm An DACA ABE FAA E ef Bi PTEROLARE iB EERO ORR Btn Sim ES Le MAMAS ps TN PO ND CO Aia Cr VD ZIARE PBB 402518 RB PBDE Bj uid TE JE Table B 10 f Table B 11 Table B10 5A Wi sux SEES IS Affymetrix GeneChip GCS3000 AutoLoaderDx D x aye eet e Pe Bra X RRBAS AEH AS DEBRA R DAHA RAIS 2 Bu 1000 ppm n Pb 1
21. Next to the Export File Size field click Clear View or change the HDD Space Warning Limit or HDD Space Alert Limit NOTE These warnings and alerts notify you when the workstation hard drive is nearing capacity You should archive and purge data before you reach your limit Once AMDS hits the alert limit you will no longer be able to scan any arrays until you have archived and purged enough data to stay below your limit n Set these values in the System region o The space alert limit must be less than the warning alert limit o It is recommended to change the alert first and then the warning o Your system will prevent you from setting the alert below a certain percentage Chapter 5 AMDS Administrative Features 55 View and configure RAID storage settings For more information see Viewing RAID Storage Status on page 55 After each of these procedures click Save When the Confirm Step dialog box displays you need to confirm the change with your password and the reason for the change Figure 5 11 The System Region of the User Performed Services Screen System Configuration HDD Space Available 459 GB HDD Space Warning Limit ile Si Clea 1 Export File Size D MB lear m GB HDD Space Alert Limit 8 37 2 GB Restart Scanner RAID Storage Console Restarting the Scanner Clicking this button will attempt to restart the scanner and establish communication between the
22. Plastic cartridge Front Probe array on glass substrate Although the inner glass surface is protected any contamination or scratches on the outer surface of the glass can compromise the integrity of the scan Avoid touching the surface of the glass with your fingers Skin oils and other substances such as lotions or ink can fluoresce If the surface of the array is noticeably dirty you should carefully clean it with a nonabrasive laboratory tissue E Signatures At times after completing procedures in AMDS you will be prompted to confirm a change with your password and the reason for the change These e signatures help track user activity on the system Figure 3 5 E Signature Confirmation Dialog Confirm Step User Credentials User Name dx2labsuper Password Event Reason Default Reason Normal Workflow v Additional Info Test Request Processing Introduction A test request is a unique record of an assay performed on a particular specimen Repeated runs of the same specimen would be represented by multiple test requests Each test request is associated with a specific array cartridge To process test requests follow these steps that correspond to the buttons in the workflow pane 1 Create test requests See Active Worklist Entering Editing or Canceling Test Requests on page 30 Register test requests See Registration Registering Test Requests on pa
23. Resume All Managing Fluidics Stations Lu IMPORTANT When performing fluidics management procedures make sure you select a fluidics station first NOTE For greater detail on using troubleshooting and maintaining fluidics stations see GeneChip Fluidics Station FS450Dx on page 66 On the Fluidics Station region of the User Performed Services screen Figure 5 10 on page 54 you can In the Elapsed Time fields see how many days have elapsed since the last bleach or tube change took place for the selected fluidics station Perform a bleach protocol A Select Bleach in the Procedure dialog box B Follow the procedures provided in The Bleach Cycle on page 78 C Click Perform Change the tubing A Select Change Tubing in the Procedure dialog box B Follow the procedures provided in Peristaltic Tubing Maintenance on page 83 C Click Perform Troubleshoot or test communication between the workstation and the fluidics station A Select Home in the Procedure dialog box Chapter 5 AMDS Administrative Features 54 B Click Perform If the operation is unsuccessful see Troubleshooting the Fluidics Station Connection to the Workstation on page 70 View or change the Bleach Interval Warning Limit and Bleach Interval Alert Limit o The bleach reminder is preconfigured on to a schedule recommended by Affymetrix o Set these limits in the Fluidics Station Configuration region n Th
24. The instrument must be surrounded by adequate airspace Slots and openings in the instrument and the electronics compartment covers are for ventilation Do not block or cover them Never push an object into the instrument ventilation slots equipment damage or injury may result Do not set liquids on top of the instrument The instrument has an AC receptacle with a safety ground appropriate for the country of destination The plug is designed to connect only to a 3 prong ground receptacle This safety feature should not be compromised in any way If the instrument AC plug does not mate with the available power source receptacle consult a licensed electrician to install one that does When to Contact Affymetrix Under any of the following conditions unplug the instrument from the power source and contact technical Support When the power cord is damaged or frayed a If any liquid has been spilled into the instrument If the instrument has been penetrated by water If after service or calibration the instrument does not perform in accordance with the capabilities stated in the specifications a If the instrument has been dropped or otherwise damaged If the instrument must be returned for repair call Affymetrix technical support Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 103 Laser Safety The laser is equipped with an automatic shutter that inhibits its output beam and ensures safe operation under conditio
25. as unknown Appendix A GeneChip Fluidics Station FS450Dx 89 Problems and Solutions This section lists some alert messages the possible causes and solutions Table A 2 AMDS may display these as alerts To resolve these alerts follow the recommended resolution in the current Worklist screen on the alert pane Table A 2 Problems and Solutions Error Message Problem Possible Cause Possible Solution Follow the recommended resolution in the current Worklist screen on the alert pane Missing Fluid Error Cartridge not filling completely with sample solution or buffer during initial stages of hybridization wash or staining protocol Possible holes in the septa of the cartridge Sample or staining solution not in place properly In the current Worklist screen on the alert pane follow the recommended resolution In the current Worklist screen on the alert pane follow the recommended resolution Make sure sample or stain vial is in the sample holder In the current Worklist screen on the alert pane follow the recommended resolution You may need to add more sample solution to the sample vial Blocked sampling tube or line of the fluidics station Failure of one of the fluidics sensors Pump tubing stretched too tightly around the pump Call Affymetrix technical support for service In the current Worklist screen on the alert pane follow the recommended resolutio
26. continue to process them Shutting Down This function allows you to shut down AMDS The shut down functionality is available at all times to users with permission to shut down In the User Details pane Figure 3 2 on page 27 click Shut Down Chapter 3 Affymetrix GeneChip System 3000Dx v 2 Operation Basics 27 Lu IMPORTANT If there are test requests in progress the system asks for confirmation before shutting down Clicking Yes to confirm the shut down will begin an orderly shut down of the system and cause all tests requests with a state of In Progress to go into an error state NOTE When you shut down the workstation the instrumentation does not shut down automatically You will need to shut them down separately Changing Your Password You can change your password at any time while you are logged onto the system 1 In the User Details pane Figure 3 2 on page 27 click Change Password Figure 3 2 The User Details Pane User Details User ID Role Lynn Laboratory Supervisor Date Time 2011 02 11 16 47 07 2 After the Change Password dialog displays enter your old password 3 Enter and confirm your new password Click OK to apply the change Using the Barcode Reader You can use the barcode reader to a Enter a Specimen ID for a test request a Associate a test request with an Array ID Associate a test request with reagent lot numbers a Associate an array w
27. firewall and write a temporary file to share a If the test fails an error message provides assistance troubleshooting the problem a If the test succeeds check Enable archiving to network For read feedback verification of archived files check Use MDS5 checksums to verify transfers 5 Click Save Changes AMDS Troubleshooting Introduction There are generally three categories of problems that can be encountered when executing test requests a Instrument related errors such as communications issues with the hybridization oven problems with a fluidics station or module or problems with the scanner a Problems with a particular test request for example the bar code of the array associated with a test request could not be read or gridding fails for a test request a Operational errors including data input errors The system tracks and reports on all three categories of problems This section provides information as to how to identify that a problem has occurred and provides some general guidance as to how to try to resolve a problem For more specific troubleshooting information related to the fluidics station and the scanner see a Fluidics Station Troubleshooting and Assistance on page 86 Troubleshooting the Scanner on page 114 Instrument Related Errors If you suspect an issue with an instrument check the Device Status pane as seen in Figure 6 1 on page 62 The pane provides you with three pieces of information a The de
28. in troubleshooting 2 4 If the test succeeds check the Enable archiving to network checkbox User Name TestConnection 5 For read back verification of archived files check the Use MD5 checksums to verify transfers checkbox otherwise archived files will be checked by confirming file sizes Enable archiving to network 6 You may save new settings at any lime C Use MD5 checksums to verify transfers Viewing and Configuring Time Zone Setting NOTE Do not change the local time or time zone if there are any test requests in progress on any worklist To view time zone current settings 1 From the System Management menu select General Configuration See Changing System Management Screens on page 52 2 On the General Configuration screen view the Time Zone Current Settings region Figure 5 16 on page 59 Chapter 5 AMDS Administrative Features 60 To configure time zone settings 1 On the Time Zone Editable Settings region A In Editable Local time set the local time B In Time Zone set your local time zone 2 Click Save Changes Configuring Scanner Settings In the System Configuration Flags screen Figure 5 16 on page 59 you can configure the scanner to 1 Select Turn on Laser to turn on the scanner laser automatically when you launch the AMDS application 2 Select Disable AutoLoader box to disable the scanner and manually load unload arrays from t
29. installing the assay The Affymetrix service technician should have installed a certificate at the time of the system s installation If for some reason the service technician did not install a certificate or if the server has changed after the system s initial installation you must install a certificate If a proper certificate has not been installed you can still install the assay and process test requests however you will have no permission to access the remote server and you cannot transfer test request data to the remote server If you cannot access the remote server and have already installed a certificate contact Affymetrix technical support To install a certificate Chapter 5 AMDS Administrative Features 49 Click the Assay Management button Figure 5 1 on page 44 on the Administrator pane Click Install Certificate The Server Certificate dialog appears Figure 5 5 on page 49 Select either Install from CD or Install from local disk drive Browse for and select the desired cer file The certificate you want to install has a cer extension Click OK to continue or Cancel to end the installation a If the installation is successful you will receive the message You have successfully added the server certificate x cer to the AMDS trusted certificate store a If the installation fails AMDS will notify you with a particular algorithm message The software will prevent you from accessing the server and from transf
30. managements systems requirements for regulatory purposes Electromagnetic Compatibility EMC Directive 2004 108 EC EN 61326 1 2006 EN 55011 2007 Amendment A2 2007 Class A EN 61000 4 2 1995 Amendment 2 2001 EN 61000 4 3 2006 Amendment 1 2008 EN 61000 4 4 2004 EN 61000 4 5 2006 EN 61000 4 6 2007 EN 61000 4 8 1993 Amendment 1 2001 EN 61000 4 11 2004 EN 61000 3 2 2006 Class A EN 61000 3 3 1995 Amendment 2 2006 EU Low Voltage Directive 2006 95 EC EN 60825 2 2004 IEC 61010 1 2001 IEC 61010 2 101 A1 2003 Electrical equipment for measurement control and laboratory use EMC requirements Radiated and Conducted Emissions Electrostatic Discharge Radiated Immunity Electrical Fast Transient Burst Immunity Surge Immunity Conducted Immunity Magnetic Field Immunity Voltage Dips and Interrupts Harmonic Current Emissions Limits Voltage Changes Fluctuations and Flicker Safety of laser products Safety of optical fibre communication systems OFCS Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements Safety requirements for electrical equipments for measurement control and laboratory use Particular requirements for in vitro diagnostic medical equipment EN 61010 1 2001 EN 61010 2 081 A1 2003 EN 61010 2 101 2002 UL 61010 1 R 2005 07 CAN CSA C22 2 No 61010 1 2004 C
31. on the instrument label Voltage fluctuations shall not exceed 10 nominal supply voltage Altitude lt 2000m Regulatory Compliance Appendix A GeneChip Fluidics Station FS450Dx 97 CE Mark Declaration of Conformity We Affymetrix Inc 3420 Central Expressway Santa Clara CA 95051 Declare under sole responsibility that the Affymetrix Fluidics Station model FS450Dx v 2 conforms to the relevant provisions of the following standards of safety amp compliance and or other normative documents EU In Vitro Diagnostic Medical Devices Directive 98 79 EC Annex III CE Declaration ISO 13485 2003 Medical Devices Quality managements systems requirements for regulatory purposes Electromagnetic Compatibility EMC Directive 2004 108 EC EN 61326 1 2006 EN 55011 2007 Amendment A2 2007 EN 61000 4 2 1995 Amendment 2 2001 EN 61000 4 3 2006 Amendment 1 2008 EN 61000 4 4 2004 EN 61000 4 5 2006 EN 61000 4 6 2007 EN 61000 4 8 1993 Amendment 1 2001 EN 61000 4 11 2004 EN 61000 3 2 2006 EN 61000 3 3 1995 Amendment 2 2006 Electrical equipment for measurement control and laboratory use EMC requirements Class A Radiated and Conducted Emissions Electrostatic Discharge Radiated Immunity Electrical Fast Transient Burst Immunity Surge Immunity Conducted Immunity Magnetic Field Immunity Voltage Dips and Interrupts Class A Harmonic Current Emissions Limits Volta
32. page 35 in the Workflow pane to view the Hybridization Oven Worklist Figure 4 7 Hybridization Oven Button Hybridization Oven Oven hybridization consists of multiple steps 1 Entering oven information 2 Starting and monitoring the oven hybridization process 3 Ending oven hybridization and removing the arrays from the oven Chapter 4 Test Request Processing 36 Hybridizing in an Oven vs Hybridization on a Fluidics Station Depending on the assay hybridization can be performed in a hybridization oven or on the fluidics station If your assay does not perform oven hybridization your test requests will appear on the Fluidics Worklist at this time Consult your assay software module manual for more information Entering Oven Data NOTE You cannot change any parameter in the Time Rotation Duration field displayed on the Hybridization Oven Worklist These values inform you of the optimal hybridization parameters for the assay To enter oven information 1 Click Hybridization Oven Figure 4 7 on page 35 The Hybridization Oven Worklist displays Figure 4 8 on page 36 Hybridization Oven Worklist 2 Associate test requests with a particular oven tray Follow these steps only if you are using an oven tray You may want to perform this task for multiple test requests at a time For more information see Editing Multiple Fields in AMDS on page 28 A To enter the tray ID with
33. slide the slot pin Step 7 back to the left This should open up the pinch rollers Pull the array out Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 119 11 If you do not see the array after turning the hex driver for 10 seconds stop 12 Using tool Affymetrix P N 13 0256 with the hook down and toward the back slide it vertically down against the front of the array opening about 1 5 inches There is a small groove made for this tool in the middle of the front array guide 13 Pull the top finger grip of the tool toward the front of the unit and then pull it up while still putting pressure towards the front The array should come up with the tool When you see it grab the array and pull it out of the unit 14 If you cannot get the array out after doing this procedure call for Affymetrix technical support 15 Put the hole plug back into the hole in the base piece of insulation 16 Plug the scanner back in and turn it on 17 Load the carousel after the scanner boots up 18 If arrays continue to become lodged in the AutoLoaderDx you should call technical support GCS3000Dx Specifications Table B 6 The Specifications of the Scanner 3000Dx with AutoLoaderDx Table B Table B Table B Item Param Value eter Weight Shipping approx 115 pounds 52 2 Kg Free standing approx 100 pounds 45 4 Kg Dimensions Width 13 25 in Depth 21 25 in Height 32 in Power Voltage 100 240 V Current 4 2A Line Frequency
34. the array Autofocus should begin about 90 seconds after you click Manual Scan Cleaning and Maintenance The scanner requires little in the way of customer maintenance The instrument must be kept clean and free of dust Dust buildup can degrade performance Wipe the exterior surfaces clean using a mild dish detergent solution in water Do not use ammonia based cleaners or organic solvents such as alcohol or acetone to clean the system because they may damage the exterior surfaces Clean the carousel by hand using warm water and if necessary mild detergent The GCS3000Dx v 2 requires calibration and maintenance twice a year by authorized Affymetrix personal to ensure the system performance Failure to maintain the system as recommended may result in the failure of the system to perform in accordance with specifications published by Affymetrix Configuring the Scanner If you are an administrator you can configure two scanner functions Set the scanner to turn on and warm up when AMDS launches a Disable the AutoLoaderDx so you can continue processing arrays if the AutoLoaderDx fails For instructions for these two functions see Configuring Scanner Settings on page 60 Troubleshooting This section deals with issues and problems that might occur with the scanner Troubleshooting the Scanner This section deals with issues relating primarily to the scanner especially when the scanner is in Manual Mode Table B 2 Scanner Troublesho
35. the barcode reader 1 Scan the barcodes of the arrays you will be placing in the tray This will select the test requests 2 Scan the tray s barcode B To enter the tray number by hand 1 Select the test requests 2 Enter a tray ID 3 Associate test requests with a particular oven NOTE If you are using a third party oven or the GeneChip Hybridization Oven 640 enter E for external in the Oven field 1 Select all test requests for the arrays you will place into the oven If you have entered tray numbers for your test requests you can select all the test requests for a particular tray by selecting one of the test requests and clicking Select Tray Chapter 4 Test Request Processing 37 2 Click and hold the Ctrl key 3 Place the cursor into a selected oven number field 4 Release the Ctrl key 5 Enter the oven number For the GeneChip Hybridization Oven 645 the value will be either 1 or 2 depending on your oven setup 6 Click Enter AMDS populates the oven number for all selected Specimen IDs You can also enter the oven number by hand for each test request Starting and Monitoring Oven Hybridization IMPORTANT The background color of the Reported Elapsed Hybridization Time cell will be yellow when the time is less than the minimum time required by the assay parameters green when it falls within the acceptable range and red when it exceeds the maximum allowable time You
36. the chip after the staining process performed by the Fluidics Station Array cartridges are loaded into the scanner by an automatic handler the AutoLoaderDx prior to scanning and returned to the handler after scanning is complete NOTE Throughout this manual the images of the scanner are pictures of the RUO version of the product The GeneChip Scanner 3000Dx with AutoLoaderDx differs from RUO version of the product in labeling and skin color Figure 2 3 GCS 3000 with AutoLoader Barcode Reader Use the barcode reader Figure 2 4 on page 15 to enter barcode encoded information found on the following items the GeneChip array cartridge the fluidics station the specimen identification the reagent lot number and other identification information Figure 2 4 Barcode Reader Chapter 2 Affymetrix GeneChip System 3000Dx v 2 System Overview 16 Hardware Firewall The hardware firewall Figure 2 5 on page 16 protects against unauthorized access to the workstation Figure 2 5 Hardware Firewall Additional Optional Hardware Components You must purchase a data transfer server from Affymetrix if you are going to transfer data out of AMDS for downstream analysis If you are going to use an uninterruptible power supply you must buy it from Affymetrix The printer you purchase must meet Affymetrix specifications In each case contact Affymetrix for information about the compone
37. while slowly turning the pump d Insert the free end of the tubing into the other clamp and attach it to the other fitting 5 Close the drop down module door 6 Order more replacement tubing P N 400110 NOTE At this point you can in the Configuration area set the Change Tubing Warning Limit and Change Tubing Alert Limit Click Save to save your configuration Fluidics Station Troubleshooting and Assistance If problems arise with the fluidics station use the following tables to locate the description that matches the problem If you cannot find a solution call Affymetrix Technical Support for assistance Troubleshooting Decision Tree The following simple flow charts Figure A 23 and Figure A 24 show you how to begin troubleshooting the fluidics station for a Missing Fluid Error MFE Appendix A GeneChip Fluidics Station FS450Dx Missing Fluid Error Workstation says Motor Contact Affymetrix Motion Error Yes Technical Support No Cartridge full No Yes a of f Sos Insufficient sample stain or wash buffer Remedy insufficiency Sepege Record cause of MFE as unknown 87 Appendix A GeneChip Fluidics Station FS450Dx 88 Stain bad MFE on several modules at once sensor readings above threshold Valve selecting a wash buffer Yes Module primed sensor reading not near 1000 Wash buffer bad above threshold Record cause of MFE
38. 00 ppm f ae BUE ii o TENERE CXBFER J PSB 1000 ppm A Pb sk He Wits Cr VID SRR PBB 25 2 BE PBDE 100 ppm dm Cd BYE MEO BRR LT Be BFS SaaS HPO Marking for Control of Pollution Caused by Electronic Information Products SJ T11364 2006 Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 128 Table B11 ASASVARREAMRSS ize Affymetrix GeneChip GCS3000 ScannerIx mass x o x o oj o Ed IE mem o ojejeje eo o o e oe oo gem mew 2 2 2 t EIE RES x ERRASASVRSLRE iH Pb 100 ppm fH Cd ADS Erne niu Tera ppm fm Cd AVE MEARE FER LL TS o A SSE Ste HER Marking for Control of Pollution Caused by Electronic Information Products SJ T11364 2006 STRAPS BH 1000 ppm ee Rim RM ahh aD ee ee Pine P pr AU e Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 129 Labeling Symbols Table B 13 Graphic Symbols for use in Labeling Symbol Label Statement Part Catalog Number Lot Number Expiration Date YYYY MM Kit will expire on the last day of the month Temperature Limitation Contains Sufficient for n Tests Irritant Hazards Consult Instructions for Use Manufacturer E Sx In vitro Diagnostic Medical Device lt o European Conformity fN Authorized Representative in the European Community BIA a Index A Add user 50 Adding arrays during a scan 42 Administrative features 44 Alerts re
39. 06 95 EC EN 60825 2 2004 IEC 61010 1 2001 Electrical equipment for measurement control and laboratory use EMC requirements Radiated and Conducted Emissions Electrostatic Discharge Radiated Immunity Electrical Fast Transient Burst Immunity Surge Immunity Conducted Immunity Magnetic Field Immunity Voltage Dips and Interrupts Harmonic Current Emissions Limits Voltage Changes Fluctuations and Flicker Safety of laser products Safety of optical fibre communication systems OFCS Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements IEC 61010 2 101 A1 2003 EN 61010 1 2001 EN 61010 2 081 A1 2003 EN 61010 2 101 2002 UL 61010 1 R 2005 07 CAN CSA C22 2 No 61010 1 2004 CAN CSA C22 2 No 61010 2 101 2004 CAN CSA C22 2 No 61010 2 081 2004 Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 121 Safety requirements for electrical equipments for measurement control and laboratory use Particular requirements for in vitro diagnostic medical equipment Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements Safety requirements for electrical equipment for measurement control and laboratory use Particular requirements for automatic and semi automatic laboratory equipment for analysis and other purposes Safety requirements for electri
40. 1 System Workstation Chapter 2 Affymetrix GeneChip System 3000Dx v 2 System Overview 14 GeneChip Fluidics Station 450Dx The Fluidics Station 450Dx Figure 2 2 on page 14 is an instrument consisting of four modules installed in a single Station or housing Each module holds a single GeneChip microarray and performs functions required for hybridization washing and staining of that array Up to 8 stations communicate with a single workstation Each module controls the addition of target and staining fluids to the array cartridge and subsequent washing of the array The module contains a pump valve thermo electric system and LCD that are controlled by scripts provided in the assay software module and automatically downloaded to each module then stored in the module s electronic memory For more information see GeneChip Fluidics Station FS450Dx on page 66 NOTE Throughout this manual the images of the fluidics station are pictures of the RUO version of the product The Fluidics Station 450Dx differs from RUO version of the product in labeling color of the levers and the presence of a barcode next to the LCD screen for each module Chapter 2 Affymetrix GeneChip System 3000Dx v 2 System Overview 15 GeneChip Scanner 3000Dx with AutoLoaderDx The GeneChip Scanner 3000Dx with AutoLoaderDx Figure 2 3 on page 15 is a wide field epifluorescent confocal scanning laser microscope which scans
41. 2 Affymetrix GeneChip System 3000Dx v 2 System Overview The Affymetrix GeneChip System 3000Dx v 2 consists of the hardware and software components that are required to process microarray based on assay parameters and to manage assay workflows This section describes the system hardware components and explores the AMDS User Interface Hardware Components The Affymetrix GeneChip System 3000Dx v 2 Instrument System includes standard hardware components that are delivered with all systems required components that may be purchased directly from Affymetrix or purchased separately and optional hardware components Standard Hardware Components The Affymetrix GeneChip System 3000Dx v 2 comes with these standard hardware components a A system workstation Figure 2 1 on page 13 GeneChip Fluidics Station 450Dx Figure 2 2 on page 14 GeneChip Scanner 3000Dx with AutoLoaderDx Figure 2 3 on page 15 a A barcode reader Figure 2 4 on page 15 A hardware firewall Figure 2 5 on page 16 System Workstation Monitor and Soundbar The system workstation Figure 2 1 on page 13 hosts the AMDS software and provides the hardware interface to other system components The workstation is a dedicated system for running AMDS and supporting the instruments of the GeneChip System 3000Dx v 2 As a result it is locked down to prevent other uses A monitor and sound bar not pictured are part of the workstation system Figure 2
42. AN CSA C22 2 No 61010 2 101 2004 CAN CSA C22 2 No 61010 2 081 2004 Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 123 Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements Safety requirements for electrical equipment for measurement control and laboratory use Particular requirements for automatic and semi automatic laboratory equipment for analysis and other purposes Safety requirements for electrical equipment for measurement control and laboratory use Particular requirements for in vitro diagnostic IVD medical equipment Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements Safety requirements for electrical equipments for measurement control and laboratory use Particular requirements for in vitro diagnostic medical equipment Safety requirements for electrical equipment for measurement control and laboratory use Particular requirements for automatic and semi automatic laboratory equipment for analysis and other purposes Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 124 Regulatory This device complies with Part 15 of FCC Rules Table B 10 Operation is subject to the following two conditions 1 This device may not cause har
43. Click the Restart Scanner button to restart the scanner You may need to close AMDS and restart screens then restart AMDS If the system remains unresponsive disconnect and reconnect power to the scanner restart the scanner normally close and restart screens and AMDS Laser warm up lasts for ten minutes during which time the Turn Laser On button will remain unchanged and AMDS will display the status message Warm up Simply note that this is normal operation Autofocus will fail if salt deposits accumulate on the array Use Tough Spots to prevent leaks in the GeneChip array See the quick reference card p n 08 0076 or the section Using Tough Spots to Prevent Leaks on page 109 Troubleshooting the Scanner This section deals primarily with diagnosing problems that may occur to the scanner Table B 4 Scanner Troubleshooting Guide Problem Possible Cause Corrective Action scanning Intermittent problems Loose cable Check all rear connections inside Scanner fails with array Power failure Manually extract array Check all connections to scanner Turn scanner on restart software Carousel does not automatically home a Check for stuck array Carousel not seated on D ring Alignment Pin not engaged in Carousel Door is open or ajar a Door is open when blue LED is off Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 116 Table B 4 Scanne
44. ID Corey Fast Name Cas Last Name Oms Comment Change Password Confirm Password reeceneed Select Assay Groupia v HGU133Plus2 v22 C OMoScan HD v1 0 SNF6 0 2 2 Save Add User a Decard LU i About Managing the System Click the System Management button Figure 5 1 on page 44 on the Administrator pane to access these system management functions Chapter 5 AMDS Administrative Features 52 a User Performed Service view the system s configuration 1 e the device and instrument settings and manage the fluidics station workstation scanner printer and firewall Service Logs view logs detailing user performed services Archive Test Request archive and then purge test request data General Configuration change the time and time zone settings for your particular location change the configuration flags for your instruments and set up network archive location Each of these functions has a separate screen To switch screens follow the instructions in Changing System Management Screens on page 52 Changing System Management Screens The System Management Menu located on the System Management toolbar allows you to switch between system management screens When you click on the System Management button in the Administrator pane the default screen is the User Performed Service screen User Performed Service Screen on page 53 To change system management screens
45. KG Affymetrix ilser Guide Affymetrix GeneChip System 3000Dx v 2 Trademarks Affymetrix GeneChip Flying Objective Powered by Affymetrix and GeneChip compatible are trademarks of Affymetrix Inc All other trademarks are the property of their respective owners Limited License Subject to the Affymetrix terms and conditions that govern your use of Affymetrix products Affymetrix grants you a non exclusive non transferable non sublicensable license to use this Affymetrix product only in accordance with the manual and written instructions provided by Affymetrix You understand and agree that except as expressly set forth in the Affymetrix terms and conditions no right or license to any patent or other intellectual property owned or licensable by Affymetrix is conveyed or implied by this Affymetrix product In particular no right or license is conveyed or implied to use this Affymetrix product in combination with a product not provided licensed or specifically recommended by Affymetrix for such use Patents for Arrays Instrument and Software Cartridge Arrays Products may be covered by one or more of the following patents U S Patent Nos 5 445 934 5 744 305 5 945 334 6 140 044 6 399 365 6 420 169 6 551 817 6 733 977 7 629 164 7 790 389 and D430 024 and other U S or foreign patents Products are manufactured and sold under license from OGT under 5 700 637 and 6 054 270 Fluidics Stations Product
46. R ROLE QU AD a EC AUR ERR REOR RR URN Re Ra 64 Instrument Troubleshooting lsssssessei s 64 Troubleshooting the Fluidics Station 2 0 0 ee 64 Troubleshooting the Scanner iilii 65 GeneChip Fluidics Station FS450DX uic mh 9 E vex Rn 66 ajirerelS eno MERE E ERREUR LU ONERE LEER 66 Warnings and Precautions nnana aaan eee eee 66 When to Contact Affymetrix 0 hes 67 Instrument COMPONeNIS s pss cock he dep pm Me Ba edo HEC Rad bao ww its dade 67 Using the Fluidics Station 450DX cerce ek e EORR ERES xen WE 69 Assay DOCUMENTATION ssscskRREReRREE PVP PRPRRE ReR Pi n E e Pig 69 Using the Barcode Reader with the Fluidics Station 0 0 0 0 cece eee 69 Fluidics Station 450Dx Protocols 000 0 eee 70 Operating the Fluidics Station s se 0 0 cece ee 70 Starting the Fluidics Station 2 eee 70 Running a Fluidics Station Protocol 0 00 eee 71 Shutting Down the Fluidics Station 0 0 00 0c ses 75 Priming the FIUIGICS Station eae e ee g Sods hd PR ODER RE E E ER ds 75 Fluidics StationDx Care and Maintenance lslsissl ee 77 Instrument Care lll ss 77 Appendix B Contents 6 Fluidics Station Bleach Protocol n sasaaa aana eee 78 The Bleach Cycle nnana nannaa 78 THe RINSE Cycle ec ke ee e RICE Peed da ddd ee UPC Dc ek OR aii 81 Peristaltic Tubing Maintenance 00 000 eee eee 83 Setting the Peristaltic Tubing Maintenance Parameters
47. RAEH pESZSENSZASDNEZT es SRESHSTFREFK SSREMLECLZRARMSERAIHUSER AK B EIC IXPEDLE RU HBAME DEAT HERNAN Hey amp 2S 39 SHES HH SBS UIHA BHSFRPSEPSEREMILE SENS FRPP RAR Rit EF SS SOSHARAIRSLERLRKRASASDRATK 1 ATH FRER FET FKARMASASHRAT FEST ES RCRRDHE CEREAIS E BR STEERER S RAN RRSP LANKRASASDRARRERE Pb eS Cr gn SAEZ PER AFR FE CPEDE HNARR TPA HFRFE BelISE a 36 a T ili 5 ag ha H y n Z7 ur Table A7 ABHRMARTKARR AM LH Affrmetriz GeneChip Fluidics Station 450Dx SPS RL om m ere Ge ASV EME Ce m m PEDE 100 ppa Ca ARAA ETTA STREP SHRM MER Marking for Control of Pollution Caused br Electronic Information Products SJ T11364 2005 GeneChip Scanner 3000Dx with AutoLoaderDx Introduction This section describes how to use the GeneChip Scanner 3000Dx with AutoLoaderDx aka the scanner The scanner is used as part of the overall assay workflow Affymetrix has designed the scanner expressly for scanning multiple array cartridges The scanner can scan up to 48 arrays automatically without operator presence Figure B 1 GeneChip Scanner 3000Dx with AutoLoaderDx WARNING Do not remove the external case or skin or scanner cover of the AutoLoaderDx Use the scanner only as instructed in this user guide Do not attempt to service the instrument Only qualified service engineers can open and service the scanner There are no customer servicea
48. S Troubleshooting on page 61 NOTE Older models of the workstation will not give Hard Drive Health status in the Device Status pane Alert Pane and Alert Details Pane The Alert pane Figure 2 17 on page 23 provides alerts if a component or process is not operating as expected By clicking on a specific alert information about the alert displays in the Alert Details pane Figure 2 18 on page 24 Depending on the type of alert you may see information related to Specimen ID Assay Name Workflow Step Date Time Alert details Recommended resolution See Device Status and Alert Icons on page 62 for more information about different types and levels of alerts Figure 2 17 Alerts Pane Chapter 2 Affymetrix GeneChip System 3000Dx v 2 System Overview 24 Alert Details Specimen ID Assay Name Workflow Step Date Time 2011 02 12 17 29 Details The hard drive health has degraded There has beena loss of hard drive redundancy and you should take the necessary precautions while waiting for the hard drive health to be restored Recommended Resolution Please contact your Dell service representative Affymetrix GeneChip System 3000Dx v 2 Operation Basics Introduction This section shows you how to Start the system including o Starting the workstation o Logging on and off of the system o Starting the fluidics station and scanner Shut down the s
49. Specimen IDs do not need to be unique Specimen IDs can have up to 40 characters 4 In the Assay name column select the required Assay Name from the drop down list Chapter 4 Test Request Processing 32 Click Submit or Delete Youcan submit one or more test requests at the same time once the Specimen ID and the assay name is selected a Submitting your test request will create it and make it active If you delete your test request before submitting no test request will be created a In either case the Enter Test Request screen closes Youcan identify your newly created test request in the Active Worklist based on the Specimen ID Assay Name and current status Editing Test Requests You can edit the Specimen ID for a test request if you have not yet completed its registration Once you register a test request you cannot edit it To edit a test request 1 From the Active Worklist select a test request to be edited The edit button displays on the Active Worklist toolbar Click Edit The Edit Test Request pane displays Figure 4 4 on page 32 Figure 4 4 The Edit Test Request screen Edit Test Request Total 1 Modify the Specimen ID a This is the only field you can edit a Click anywhere on the tool bar or Specimen ID row to indicate you have finished changing the ID You can now choose to save changes discard changes or cancel edit to continue To save your changes click Save Ch
50. a network location from a non AMDS workstation To purge test requests 1 Select the test requests you wish to purge 2 Click Purge Chapter 5 AMDS Administrative Features 59 Setting General Configurations In the General Configuration screen you can View and configure time and time zone settings Configure scanner settings Require users to approve or reject analysis results before proceeding Configure network archive location settings System Management General Configuration a ia ent 2 v A 2x Time Zone Editable Settings Editable Local Time 3 37 45 PM 20011 02431 Time Zone E cific Time US amp Canada Time Zone Current Settings Local Time 2 3 37 45 PM 2011 02 11 Current Time Zone Pacific Standard System Configuration Flags Turn On Laser Ifthe scanner laser is off on system startup turn it on O Disable AutoLoader Disable the scanner AutoLoader v Require User Approval Require the userto approve or reject analysis results once available before proceeding Network Archive Storage Configuration e g RemoteFileServer Share UNC Share To setup the Network Archive Storage device please do the following 1 Enter a valid UNC Share User Name and Password Password 2 Click the Test Connection button to configure the firewall and write a temporary file to the share 3 If the test fails a message will be displayed to assist
51. ach of the fluidics stations that will be used at this time 4 Ifrequired enter Wash Buffer A and Wash buffer B lot numbers Information entered in these fields will be saved into the logs for test requests NOTE You need to use the module check boxes only if the fluidic station contains faulty modules Unchecking a fluidics module will cause that module to be skipped and it won t be available for processing arrays 5 Select the fluidics station s and click Prime See Priming the Fluidics Station on page 75 for details 6 Click Close Setup on the toolbar IMPORTANT You must prime the fluidics station when you first start the fluidics station when you change the wash buffers if you have performed a shutdown on the station since it was last used or if resolution to an alert tells you to prime You DO NOT need to reprime the fluidics station when using assays that use the same wash buffers Associating Test Requests with Fluidics Stations To associate test requests with a fluidics station 1 Click Fluidics The Fluidics Worklist displays Figure 4 10 on page 38 2 Place the array in the fluidics station module Do not load the cartridge at this time 3 Associate the test request with a fluidics station module A If you are using a barcode reader repeat the following steps for each array you wish to process 1 Scan the array barcode AMDS selects the array associated with the test request You will hear a single
52. al for more information about how to enter the Reagent information for your specific assay 5 Click Save to save your registration information and remain in the Registration Worklist This step allows you to save your work and pause before proceeding with the workflow 6 Click Complete Step This step will complete registration and move the test requests to the next step in the workflow which will depend on the type of assay you are using Consult your assay software module manual for more information Troubleshooting Registration AMDS will check your data as you enter Array IDs and Reagent Kit IDs You must correct the data if you get a message regarding one of the following errors The Array ID already exists a You have entered an invalid Array ID a The array is expired The Reagent Kit ID entry is disabled for this assay a The Reagent Kit ID entered is invalid for this assay Until you correct the error you cannot complete registration Hybridization Oven Hybridizing Arrays in the Hybridization Oven m IMPORTANT Make sure you understand how to operate your hybridization oven If you are using the GeneChipe Hybridization Oven 640 refer to the GeneChip Hybridization Oven 640 User s Guide P N 700281 for detailed instructions If you are using the GeneChipe Hybridization Oven 645 refer to the GeneChipe Hybridization Oven 645 P N 08 0255 for detailed instructions Click the Hybridization Oven button Figure 4 7 on
53. and process test requests and generate test results Perform administrative tasks such as u Viewing logs o Managing assays n Managing users o Maintaining the system Troubleshoot the system The appendices also provide information for using the GeneChip Fluidics Station 450Dx as well as the GeneChip Scanner 3000Dx with AutoLoaderDx Intended Use Indication s for Use The Affymetrix GeneChip Microarray Instrumentation System consisting of GeneChip 3000Dx scanner with autoloader FS450Dx fluidics station and GCOSDx AMDS software is intended to measure fluorescence signals of labeled DNA and RNA target hybridized to GeneChip arrays Special Condition for Use Statement For use only with separately cleared GeneChip microarray assays n WARNING Operators are responsible for following internal security policies to ensure security of patient data Other Documentation The Affymetrix Molecular Diagnostic Software AMDS Quick Reference Card is available Part Number 08 0271 The AMDS software also has online help Tooltip help is available for many interface elements just hover over an interface element to view a description of the item or to view truncated data About Online Help While the online help system is designed to provide content sensitive help you can access the complete content of the user guide as well When you click Help the cursor displays as a question mark as seen in Figure 1 1 on page 9
54. anges When the Confirm Step dialog displays enter your password and the reason for the change a Click OK The modified Specimen ID appears on the Active Worklist To discard your changes click Discard Changes The Confirm Step dialog box displays a After you click Yes you remain on the Edit Test Request Screen and can continue editing the Specimen ID To cancel all edits and to leave the Edit Test Request Screen click Cancel Edit Canceling a Test Request After you have submitted a test request you cannot delete it but you can cancel it and send it to the Non Active Worklist You can only cancel one test request at a time You can cancel it during processing up until the point of generating results To cancel a test request 1 From the Active Worklist select the test request you would like to cancel Chapter 4 Test Request Processing 33 2 Click Cancel Test Request on the Active Worklist toolbar The Confirm Step dialog box displays Enter your password Select a reason for canceling from the list Enter any other necessary information Au Pw Click OK to confirm cancelation AMDS moves the test request to the Non Active Worklist Adding Additional Information to a Test Request NOTE See your assay software module manual for more details After you create a test request and any time before the array associated with it begins scanning you can add data to it The dialog box for addi
55. anufacturer the system may require additional information for each test request in order for that test request to run successfully Failure to enter the additional information prior to starting to scan the array will cause a failure when attempting to execute the analysis algorithm following the scanning step See your assay software module manual for details Click on the Scanner button Figure 4 12 on page 40 in the Workflow pane to view the Scanner Worklist Figure 4 12 The Scanner Worklist Button Scanner Scanning Arrays in Normal Operational Mode To scan an array in normal operational mode Chapter 4 Test Request Processing 41 1 Click Scanner Figure 4 12 on page 40 The Scanner Worklist displays Figure 4 13 on page 41 Figure 4 13 The Scanner Worklist Scanner Worklist Total 0 ee ELLE essa si 2 Load the array cartridges into the AutoLoaderDx starting with slot 1 NOTE During a scanner run always start with the array in slot 1 It is most efficient to remove all scanned arrays and shift any unscanned arrays in the carousel to slot 1 so there are no empty slots 3 Add any additional arrays in the remaining slots in a contiguous manner Click Start As each array is encountered the scanner will pass the Array ID to AMDS AMDS will find the associated test request 5 When the scan completes as indicated by the status for the test request showing complete cl
56. artridge holder Engage the washblock by pulling up on the cartridge lever to the closed position The fluidics station drains the cartridge and then fill it with a fresh volume of the last wash buffer used When it is finished if the LCD screen displays EJECT CARTRIDGE again remove the cartridge and inspect it again for bubbles If no bubbles are present it is ready to scan proceed to step 13 12 Flip up the cartridge holder lever to re engage the wash block 13 Lift up on the needle lever to remove the needles from the vials 14 Replace the used vials with new empty vials 15 Press down on the needle lever The fluidics station automatically performs a Cleanout protocol The LCD screen indicates the progress of the Cleanout protocol When the Cleanout protocol is complete the LCD screen should display the following REMOVE VIALS 16 Lift the needle lever and remove the sample vials from the sample holder Shutting Down the Fluidics Station You should perform the Shutdown protocol at the end of a session Run the shutdown protocol any time you will not use the fluidics station within the next twelve hours 1 2 3 4 The shutdown protocol requires three 1 5 mL sample vials for each module Place the wash lines into a bottle filled with deionized water Run the Shutdown protocol and follow the instructions on the LCD screen After the Shutdown protocol is complete flip the ON OFF switch to the OFF pos
57. ble parts Removing the case exposes the customer to laser and electrical shock hazards Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 102 n WARNING ONLY authorized personnel may service this equipment The GCS3000 Scanner contains an incorporated Class 3B laser Use of controls or adjustments or performance of procedures other than those specified herein may result in hazardous radiation exposure nn WARNING The GCS3000 Scanner contains an incorporated Class 3B laser with the following specifications Wavelength 532nm 1 nm Beam Divergence full angle 8mrad Output Duration Continuous Wave Maximum Power Output 500mW Safe Operation To ensure safe operation of the scanner bu IMPORTANT Shutting down the scanner To preserve the lifetime of the scanner s internal laser we recommend that you turn the scanner OFF when it is not in use for any extended period of time such as overnight or a weekend Read this section completely before operating the instrument Do not attempt to service this instrument Any attempt at unauthorized service may damage the instrument and or void the warranty a The instrument weight is approximately 63 pounds 28 6 Kg Do not place it on an unstable cart stand or table Failure to properly support the instrument may cause serious damage or injury and may void the warranty CAUTION Heavy object Two people are required to lift the scanner
58. bs from the print queue Resume all queued print jobs To resume jobs in the queue click Resume All Chapter 5 AMDS Administrative Features 56 Figure 5 12 The Printer region of the User Performed Services screen Printer Printer Name AMDSPrinter Online Offline Number of Jobs in Queue 0 Purge All Resume ll NOTE You cannot change the printer An Affymetrix service engineer sets up the printer as part of the AMDS installation process Backing Up and Restoring Firewall Settings The AMDS firewall monitors incoming and outgoing messages from the workstation and protects the workstation from malicious intrusion Figure 5 13 on page 56 On the Firewall region of the User Performed Services screen you can View the last firewall backup Backup current firewall settings a Restore firewall settings from the last backup Some assays access servers on an intranet or on the internet When these assay software modules are installed a rule is written to the firewall This rule permits communication between the AMDS workstation and the remote server Restoring firewall settings may overwrite these rules and prevent AMDS from communicating with the server In this case reinstall any assay software modules that communicate with remote servers in order to restore communication between the workstation and server Figure 5 13 The Firewall region of the User Performed Services screen
59. cal equipment for measurement control and laboratory use Particular requirements for in vitro diagnostic IVD medical equipment Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements Safety requirements for electrical equipments for measurement control and laboratory use Particular requirements for in vitro diagnostic medical equipment Safety requirements for electrical equipment for measurement control and laboratory use Particular requirements for automatic and semi automatic laboratory equipment for analysis and other purposes Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 122 GCS 3000Dx v 2 GeneChip Instrument System We Affymetrix Inc 3420 Central Expressway Santa Clara CA 95051 Declare under sole responsibility that the Affymetrix GeneChip GCS 3000Dx v 2 GeneChip Instrument System including the Scanner GCS3000Dx v 2 the AutoloaderDx the Fluidics Station FS450Dx v 2 and associated Workstations with Affymetrix Molecular Diagnostic Software AMDS and conforms with the relevant provisions of the following standard s of safety and compliance and or other normative documents EU In Vitro Diagnostic Medical Devices Directive 98 79 EC Annex III CE Declaration ISO 13485 2003 Medical Devices Quality
60. can place your arrays into an oven that is hybridizing other sets of arrays as long as the oven temperature and rotation speed are correct for your arrays Monitor your arrays using data from AMDS To start and monitor oven hybridization 1 Turn on the oven and wait for it to reach the correct hybridization temperature Place the array cartridges into trays Place the trays into the hybridization oven Select the test request s in the Hybridization Oven Worklist and click Start on the toolbar m RWN Monitor the hybridization process You can monitor elapsed time for all oven hybridization processes on the Hybridization Oven Worklist a If you are using a GeneChip Hybridization Oven 645 you can monitor the temperature rotation speed and oven door status in the Device Status pane Alerts related to your process display in the Alerts pane and Alerts Details pane For more information about device status and alerts see AMDS Troubleshooting on page 61 Ending Oven Hybridization To end oven hybridization 1 When the correct amount of time has elapsed remove the arrays from the oven 2 Select the test requests associated with the arrays and click End 3 Click Complete Step This completes oven hybridization and moves the test requests to the Fluidics Worklist Troubleshooting Oven Hybridization AMDS will check your data as you enter Tray and Oven information You must correct the issue if you get a message regarding on
61. case character two special characters and two numerics The numerics and the special characters may repeat Select the user s role Select the assay groups you want for the user 3 Click Save Changes AMDS commits the information and creates the user in the system with the associated roles and permissions Editing a User You can change any user attribute other than the user ID Chapter 5 AMDS Administrative Features 51 1 In the User Management screen Figure 5 6 on page 50 select a user 2 Click Edit User The Edit User screen displays The Edit User screen looks like the Add User screen Figure 5 7 on page 51 displaying the user s current data and disabling the User ID field 3 Youcan Select Active to activate or deselect to deactivate the user Edit the user s first and last name Enter or edit a comment new password in the Confirm Password dialog box Change the user s role Change the assays groups to which the user has access 4 Click Save Changes Change a password by selecting the Change Password box and then entering and confirming the AMDS commits the information and change the associated roles and permissions of the user Deactivating a User To deactivate a user uncheck the Active box on the Edit User screen You can reactivate the account at a later date Figure 5 7 The Add User screen Details Select Role O Guest Iv Active User
62. connections Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 105 Figure B 2 Workstation rear cable connections 3 Pronged Electric Power Plug Fluidics Station 450Dx Connection unusssuca AutoLoaderDx Ethernet A Connection we wn S8eeeeeee Y 1 Firewall Connection Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 106 Figure B 3 Scanner Rear Connections Circuit Breaker Reset Button Power Cable Cable Receptacle to Workstation Upper Drain Tube Lower Drain Tube Scanner Indicator Lights and On Off Button The front panel has the following button and indicators Figure B 4 on page 107 Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 107 Figure B 4 Scanner Indicator Lights 1 Blue AutoLoaderDx Indicator Light 2 Blue Scanner Indicator Light 3 Green light 4 1 0 on of button 5 Yellow light 1 Blue indicator light on AutoLoaderDx running vertical at front center This light appears to be merely an extension of the lower scanner light However when on it indicates that the AutoLoaderDx door is closed and locked It will turn off when the door is unlocked 2 Blue scanner indicator light on the scanner body running vertical at front center This light extends to the bottom of the scanner and is always on when the scanner is on 3 Green light a On System is r
63. cordance with the Chinese RoHS Restriction of Hazardous Substances Table B 11 and Table B 12 contain information identifying the specific hazardous material s and the components parts in which they are found Table B 11 Table Containing Names and Contents of Toxic or Hazardous Materials Instrument Affymetrix GeneChip GCS3000 ScannerDx with AutoLoaderDx Printed Circuit X O X O O O Boards Rubber amp Plastic Parts o O o o o o CN X o o o o O omponents um Metal o o o o o o arts External Metal Parts o o o o o o Labels 0 O O O Oo O Packaging Shipping O O O O Oo O Materials Internal Lasers Optics O O O O Oo O amp Sensors Adhesives O O O O O O Internal Power O O O O O O Supplies m and o o o o o o umps X Indicates that the toxic or hazardous substance contained is above the limit of 1000 ppm for lead and above 100 ppm for cadmium O Indicates that the toxic or hazardous substance contained is below the limit of 1000 ppm for lead mercury hexavalent chromium polybrominated biphenyls and polybrominated diphenyl ethers and below 100 ppm for cadmium Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 126 Table B 12 Table Containing Names and Contents of Toxic or Hazardous Materials Instrument Affymetrix GeneChip GCS3000 ScannerDx Printed Circuit Boards Rubber amp Plastic Parts Electrical Components Internal
64. d by your user role For information about user roles see About User Roles on page 50 Figure 5 1 Administrator Pane Administrator Viewing Logs The View Logs function allows you to View system logs and audit logs a Filter logs according to specific criteria Export and burn logs files to CDs or DVDs for troubleshooting or retention System Logs System logs contain system level algorithm and computer messages as well as recorded parameters of completed assays such as date and time the component type user etc The View System Logs screen Figure 5 2 on page 45 displays the system log in the upper half of the View Logs screen See also Exporting and Burning Log Files to CD or DVD on page 46 To view a system log 1 Click the View Logs button Figure 5 1 on page 44 in the Administrator pane The log view displays the current system log 2 Optional If you wish to view a system log other than the current one select one from the System Log list Chapter 5 AMDS Administrative Features 45 View Logs Exported File Size 0 MB Files Exported 0 0x2 Business Enifies User 2011 02 12 ScaneelistrumeniWarneger Seri number Crack gt eystem stardup success Scanner serial number WTOSIM v2 16 47 58 Method cid VscilrScsmee Senis Namber System Device configuration scanner seris number MT SIM v2 Collections Generic List Attymetrx D2 Business AedrumeriCartrcl ple IMereoer Close
65. d Seta Mumbo 1825000002220 Oven Mumba 1 i angaditerop HetrumentContral j 2011202412 meniMereger i Seis number chak st system startup successful Hyva 1629000000000 Davies 16 47 58 Method yoOvenSerisiNumber System Config HybOvent 1626000000000 Specimen ID H919802 Assay Name HCHJ123 Plus 20 v2 2 bea ooo Eua umm inimicum CM e pemen 2011 0242 EMIL Drrmuitectetr mic Filtering the System Log To filter log entries 1 After selecting a system log enter filter criteria in the row that is just below the system log column headers You can filter the log according to Date Time System component Log message type User 2 Click Remove Filter to display all log entries Chapter 5 AMDS Administrative Features 46 Audit Logs Audit logs contain information messages and parameters related to a specific test request for each step of the workflow See also Exporting and Burning Log Files to CD or DVD on page 46 Viewing Audit Logs To view an audit log 1 Click the View Logs button Figure 5 1 on page 44 on the Administrator pane The Audit Log displays in the lower half of the View Logs screen In the Audit Logs toolbar click Browse for Audit Logs to locate a specific test request s log 3 Select the test request you want to view Click Display Filtering Audit Logs To view audit log entries related to specific types of information 1 After selecting an audit log enter filte
66. d of entering the tray number for each array separately you can add the tray number to all ten arrays at once Contiguous Select and Enter Click on the first row of the desired selection Hold down the Shift key Click on the last row of the desired selection Hold down the Ctrl key and A Select from the drop down in the last row OR B Click in the field in the last row and scan the barcode OR C Click in the field in the last row release the Ctrl key and enter the value 5 Click out of the field or press the Enter key PWN Non Contiguous Select and Enter 1 Click on the first row of the desired selection 2 Hold down the Ctrl key 3 Select each desired row individually Chapter 3 Affymetrix GeneChip System 3000Dx v 2 Operation Basics 29 4 While still holding the Ctrl key A Select from the drop down in the last row OR B Click in the field in the last row and scan the barcode Or C Click in the field in the last row release the Ctrl key and enter the value 5 Click out of the field or press the Enter key Handling the Array Cartridge The array comes mounted in a plastic package to form an array cartridge Figure 3 4 on page 29 The array contains a collection of oligonucleotide probes that have been arrayed on the inner glass surface A chamber in the plastic package directly under the chip acts as a reservoir where hybridization and washing staining occur Figure 3 4 The Array Cartridge
67. d on the back of the fluidics station See Figure A 3 on page 69 Flip the ON OFF switch for the fluidics station to the ON position The switch is located on the left side of the fluidics station The LCD screen should display the following Power On Done NOT PRIMED 25 C If you have not done so already turn on the workstation and log onto AMDS Troubleshooting the Fluidics Station Connection to the Workstation To troubleshoot or test communication between the workstation and fluidics stations 1 Select Home in the Procedure dialog box and click Perform The Confirm Step dialog box displays Enter your password and the Event Reason Click OK o AMDS instructs the fluidics station to home the valves o If successful the LCD on the fluidics station informs you o If homing fails the Device Status region on a worklist screen alerts you o If you fail after several unsuccessful tries to home the fluidics station turn off the fluidics station Then turn the fluidics station back on and restart the AMDS workstation o If these failures continue call Affymetrix technical support Appendix A GeneChip Fluidics Station FS450Dx 71 Running a Fluidics Station Protocol The following steps represent a general procedure Your specific protocol may indicate steps different from these outlined below 1 Check to ensure that all the wash lines are in the appropriate wash bottles Please consult the array package insert
68. ding sound 2 Scan the barcode for the fluidics station module that will process the array The fluidics station and module information will be entered for the test request You will hear a double ding sound Chapter 4 Test Request Processing 40 B If you are entering the information manually 1 Select a test request record with the desired Array ID 2 Enter the fluidics station number in the Station field and module number in the Module field You are ready start the fluidics run Starting the Fluidics Run To start the fluidics run 1 Select the test requests on the Fluidics Worklist 2 Click Start on the toolbar of the Fluidics Worklist 3 Follow the instructions on the fluidics station LCD 4 After you remove the arrays from the fluidics station click Complete Step This step completes washing and staining arrays with the fluidics station and moves the test request s to the Scanner Worklist The fluidics stations will continue running for a few minutes after you remove the arrays If you are done processing arrays for this assay or won t be processing any more arrays on this fluidics station for several hours perform the shut down procedure See Shutting Down the Fluidics Station on page 75 Scanner Scanning Arrays Lu IMPORTANT Make sure you know how to operate the scanner See GeneChip Scanner 3000Dx with AutoLoaderDx on page 101 NOTE For certain assays as determined by the assay m
69. e fluidics station Using the Fluidics Station 450Dx This section shows you how to run the fluidics station Assay Documentation You must configure the fluidics station for the type of assay that you want to run on the fluidics station The partner who provides the assay determines the assay type and provides the relevant documentation in the form of a package insert or other type of document Each assay package insert or assay document describes the fluidics station configuration requirements for that assay The system ensures that the fluidics station is configured properly for the assay being run If the station is not configured properly for the assay you will be notified You may then configure the station for that assay or run the test request on a fluidics station that is correctly configured for that assay Using the Barcode Reader with the Fluidics Station 1 Open the Fluidics Worklist 2 Hold the array or insert the array into the fluidics station module 3 Aim the barcode reader at the barcode of the array and record the barcode number 4 Aim the barcode reader at the barcode of the fluidics module and record the barcode number AMDS locates the appropriate fields in the Fluidics Worklist and add the numbers The barcode reader emits three distinct sounds depending on the sound s function a A good sound that indicates that the barcode reader selected the correct test request Appendix A GeneChip Flu
70. e fluidics station Loose cables No user response to Remove Vial prompt or other prompt Turn fluidics station power on and then try to connect again Firmly connect cables to fluidics station In the current Worklist screen on the alert pane follow the recommended resolution Error While Draining Error While Filling Cartridge is not filling or draining properly Defective septa in cartridge Insufficient sample or stain volume Excessive bubbling in cartridge Buffer conductivity too low Failure of one of the fluid sensors In the current Worklist screen on the alert pane follow the recommended resolution You may need to use a new cartridge Add more sample solution to sample vial Change the buffer reduce detergent Use fresh buffer Call Affymetrix technical support for service Error While Filling System detects improper conditions while filling Note where in protocol error occurred Missing or insufficient stain or antibody in vial Wash or DI water empty Air bubbles in line Leaks Identify if chip is filled In the current Worklist screen on the alert pane follow the recommended resolution Appendix A GeneChip Fluidics Station FS450Dx 91 Table A 2 Problems and Solutions Continued Error Message Problem Possible Cause Possible Solution Follow the recommended resolution in the current Worklist screen on the alert pane
71. e of DI water Insert the waste line into the waste bottle Figure A 14 on page 79 4 Immerse all three wash and water lines of the fluidics station into the 500 mL of bleach solution Figure A 14 on page 79 DO NOT IMMERSE THE WASTE LINE INTO THE BLEACH Ls IMPORTANT The bleach protocol requires approximately one liter of deionized water Figure A 14 Immerse the tubes into the 0 52596 sodium hypochlorite solution The waste line remains in the waste bottle 5 Click the System Management button Figure A 15 on page 80 on the Administrator pane 1 Affymetrix also recommends the new Clorox Ultra Bleach with 6 15 sodium hypochlorite but your mixing calculations will be different Figure A 15 Sample Figure Administrator View Logs m Assay Management m User Management System Management Appendix A GeneChip Fluidics Station FS450Dx 80 6 The System Management screen displays The User Performed Service screen should be the default screen If not select In House Service gt User Service The User Performed Service screen displays Note the fluidics station maintenance area Figure A 16 on page 80 Figure A 16 Sample Figure Fluidics Station Station E Time Elapsed Since Last Bleach 105 d Last Change Tubing 105 ld Procedure Bleach J Configuration Bleach Interval Warning Limit 10 d Bleach Interval Alert Limit 100 d Change Tubi
72. e of the following errors a Arrays are not compatible for inclusion on same tray Arrays are not compatible for current temperature and rotation speed of oven Chapter 4 Test Request Processing 38 Fluidics Washing and Staining Arrays in the Fluidics Station IMPORTANT Make sure you know how to operate the fluidics station See GeneChip Fluidics Station FS450Dx on page 66 Click on the Fluidics button Figure 4 9 on page 38 in the Workflow pane to view the Fluidics Worklist Fluidics AMDS provides the tools to set up the fluidics station and then to complete washing and staining of the arrays You can monitor the fluidics station and the washing and staining process on the LCD on the fluidics station a Fluidics Worklist Device Status pane a Alerts and Alert Details panes Consult AMDS Troubleshooting on page 61 for information regarding alerts and instrument error messages Setting Up the Fluidics Station To set up the fluidics station 1 Click Fluidics The Fluidics Worklist displays Figure 4 10 on page 38 Fluidics Worklist 2 Click Station Setup The Fluidics Station Setup screen displays Figure 4 11 on page 39 Chapter 4 Test Request Processing 39 Figure 4 11 The Fluidics Station Setup screen Fluidics Station Setup cs ics Sis Mot Pamad 3 Select the desired assay from the Assay Name field for e
73. e second category of troubleshooting relates to problems with an individual test request These issues generate an alert with an associated Specimen ID and module Potential alerts include Scanner could not read the bar code a Autofocus error a Gridding error Analysis algorithm error as a result of missing information Chapter 6 AMDS Troubleshooting 64 Refer to the individual alert for additional information and a suggested course of action for resolving the error For more information see Resolving Alerts on page 64 Operational and Data Input Errors The third and final category of error consists of operational or data input errors These type of errors are relatively easy to detect and correct as the User Interface is designed to provide immediate feedback and prevent incorrect operation and or data input Some examples of incorrect operation or data input include Entry of an invalid Array Barcode Loading of an array into a fluidics station that is not primed Loading of an array into a fluidics station that is configured for a different assay type Scanning an array that array s test request is still displayed in the Fluidics Worklist In each of these cases AMDS immediately displays an error message that informs you the action or data entered is inappropriate and prevents you from proceeding Resolving Alerts To resolve an alert 1 Click on the Alert in the Alerts pane Figure 6 2 on page 63 The al
74. e vials containing reagents into the sample holders 1 2 and 3 on the fluidics station in accordance with the assay instructions Figure A 7 on page 73 Figure A 7 Sample Figure Needle Lever in Up Position Appendix A GeneChip Fluidics Station FS450Dx 74 NOTE When you place the vials into the holders orient the vial caps toward you so that the vials seat snugly into their respective holders d When you have loaded the vials gently but firmly press down on the needle lever to insert the needles into the vials The run commences automatically See Figure A 8 and Figure A 9 Figure A 8 Press down on the needle levers to start the protocol Figure A 9 The sample vials on the sample holder with the needle lever down note the orientation of the vial caps As the run progresses check to ensure that the cartridge is filling properly and that bubbles are not forming If it is not filling properly see the note below in this section Appendix A GeneChip Fluidics Station FS450Dx 75 10 When you have completed the hybridization or washing and staining protocols the LCD screen should display the following EJECT CARTRIDGE 11 Eject and remove the cartridge by pushing down on the cartridge lever The LCD screen should display the following ENGAGE WASHBLOCK NOTE If air bubbles are present in the cartridge return it to the c
75. e warning times must be less than the alert times o It is recommended to change the alert first and then the warning o Click Save after you have changed the values View or change the Change Tubing Warning Limit and Change Tubing Interval Alert Limit o The change tubing reminder is preconfigured on to a schedule recommended by Affymetrix o Set these limits in the Fluidics Station Configuration region o The warning times must be less than the alert times n It is recommended to change the alert first and then the warning n Click Save after you have changed the values After each of these changes the Confirm Step dialog box displays Confirm the change with your password and the reason for you performed the action Figure 5 10 The Fluidics Station region of the User Performed Services screen Fluidics Station Configuration Station vi Bleach Interval Warning Limit e ES d Time Efapsed Since Bleach Interval Alert Limit ld Last Bleach d Last Change Tubing m idl Change Tubing Warning Limit d Change Tubing Alert Limit d Procedure Bleach v Perform Managing the Workstation Hard Disk On the System region of the User Performed Services screen Figure 5 11 on page 55 you can View how much space is available on the workstation hard disk View the size of the current export files a Clear the exported file list o Clearing this list removes all exported logs from the system without burning them to disc o
76. eady to scan yellow off b Flashing Scan in progress I O on off button in the center 5 Yellow light a On Idle laser is warming up laser not ready green off b Off System ready no errors Green on c Flashing Error Summary of Indicator Lights Table B 1 below summarizes the light conditions and their meaning Table B 1 Light colors and meanings Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 108 Initial Off Off On Off Initial power up embedded PC takes control boot up Scanner On On On Off Embedded PC takes control of scanner boot up boot up Laser Off On On Off Software enabled and laser is warming up warm up System On Off On Off scanner ready for use and scanner door is ready unlocked waiting to receive a carousel Error Off Flashing On Off Fatal error reboot scanner and software scanner door is unlocked to remove carousel if necessary Scanning Flashing Off On On Scanning is in progress and scanner door locked Scanning Flashing Off On Off Scanning is in progress and scanner door is unlocked Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 109 Scanning Arrays This section shows you how to scan multiple arrays using the AutoLoaderDx The GeneChip arrays are similar to those shown in Figure B 5 Figure B 5 The array or cartridge note the location of the flange The AutoLoaderDx will accept the array in only one orientation Plastic ca
77. ected test requests Exported log files are not burned to a disc when archiving test requests You can archive test requests to a A network drive See Configuring Network Archive Storage on page 60 a A DVD or CD To archive test requests 1 If necessary use filters to locate the test requests you want to archive 2 Select the test requests a You can use Select All if you want to archive all of the displayed test requests When you select test requests you see the number of selected test requests on the toolbar 3 Click DVD Archive to burn the selected test requests to CD or DVD Click Network Archive to archive to a remote drive The network drive must be configured for this feature to be available a For more information see Configuring Network Archive Storage on page 60 Figure 5 15 The Archive Test Requests Screen System Management Archive Test Requests Display All Display All Display All 2011 02 12 16 39 A4435 HG U133 Plus 2 0 v2 2 52001900456789122015232937903114 2011 02 12 16 41 A4436 HG U133 Plus 2 0 v2 2 852001300456783122015232337303098 Purging Test Requests You can only purge a test request record after it has been archived Once the test requests have been purged they are no longer available on the AMDS system You can view test requests that have been archived to CD DVD by using the DVD Index button a You can view test requests archived to either CD DVD or
78. erring data without the proper certificate installed Click OK to dismiss the message and return to the Assay Management screen Figure 5 5 Server Certificate Dialog ES Please select a server certificate to install 9 Install from CD O Install from local disk drive ajf dtsd5pfrbf1_05132008 cer Managing Users The User Management button allows you to add users or to change user privileges To open the User Management screen 1 Click the User Management button Figure 5 1 on page 44 on the Administrator pane The User Management screen displays Figure 5 6 on page 50 Chapter 5 AMDS Administrative Features 50 Figure 5 6 User Management screen User Management About User Roles Each user has a defined role that specifies the actions the user is allowed to perform on the system Guest Users with this role are allowed to view non patient information on the system and are not allowed to perform any of the processing steps for a test request When assigning the Guest role to a user we recommend not assigning them access to any assay software modules Technician A user with a Technician role can create test requests and process them through the workflow A technician cannot approve or reject the results for test requests Technologist Users with the role of Technologist can create and process test requests through the workflow and can approve or reject results
79. ert details display Figure 6 3 on page 63 2 Follow the suggested resolution procedure a The resolution procedure varies depending on the alert If the alert is associated with a Specimen ID use the Go to test request button to select the row in the worklist that contains the related test request 3 After resolving the issue click Resolve 4 Atthe prompt enter your password and additional information and click OK to remove the alert from the list NOTE If after completing the recommended resolution procedure you are unable to resolve the error call Affymetrix support Instrument Troubleshooting Many instrument errors require the attention of a qualified Affymetrix field service engineer However there are some errors related to the fluidics station and scanner that can be resolved Troubleshooting the Fluidics Station There are several fluidics station errors you can correct Fluidics Station is Not Primed You can access the fluidics setup pane to prime the fluidics station for the selected assay class See the section Priming the Fluidics Station on page 75 Fluidics Station Configured for a Different Assay Open the Fluidics Station Setup screen to prime the station for the correct assay type or determine which fluidics station is configured for the assay type See Setting Up the Fluidics Station on page 38 for details on changing the assay type Chapter 6 AMDS Troubleshooting 65 Missing Fluid Error
80. ert pane Temperature Timeout The Re attempt command timed out before the set point temperature was reached Sensor Timeout The Await Sensors command timed out before the anticipated sensor pattern was seen Valve not Homed The Home command did not result in the valve reaching it HOME position Valve Motion Error The Valve command did not result in the valve reaching it target valve position Valve out of Position According to the outer valve encoder the valve did not reach a valid position when it was last rotated Error while Filling While filling the cartridge the AwaitMotor command terminated because of the step count not the expected sensor pattern and that the same error had occurred several times consecutively Error while Draining While draining the cartridge the AwaitMotor command terminated because of the step count not the expected sensor pattern and that the same error had occurred several times consecutively Missing Fluid Error Examples Stage C WashA Sense Threshold 960 890 Stage C WashA Sense Threshold 960 890 The Pump command completed its step count before the conductivity sensor determined that the cartridge contained a solution with conductivity below the set threshold value The Missing Fluid Error MFE Display not only gives a visual notification of an error condition to the operator but gives you information that enables you to deter
81. est requests to AMDS The only place test request data exists is on the CD DVD containing the archive any print outs or similar material On the Archive Test Requests screen you can View test requests o That are within AMDS ready to be archived o Ona CD DVD containing an archive a Filter the archive a Archive test requests to CD DVD or network location a Purge selected test requests Viewing and Filtering Test Request Archives You can view test requests that are in AMDS that are ready to be archived or those that have already been archived to a CD DVD To view test request archives 1 From the System Management menu select Archive Test Requests See Changing System Management Screens on page 52 The Archive Test Request screen displays Figure 5 15 on page 58 Chapter 5 AMDS Administrative Features 58 a If a test request has a green checkmark in the Archived DVD or Network column it has been successfully archived a The System Management toolbar displays the total number of tests that are ready to be archived Click AMDS Index to view test requests in AMDS that are ready to be archived 3 Click DVD Index to view test requests from an archive CD DVD The disc must be in the workstation disc drive 4 Youcan filter the index by Date completed a Assay name Array ID Archiving Test Requests Archiving is not the same process as exporting logs When you archive to CD or DVD you only archive the sel
82. etrix Molecular Diagnostic Software Pligte Station 1 Fuss Station 2 Facies Station 3 Phaches Staton 4 Fiches Sison 5 Fhuscics Staton 6 Fluss Shaun 7 Fides Staten 8 Scanner Center Panel Reais Printer Role Time 132950 T S CC Ps SOR PH Closed Mode 1 Stopped Modde Stopped Modden 1 Shopped Modden 1 Stopped Mode 1 Stopped Mode 1 Stogoed Modde 1 Stopped Modde 1 Stopped Aufolosder Standby Hord Drive Heath Optimal Ready Laboretory Supemsor Left Panel Right Panel Specimen ID Array Name Workflow Step Date Time 4 Details Administrator Recommended Resolution Asse Management lt 3 User Management System Management P Workflow Pane In the left panel you see the Workflow Pane which contains six buttons Active Worklist Registration Hybridization Oven a Fluidics Scanner Non Active Worklist When you click on a button in this pane a worklist corresponding to the button you clicked displays in the center panel A blue arrow also displays next to the button you have clicked Click the next button in the pane to view the next step in a workflow Each button on the Workflow pane is defined below Instructions for completing a workflow appear in Test Request Processing on page 30 Active Worklist A test request is active until it has completed processing or has been canceled While a test request is active
83. ewdriver is inserted into this hole 5 Using a standard flat screwdriver 13 0257 gently slide it down through the hole making sure not to damage the shaft and spring that are protruding into the hole When the screwdriver stops it should be in contact with the Scanner Y stage screw Slowly turn the screwdriver until you feel it engaging the slot on the screw of the scanner Y stage 6 Slowly turn the screw clockwise until it hits a hard stop and cannot turn further Do not try to turn it further or use excessive force because it will break the Y stage in the AutoLoaderDx The Y stage has now ascended to its maximum position Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 118 7 Using your fingers slowly slide the slot pin which is sticking through the slot in the base piece of insulation to the right until it stops You should see the little pinch rollers near the array slot close a little as you do this 8 Insert a 3 16 hex driver Affymetrix P N 13 0255 into the hole that is located on the front of the AutoLoaderDx housing on the left You should feel it engage a coupling 9 Turn the hex driver counter clock wise until you see the array appear through its opening The array should stay up if you stop turning the hex driver If you don t see the array after turning the hex driver ten seconds go to step 11 10 Grab and hold the array with your fingers Using your other hand slowly
84. ffymetrix GeneChip System 3000Dx v 2 System Overview 21 Non Active Worklist Click Non Active Worklist Figure 2 13 on page 21 to display non active test requests The system moves test requests to the Non Active Worklist when they have completed processing in AMDS e g when the results have been viewed and approved or when you cancel them Figure 2 13 Non Active Worklist Button Non Active Worklist Administrator Pane The Administrator Pane Figure 2 14 on page 21 is located below the Workflow Pane While the Administrator Pane is visible to everyone only Laboratory Supervisors and System Maintainers are able to interact with its features Figure 2 14 The Administrator Pane Administrator View Logs Assay Management 3 UserManagement 4 System Management Y The Administrator Pane contains these buttons View Logs a Assay Management a User Management a System Management Clicking on one of these buttons displays related data in the center panel For more information see AMDS Administrative Features on page 44 Chapter 2 Affymetrix GeneChip System 3000Dx v 2 System Overview 22 User and System Information Panes The right panel of the user interface has four panes that give you up to date information related to user details and device status User Details Pane You can view the User Details pane Figure 2 15 on page 22 in the upper portion of the right panel You can L
85. fications If the instrument has been dropped or otherwise damaged If the instrument must be returned for repair call Affymetrix technical support Fluidics Station LCD Messages This section describes the LCD script messages and their meaning Table A 5 The following is a list of some of the common messages that appear on the fluidics station LCD throughout the course of the fluidics station operation The actual list of messages on a particular fluidics station may include some that are not listed here Table A 5 Table A 5 LDC Messages Message Meaning Changing gt Wait for temperature to reach set point Draining to Waste Empties cartridge Purging with A Purges chip with 1mL of buffer A at 25 C from bottom to top then to waste Draining to Vial 1 Recovers stain to Vial 1 for reuse or disposal Draining to Vial 2 Recovers stain to Vial 2 for reuse or disposal Draining to Vial 3 Recovers stain to Vial 3 for reuse or disposal Filling with A or Filling with B Drains and fills cartridge with last wash solution used if any EJECT WASHBLOCK Disengage washblock LOAD CARTRIDGE Prompt for loading cartridge REMOVE PREVIOUS VIALS Prompt to remove vials LOAD VIALS 1 2 3 Prompt for loading vials 1 2 and 3 LOAD VIALS 1 amp 2 Prompt for loading vials 1 and 2 LOAD VIALS 1 amp 3 Prompt for loading vials 1 and 3
86. g the Carousel into the AutoLoaderDx 0 00 00 110 Starting the Scanner 2200 adete ec itamhohardedt Ime duke 6 SEENE eR ae ES 112 Shutting Down the Scanner 2 2 0 0 0 es 112 Disabling the AutoLoaderDx 6 0 eee 112 Cleaning and Maintenance 0 0000s 113 Configuring the Scanner 2 ete eee 113 TROUBIESHOOUNG se ua a hates ey aus eem HBA Cow ere ots DR UR ded Re god den e o bb s 113 Troubleshooting the Scanner sce EE Ei RIXA ERE REESE 113 Issues Relating to Scanner Operation 0 00000 cee 114 Troubleshooting the Scanner cec EE su rere pev Lee SS 0 SENE 114 Scanner Error Messages 0000 cece eee eee eee 115 Manually Removing a Lodged Array Cartridge 0 eee 116 GCS3000DX Specifications ix acc iplo edere biz XXE d ELS Pe ade ans 118 Regulatory Compliance 0 0 es 119 dseUunEmPPCC crcEEELDIUUMTT 123 Contents 7 China RoHS Restriction of Hazardous Substances Compliance 000 124 Labeling Symbols 2 0 2 0 hr 128 129 Welcome to AMDS Introduction Welcome to the Affymetrix Molecular Diagnostic Software AMDS User Guide The AMDS User s Guide provides details concerning both the workflow and administrative functions of AMDS as part of the Affymetrix GeneChip System 3000Dx v 2 GCS 3000Dx v 2 For a system description see Affymetrix GeneChip System 3000Dx v 2 System Overview on page 13 This manual explains how to use the AMDS to Create
87. ge 34 Hybridize tests requests See Hybridization Oven Hybridizing Arrays in the Hybridization Oven on page 35 Some assays perform hybridization in an oven other perform it on the fluidics station Consult your assay software module manual for more information on this step 4 Wash and stain test requests See Fluidics Washing and Staining Arrays in the Fluidics Station on page 38 Scan arrays See Scanner Scanning Arrays on page 40 Approve or reject results See Post Scan Processing on page 42 Consult your assay software module manual for information on this step 7 View non active test requests See Non Active Worklist Viewing Non Active Test Requests on page 43 Before you begin familiarize yourself with a Terminology on page 10 a Affymetrix GeneChip System 3000Dx v 2 System Overview on page 13 a Affymetrix GeneChip System 3000Dx v 2 Operation Basics on page 25 including Using the Barcode Reader on page 27 a GeneChip Fluidics Station FS450Dx on page 66 GeneChip Scanner 3000Dx with AutoLoaderDx on page 101 Lu IMPORTANT Before attempting any assay runs you must be familiar with the operation of the fluidics station see the appendix GeneChip Fluidics Station FS450Dx on page 66 and the operation of the scanner see the appendix GeneChip Scanner 3000Dx with AutoLoaderDx on page 101 NOTE Throughout test request processing you will need to enter data related to the test request Whenever po
88. ge Changes Fluctuations and Flicker EU Low Voltage Directive 2006 95 EC IEC 61010 1 2001 IEC 61010 2 101 A1 2003 EN 61010 1 2001 Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements Safety requirements for electrical equipments for measurement control and laboratory use Particular requirements for in vitro diagnostic medical equipment Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements Regulatory EN 61010 2 081 A1 2003 EN 61010 2 101 2002 UL 61010 1 R 2005 07 CAN CSA C22 2 No 61010 1 2004 CAN CSA C22 2 No 61010 2 101 2004 CAN CSA C22 2 No 61010 2 081 2004 Appendix A GeneChip Fluidics Station FS450Dx 98 Safety requirements for electrical equipment for measurement control and laboratory use Particular requirements for automatic and semi automatic laboratory equipment for analysis and other purposes Safety requirements for electrical equipment for measurement control and laboratory use Particular requirements for in vitro diagnostic IVD medical equipment Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements Safety requirements for electrical eq
89. gineer who installed AMDS or your system administrator will have provided User IDs and Passwords a After authenticating your credentials AMDS provides functionality based on your user role For more information about user roles see About User Roles on page 50 Chapter 3 Affymetrix GeneChip System 3000Dx v 2 Operation Basics 26 Figure 3 1 AMDS User Log On Screen Affymetrix Molecular Diagnostic Software Ae a Affymetrix Affymetrix Molecular Diagnostic Software User Name l Password Logon Shadow Starting the Fluidics Station and Scanner Turn on the fluidics station and scanner when your test requests have reached the associated worklists For related information see Operating the Fluidics Station on page 70 a Starting the Scanner on page 113 z WARNING A Laser in use during scanning NOTE The scanner laser requires about 10 minutes to warm up Lu IMPORTANT To preserve the lifetime of the scanner s internal laser we recommend that you turn off the scanner when it is not in use for any extended period of time such as overnight or a weekend Logging Off This function allows you to log off of AMDS The log off functionality is available at all times to all users 1 In the User Details pane Figure 3 2 on page 27 click Log Off Logging off will not terminate the active workflow processes If there are test requests in hybridization fluidics or scanning AMDS will
90. has been dropped or otherwise damaged If the instrument must be returned for repair call Affymetrix technical support Instrument Components The GeneChip Fluidics Station 450Dx aka the fluidics station contains four modules Each module can hold one GeneChip array cartridge and up to three vials The software and computer workstation can control each of the four modules independently of the others All modules are primed as a unit Only one assay can be associated with a fluidics station at a time You can use any or all of the modules at the same time The modules are numbered 1 through 4 near the LCD screen Figure A 2 on page 68 and Figure A 3 on page 69 show the components and cable connections of the fluidics station See Figure B 2 on page 105 for the cable connection to the scanner This is for reference only Affymetrix recommends that only a qualified service engineer attempt to service this instrument or change these connections The GeneChip Fluidics Station 450Dx includes the following components 1 Sample Holders holds up to three sample vials 2 Module Door protective cover for the peristaltic pump on the module enon 10 11 12 13 Appendix A GeneChip Fluidics Station FS450Dx 68 Cartridge Holder holds the cartridge during fluidics operation Washblock part of the cartridge holder that completes the fluid path when a cartridge is not in place used for cleaning out or draining the fluidic
91. he scanner This should only be used on systems where the AutoLoader has failed and there are arrays that need to be scanned immediately For complete instructions see Disabling the AutoLoaderDx on page 113 3 Click Save Changes Requiring User Approval for the Analysis Results In the System Configuration Flags screen select Require User Approval to require the technician to approve or reject the analysis results as they become available after an assay run Figure 5 16 on page 59 This flag is meaningful only if you do not wish to have the opportunity to approve or reject the results on the AMDS system Deselecting this box will cause the test requests to immediately move to the Non Active Worklist upon completion of the analysis algorithm The user will not be able to view the results through the Active Worklist NOTE This checkbox is intended for use in conjunction with an LIS If you check this box you will need to review the results for each test request If the box is unchecked the test requests disappear from the Active Worklist upon completion of the workflow and reappear on the Non Active Worklist without user intervention Configuring Network Archive Storage To setup the Network Archive Storage device 1 On the General Configuration screen view the Network Archive Storage Configuration region Figure 5 16 on page 59 2 Enter a valid a UNC Share User Name Password 3 Click Test Connection to configure the
92. he scanner 3 Optional Click Start to resume scanning with the array in slot 1 NOTE The scanner will not rescan any previously scanned arrays and will always start its run with the array in slot 1 Post Scan Processing Once the scan is complete AMDS will a Take the resulting DAT file Apply a grid to it a Generate intensity data a Generate a CEL file The CEL file will then be analyzed in the manner specified by the assay software module When this processing is complete an Awaiting Review hyperlink Figure 4 14 on page 42 displays in the Review Results column of the Active Worklist At this time the results are ready to be reviewed Reviewing Test Results The workflow for reviewing and processing test results is assay dependent See your assay software module manual for specific instructions To review test results 1 Click Active Worklist 2 Click on the Awaiting Review hyperlink for your test request Figure 4 14 The Review Results Function Active Worklist Total 9 The assay software displays a Results screen for your particular assay See your assay software module manual for instructions on how to finalize the test request You may want to view log files or generate archives related to test requests For more information see Viewing Logs on page 44 and Archiving and Purging Test Requests on page 57 After you accept or reject a test request you can view it on the Non Active Worklist
93. ick Complete Step This step completes scanning in normal operational mode and removes the test request s from the Scanner Worklist Scanning Arrays in Manual Mode You can scan one array at a time using the manual scan function Use this function to scan arrays that have illegible or missing barcode labels AMDS will attempt to scan the barcode and if it can will validate that the selected test request is correct To scan arrays in manual mode 1 Click Scanner The Scanner Worklist displays Figure 4 13 on page 41 Open the AutoLoaderDx door Insert the array into the AutoLoaderDx carousel at slot 1 Close the door BRWN Select the correct test request on the worklist The Manual Scan button is enabled 6 Click Manual Scan The door locks and scan begins After the scan is complete the door unlocks Open the door and remove the array 7 Click Complete Step This step completes scanning in manual mode After post scan processing is complete you can review approve or reject the test results on the Active Worklist For more information see Post Scan Processing on page 42 Chapter 4 Test Request Processing 42 Stopping an Scanner Run If you want to add arrays to the carousel or if issues occur you can stop the scanner in the middle of a scanner run To stop a scanner run 1 Click Stop Scan The scanner will finish scanning the current array and then stop and unlock the door 2 Optional Add an array to t
94. idics Station FS450Dx 70 b A double good sound that indicates that the barcode reader confirms a valid association between the test request and the fluidics module C A bad sound that indicates that the barcode reader detects an error Check the Device Status and Alerts panes for information related to the error See the section Starting and Shutting Down the System on page 25 for more information See the section Scanner Indicator Lights and On Off Button on page 106 for information on connecting the barcode reader to the workstation Fluidics Station 450Dx Protocols Each assay software module contains a fluidics protocol which provides processing instructions to the fluidics station AMDS automatically selects the correct protocol for each test request Operating the Fluidics Station This section illustrates how to operate the fluidics station to process assays This discussion must be general since the number and type of steps required to process your specific array will be different depending on the specific design of the assay that the array contains Lu IMPORTANT Do not lower needles or engage the washblock until prompted by the fluidics station LCD Starting the Fluidics Station 1 4 Check to ensure that the fluidics station is connected to the power main through the power cord provided Check to ensure that the fluidics station is connected to the workstation CommLink connections are locate
95. ing Test Requests Arrays and Reagent Kit IDs during Registration 34 Troubleshooting Registration z aco ERR RII ER OECERREETE Sean lt 35 Hybridization Oven Hybridizing Arrays in the Hybridization Oven 35 Hybridizing in an Oven vs Hybridization on a Fluidics Station 00 36 Entering Oven Data 1 2 0 0 0 tees 36 Starting and Monitoring Oven Hybridization 0 0 0 000 eee 37 Ending Oven Hybridization 0 00 0 s 37 Troubleshooting Oven Hybridization 0 0 0 000 eee 37 Fluidics Washing and Staining Arrays in the Fluidics Station 0 000 38 Setting Up the Fluidics Station sics 0 daadaa eb 38 Associating Test Requests with Fluidics Stations 0 0 nee 39 Starting the Fluidics RUN 5 2 40 2 022 62444002040244 tage Rhdd be eldje44 39g 40 Scanner Scanning Arrays l ssl 40 Scanning Arrays in Normal Operational Mode 00 00 cee 40 Scanning Arrays in Manual Mode oaaao anaana aaaea e 41 Stopping an Scanner RUN 1 les 42 POST SCan PFOCESSING x ausus ii CR RR TR ye hee aa RR Yee ee Maas o d dad qos 42 Reviewing Test Results 2 0 0 000 s 42 Non Active Worklist Viewing Non Active Test Requests 0000000020 e eee 43 AMDS Administrative Features 000 ccc eee eee 44 Miis se eon pats ete Bons oe oe Eh Ee Aon ee es 44 SVStEm LOOS E ttc ado Acer eh the bee Bathe ad os iud uet eee Bee Gee Be dad os 44 PT iu ojo 46 Expor
96. ing and Shutting Down the System n asaan aana 25 Starting the Workstation 2 2 22 46344440 4 84444 i PG epp ss 29040554 aa a 25 Logging onto AMDS 1 2 2 eee 25 Starting the Fluidics Station and Scanner 2 eee 26 Chapter 4 Chapter 5 Contents 4 HOG OING ON inte aig eean ponent ata fe a E A a at nono AE Fate Alaa poke Ga dane 26 Shutting Down 0 eee ee 26 Changing Your Password 25 once cena RR Ep On RR Ro DOMO RAUS Edad 27 Using the Barcode Reader xs Eee Rena ERE Pek ee A dena eua Diui a 27 Editing Multiple Fields in AMDS ssssssss diddi dii kak BEE Ea 28 Contiguous Select and Enter spera etemas ln 28 Non Contiguous Select and Enter llle 28 Handling the Array Cartridge 0 ccc anei GERE EEE E AEREE EE 29 E SIQNAtureS ue ura dne es 544 PER E E BEd ORE OE ES ee ER ae res 29 Test Request Processing 0c cece eee eee eens 30 IntFOQU GIOI uices ace RREE E SNe S PPRRCBNM S Ob S vete Gad Sodas 30 Active Worklist Entering Editing or Canceling Test Requests 0 000 30 Entering Test Requests illiiilsssell 31 Editing Test RequestS isses R9 ee 39 3 a ELO E AG GG rds 32 Canceling a Test Request 2 0 0 hs 32 Adding Additional Information to a Test Request 0 0 0 0 2 cece eee 33 Viewing Assay Information 0 0 0 0 eee eee 33 Batch Editing Test Requests 0 2 eee ee ee 33 Registration Registering Test Requests 0 0 0 0 eae 34 Associat
97. ith a fluidics station and module As an example in the AMDS Registration Worklist for each test request you can scan the barcode for the Specimen ID to select the associated test request Then scan the Array ID barcode to associate a specific array with a test request In the Fluidics Worklist scan the array barcode to select the associated test request and then immediately scan the fluidics station module barcode AMDS will automatically place the fluidics station and module identifiers in the proper fields Figure 3 3 on page 28 Chapter 3 Affymetrix GeneChip System 3000Dx v 2 Operation Basics 28 Figure 3 3 Using the barcode reader to scan an array barcode and a module barcode Array Module Barcode See Using the Barcode Reader with the Fluidics Station on page 69 for more information on using the barcode reader with the fluidics station Instructions for when to use the barcode reader are embedded in procedures throughout Test Request Processing on page 30 NOTE If the barcode on any item is not readable for any reason you can manually enter the ID by positioning the cursor in that field and typing the information into the field The recommended method is to always use the barcode reader when possible Editing Multiple Fields in AMDS You may at times want to enter the same value into multiple data fields at once For instance if you are preparing a tray of 10 arrays for oven hybridization instea
98. ition Lu IMPORTANT To maintain the cleanliness of the fluidics station and obtain the highest quality image and data possible a weekly bleach protocol Please refer to the section Fluidics Station Bleach Protocol on page 78 for further details Priming the Fluidics Station Priming fills the fluidics station lines with wash buffers designed for that assay and deionized water You must prime the fluidics station before you can use it to run assay protocols You should prime the fluidics station When you first start the fluidics station Before you process a cartridge Appendix A GeneChip Fluidics Station FS450Dx 76 When you change the wash buffers When you change the assay associated with a fluidics station a If the LCD screen instructs you to run a prime protocol If any alert instructs you to run a prime protocol To prime the fluidics station 1 Check to ensure that all the wash lines are in the appropriate wash bottles Please consult the array package insert that came with the cartridge kit for the appropriate wash buffer solutions or contact your Affymetrix technical support representative 2 Load three standard 1 5 mL vials in the sample holders of each module that is to be primed Figure A 9 on page 74 3 In the Active Worklist pane click Fluidics Figure A 10 on page 76 Fluidics Fluidics Worklist The Fluidics Worklist displays Figure A 11 on page 76
99. l to turn on the instrument 2 Wait ten minutes for the scanner to warm up Shutting Down the Scanner 1 Press the I O button on the front panel to turn off the instrument IMPORTANT Affymetrix recommends a professional service call for maintenance at least twice a year Please contact Affymetrix technical support for details Disabling the AutoLoaderDx If you are having issues with your AutoLoaderDx and need to scan arrays with the AutoLoaderDx disabled follow these instructions exactly To disable the AutoLoaderDx 1 With the AutoLoaderDx in ready state green light solid yellow light off check Disable AutoLoaderDx on the General Configuration screen 2 Click Save Changes button and enter your credentials in the Confirm Step dialog 3 Click OK in the dialog that appears telling you to reboot the scanner Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 114 4 Atthis time the AutoLoaderDx status in the Device Status pane should appear as AutoLoader Mode has changed Turn the scanner off Wait one minute then turn it on again 5 The scanner will boot up and go through laser warm up The connection between the scanner and AMDS should be established soon after laser warm up starts When the scanner status in the Device Pane is AutoLoader Standby then restart the workstation 6 Remove the carousel from the AutoLoader drop an array into the slot and use Manual Scan from the Scanner Worklist to scan
100. material s and the components parts in which they are found Table A 6 Table Containing Names and Contents of Toxic or Hazardous Materials Instrument Affymetrix GeneChip Fluidics Station 450Dx Component Lead Mercury Cadmium Hexavalent Polybrominated Polybrominated Part Pb Hg Cd Chromium Biphenyls Diphenyl Ethers Categories Cr 6 PBBs PBDEs Printed Circuit X Oo X Oo Oo Oo Boards Rubber amp O O O O O O Plastic Parts Electrical X O O O O O Components Internal Metal O O O O O O Parts External Metal O O O O O O Parts Labels O O O O O O Packaging O O O O O O Shipping Materials Internal Lasers O O oO O O O Optics amp Sensors Adhesives O O O Internal Power X O X O O Supplies Motors and O O O O O O Pumps X Indicates that the toxic or hazardous substance contained is above the limit of 1000 ppm for lead and above 100 ppm for cadmium O Indicates that the toxic or hazardous substance contained is below the limit of 1000 ppm for lead mercury hexavalent chromium polybrominated biphenyls and polybrominated diphenyl ethers and below 100 ppm for cadmium Appendix A GeneChip Fluidics Station FS450Dx 100 SJ T11364 2006 Sj T11364 2006 BFP SF iiie iBERY Hired e oe Sr aay ae BERSKHRRHSE HEAKEDE Pb OH amp KPS Cr gt SRR PEB MSR BM PEDE Sesesneare EE low P WETS FREMNFRBRER CSR 1 s ABIESUUZWE SFPT
101. mful interference and 2 This device must accept any interference received including interference that may cause undesired operation This device complies with FDA performance standards for laser products except for deviations pursuant to Laser Notice No 50 dated July 26 2001 This Class A digital apparatus meets all requirements of the Canadian Interference Causing Equipment Regulation Cet appareil num rique de la classe A respecte toutes les exigences du R glement sur le mat riel broullier du Canada Table B 10 Regulatory Certifications Regulatory Agency Certification Class Laser Device Complies with EN 60825 1 2007 Complies with FDA performance standards for laser products except for deviations pursuant to Laser Notice No 50 dated July 26 2001 Hand held barcode Complies with EN 60825 1 2007 reader is a Class II laser Complies with FDA performance standards for device laser products except for deviations pursuant to Laser Notice No 50 dated July 26 2001 Compliant with directive 2002 96 EC WEEE E Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 125 China RoHS Restriction of Hazardous Substances Compliance Manufacturers of Electronic Information products EIPs that are sold to the People s Republic of China are required to provide information about lead cadmium mercury hexavalent chromium polybrominated biphenyls and polybrominated diphenyl ethers contained within In ac
102. mine the cause of the error It does this by displaying information about the sensor value and the fluid that caused the error It shows this internal information in a continuous loop until the machine is powered down or a script is started For example Missing Fluid Error for 4 seconds Stage A valvePos WashA for 4 seconds Sense Threshold 820 600for 4 seconds Other Problems and Solutions Appendix A GeneChip Fluidics Station FS450Dx 93 Table A 4 lists uncommon problems and their solutions AMDS may display these as alerts To resolve these alerts follow the recommended resolution in the current Worklist screen on the alert pane Lu IMPORTANT NEVER run the prime script with anything but the correct buffers Table A 4 Other Problems and Solutions Problem Possible Cause Possible Solution Follow the recommended resolution on the alerts pane Air bubbles left in Air bubble in wash line cartridge at the end of a hybridization wash script You may need to perform a Cleanout procedure or a Priming procedure Buffer leaking inside the fluidics station Loose tubing attachments inside the fluidics station Washblock requires replacement Salt buildup in the lines of the fluidics station Call Affymetrix technical support for service Call Affymetrix technical support for service Run the Shutdown script with fresh DI water to flush out salt blockage Possible defective septa o
103. n You may need to loosen the tubing clamps allow tubing to relax close the clamps Insufficient volume of sample or staining solution 500 pL Blocked sampling tube or line of the fluidics station In the current Worklist screen on the alert pane follow the recommended resolution You may need to run a Shutdown script with fresh deionized DI water to flush out salt blockage Cartridge not filling completely with buffer during wash script System detects improper conditions while filling Note where in protocol error occurred Buffer bottle empty Module not primed Missing or insufficient stain or antibody in vial Wash empty Air bubbles in line Leaks Fill buffer bottles Prime module In the current Worklist screen on the alert pane follow the recommended resolution Table A 2 Problems and Solutions Continued Appendix A GeneChip Fluidics Station FS450Dx 90 Error Message Missing Fluid Error continued Fluidics Station X Does Not Respond Sensor Timeout Problem Possible Cause Possible Solution Follow the recommended resolution in the current Worklist screen on the alert pane Recovered less sample than initial input during Recover script Loose tubing attachments inside the fluidics station Call Affymetrix technical support for service Sensor Timeout error message on workstation Power not switched on at th
104. n page 34 in the Workflow pane to view the Registration Worklist Registration Associating Test Requests Arrays and Reagent Kit IDs during Registration NOTE Not all assays require the use of a Target Preparation Reagent Lot ID For some assays you ll need to enter reagent data via the Reagent Information tab of the Assay Home Screen See your assay software module manual for more details Registration consists of associating a test request with the array to be used for the test request Depending on the assay the target preparation reagent kit information may also be collected during this step To register a test request 1 Click Registration The Registration Worklist displays Figure 4 6 on page 34 N Scan the Specimen ID barcode a AMDS will select the test request associated with this Specimen ID You can also select the Specimen ID from the list 3 Scan the array barcode from the array cartridge AMDS will populate the Array ID field a AMDS will warn you if you have already used this Array ID if the array is expired or if the array type is not compatible with the assay type You can enter this information by hand too Registration Worklist Chapter 4 Test Request Processing 35 4 Optional Enter the Target Preparation Reagent Kit ID a Target Preparation Reagent Kit IDs may be entered with the barcode reader or by hand See your assay software module manu
105. n the cartridge Cartridge needles of the fluidics station not engaging with the cartridge Extra flashing on the cartridge Salt buildup on the cartridge needles Cartridge holder aligned and attached to the fluidics station improperly Cartridge holder not properly engaged to the fluidics station Use another cartridge Use another cartridge or call Affymetrix technical support for service Run the Shutdown script with fresh DI water to flush out salt blockage Clean cartridge needles with a wet cotton swab Call Affymetrix technical support for service Place the cartridge into the cartridge holder Push the holder door shut and firmly lift the lever to engage the cartridge needles Sample needles do Bent sample needle not properly enter vial User may be pressing the needle lever down to quickly or with too much force Replace sample needle Engage sample needle lever more slowly and or with less force When to Contact Affymetrix Appendix A GeneChip Fluidics Station FS450Dx 94 Under any of the following conditions unplug the instrument from the power source and contact technical Support When the power cord is damaged or frayed a If any liquid has been spilled into the instrument a If the instrument has been penetrated by water a If after service or calibration the instrument does not perform in accordance with the capabilities stated in the speci
106. need not be concerned regarding the bleach that remains in the lines Appendix A GeneChip Fluidics Station FS450Dx 82 Figure A 18 Immerse the three wash and water lines in the DI water bottle The waste line remains in the waste bottle 3 Press down on the needle levers to begin the rinse cycle The fluidics station empties the lines and rinses the needles 4 When the rinse is completed after approximately one hour the fluidics station will bring the temperature back to 25 C and drain the lines with air The LCD display will read CLEANING DONE 5 Discard the vials employed for the bleach protocol 6 Follow these suggestions in Table A 1 after you have completed the bleach protocol Appendix A GeneChip Fluidics Station FS450Dx 83 Table A 1 Suggestions on using the fluidics station after a bleach protocol If you are Then do this Planning to use the system immediately After running the bleach protocol remove the DI water supply used in the rinse phase and install the appropriate reagents for use in your next staining and washing protocol including fresh DI water a Perform a prime protocol without loading your arrays Failure to run a prime protocol will result in irreparable damage to the loaded hybridized arrays Not planning to use the system immediately Since the system is already well purged with water you need not run an additi
107. ng Warning Limit 10 d Change Tubing Alert Limit 100 d 7 From the dropdown list select a station number The system displays the last bleach and peristaltic tube change 8 Select the Bleach procedure from the list and click Perform The Confirm Step dialog box opens Enter your password and event reason AMDS enters the time and date information into the device log CAUTION Temperature will ramp up to 50 C 9 Follow the prompts on the LCD Appendix A GeneChip Fluidics Station FS450Dx 81 Figure A 17 Press down on the needle levers to start the bleach protocol 10 The fluidics station begins the protocol and begins to empty the lines and perform the cleaning cycles using bleach solution 11 After approximately 30 minutes the LCD will prompt you when the bleach cycle is over and the rinse cycle about to begin The Rinse Cycle Once the bleach cycle has finished the second part of the protocol is a rinse step This step is essential to remove all traces of bleach from the system Failure to complete this step can result in damaged arrays 1 Follow the prompts on the LCD for each module Lift up on the needle levers and remove the bleach vials Load clean empty vials onto each module 2 Remove the three wash and water lines from the bleach bottle and transfer them to the DI water bottle Figure A 18 on page 82 At this step you
108. ng this information will vary depending on the assay software module New fields cannot be added To add additional information to a test request 1 From any worklist click on the desired Specimen ID hyperlink The Additional Information dialog box displays a This dialog will look different for different assay software modules Add information in the provided fields See your assay software module manual for details Viewing Assay Information You can retrieve the information related to specific assays by opening the Assay Home screen 1 From any worklist click on the assay name hyperlink The Assay Home screen displays See your assay software module manual for more details Batch Editing Test Requests Lu IMPORTANT Batch editing is only possible with test requests that use the same assay software module The Batch Edit button will only work if none of the arrays associated with the selected test requests have started scanning You can use the Batch Edit command to associate information with multiple test request records To batch edit test requests 1 From any worklist select one or more test requests associated with a single assay software module and click Batch Edit The Assay Batch Information dialog box displays See your assay software module manual for more details Chapter 4 Test Request Processing 34 Registration Registering Test Requests Click on the Registration button Figure 4 5 o
109. ns encountered in normal operation The instrument covers the array access port and protective shutters ensure that during instrument operation no directed or stray laser light leaves the instrument Lu IMPORTANT The scanner is a Class laser product when the laser is enclosed in scanner case The laser itself is a Class IIIB laser product DANGER Laser radiation when open Avoid direct exposure to laser beam The lasers can cause serious injury if the instrument is not operated in accordance with instructions in this user guide CAUTION Use laser safety glasses when servicing DO NOT STARE INTO LASER BEAM Ld Class Laser Product The green laser is a 532nm solid state laser This is a Class IIb laser and has visible outputs greater than 5mw but not more than 500mw It must never be operated in an exposed manner Any object in the direct path of the laser beam may be damaged Eyes and skin can be seriously damaged by direct exposure to specular reflections from or diffuse reflections from this laser If improperly used a laser of this type can cause fires When used according to the instructions in this manual and when all covers are in place the GeneChip AutoLoaderDx is classified as a Class I Laser Device per 21 CFR 1040 Always take note of laser safety labels they indicate areas where exposure to laser beams may be hazardous Electrical Safety The scanner will automatically handle any input v
110. nt you wish to buy Optional Hybridization Oven Depending on the type of assay you may need a hybridization oven to prepare arrays for testing Since you may already have a hybridization oven its purchase is optional The GeneChip Hybridization Oven 645 Figure 2 6 on page 16 provides precise temperature and rotation control to ensure the successful hybridization of as many as 64 GeneChip brand cartridges at one time It can be linked to the instrument system enabling you to monitor and log temperature and rotation speed You may also use the older model Affymetrix GeneChip Hybridization Oven 640 The Hybridization Oven 640 does not offer the same level of integration as the Affymetrix GeneChip Hybridization Oven 645 and may not support all assays i e CytoScan HD is not supported by the 640 Figure 2 6 Affymetrix GeneChip Hybridization Oven 645 Chapter 2 Affymetrix GeneChip System 3000Dx v 2 System Overview 17 Software Components The Affymetrix GeneChip System 3000Dx v 2 contains two types of software components a Affymetrix Molecular Diagnostic Software AMDS Assay software modules AMDS Software Component AMDS provides the interface between the user and instrument systems It provides control over the instruments assay software modules and the processes for data collection and management Upon completion of scanning of the array data is passed through AMDS to the assay software m
111. odule that contains the algorithms and reporting functions to produce the clinical result specified by the assay software module AMDS provides tools to a Control assay workflows and view test results a Perform administrative functions Troubleshoot the system For information how to conduct workflows see Test Request Processing on page 30 For information how to administer the system see AMDS Administrative Features on page 44 Assay Software Modules Assay software modules provide all of the parameters necessary to process a specific Affymetrix GeneChip array through its entire workflow AMDS identifies a particular assay by its assay name AMDS assists you in installing and deactivating an assay Assay management is explained in Managing Assays on page 47 Assay software module manuals provides further instructions that are unique to specific assays AMDS User Interface The AMDS user interface consists of three regions Figure 2 7 on page 18 Left Panel contains the Workflow and Administration panes each of which contains several buttons Center Panel displays information related to the button you click on in the left pane Online help also displays in the center panel Right Panel consists of the User Details Device Status Alert and Alert Details panes Chapter 2 Affymetrix GeneChip System 3000Dx v 2 System Overview 18 Active Worklist tegere Log on Stat Doum Affym
112. og off See who is logged in and their role See system time and date Change passwords Shut down the system For more information see Managing Users on page 49 Figure 2 15 User Details Pane User Details User ID Role Lynn Laboratory Supervisor Date Time 2011 02 11 16 47 07 Device Status Pane Located just below the User Details pane is the Device Status pane Figure 2 16 on page 22 Figure 2 16 Device Status Pane Device Status Hyb Oven 1 T 50 C R 60 RPM Closed Fluidics Station 1 Module 1 Stopped Fluidics Station 2 Module 1 Stopped Fluidics Station 3 Module 1 Stopped Fluidics Station 4 Module 1 Stopped Fluidics Station Module 1 Stopped Fluidics Station B8 Module 1 Stopped Fluidics Station Module 1 Stopped Fluidics Station 8 Module 1 Stopped Scanner Autoloader Standby Hard Drive Health Optimal Printer Ready Chapter 2 Affymetrix GeneChip System 3000Dx v 2 System Overview 23 This pane is an instrument status dashboard providing color coded status for each system device a Green indicates the device is operating normally Yellow indicates that AMDS detected an abnormal condition that requires attention Red indicates a communications issue or a device failure AMDS provides status for the hybridization oven the fluidics station the scanner the printer and the workstation hard drive For more information see AMD
113. oltage from 100 to 240 VAC nominal 50 to 60 Hz x NOTE The scanner s power supply will autodetect the input voltage source and configure itself Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 104 N CAUTION The power supply cord is used as the main disconnect device Ensure that the socket outlet is located and installed near the equipment and is easily accessible CAUTION If you use the scanner ina manner not specified in this user guide you may impair the protection provided by the equipment CAUTION Do not confuse your company s network connections with the dedicated Ethernet port of the scanner workstation The proper scanner connection is located near the top of the workstation CAUTION This 10 100 Base T Ethernet communications port is dedicated to the scanner workstation interface You cannot connect the scanner to your company s Ethernet communications network Lu IMPORTANT The reset button is the scanner s circuit breaker The breaker switch will be tripped whenever the scanner experiences an electrical fault condition Press to reset If you cannot reset this switch contact Affymetrix technical support Workstation AutoLoader Connections Figure B 2 on page 105 and Figure B 3 on page 106 show the cable connections of the workstation and the AutoLoader This is for reference only Affymetrix recommends that only a qualified service engineer attempt to service or change these
114. on transferable non sublicensable license to use this Affymetrix product only in accordance with the manual and written instructions provided by Affymetrix You understand and agree that except as expressly set forth in the Affymetrix terms and conditions that no right or license to any patent or other intellectual property owned or licensable by Affymetrix is conveyed or implied by this Affymetrix product In particular no right or license is conveyed or implied to use e E product in combination with a product not provided licensed or specifically recommended by Affymetrix for such use Copyright 2008 2011 Affymetrix Inc All rights reserved Contents Chapter 1 Chapter 2 Chapter 3 Welcome to AMDS 2iiiileesee deen Emu R AR ARRAS se ETAR ERR kee 8 Jajtrsie aul og MRTTRRRERCRT CRIME 8 Iriteridedd Se x iun cs mana a Redan am ea IER d ed E luti a Rat Salt RUE d RAS dee od 8 Other Doc rmentatilor o iraani i csi ERN UU e UIROS DU uuum Ne uud 8 About Online Help 14 exte Ree een Pope bbb deed obi qeeradpehei qpegi 8 Accessing Context Sensitive Help 2 0 e 9 Accessing the Complete Help System 2 0 0000 ee 9 TERMINOLOGY C ccc cc ster tng rh sehen aad ey ethene atten Gog ee ate tte mtd Sas Gad Ny ihe Uae ee anaes ee 10 L2 anos ne cat ee aes atie e ee Sr gee tenes cut dy ate eb ates aha gv eae eles tee 10 Technical SUPPONE se siste deh Besse rax wed dente Erbe ER RAN eda cies 11 Affymetrix GeneChip System 3000Dx v 2 Sys
115. onal shutdown protocol Just remove the old DI water bottle and replace it with a fresh bottle Not planning to use the system for an extended period of time longer than one week Remove the DI water and perform a dry protocol shutdown This will remove most of the water from the system and prevent unwanted microbial growth in the supply lines Also remove the pump tubing from the peristaltic pump rollers NOTE After you have completed the bleach protocol discard the vials NOTE At this point you can in the Configuration area set the Bleach Interval Warning Limit and Bleach Interval Alert Limit Click Save to save your configuration Peristaltic Tubing Maintenance You must periodically replace the peristaltic tubing because of wear contamination or to avoid salt buildup Inspect the tubing on a weekly basis if you see evidence of these conditions follow the procedure outlined below If you have AMDS administrator privileges you can set the Change Tubing Warning Limit and Change Tubing Alert Limit See the section Managing Fluidics Stations on page 53 Wear gloves when changing tubing Do not allow fluid from old tubing to spill onto surfaces Lu IMPORTANT For systems in routine use Affymetrix recommends monthly replacement of the silicone peristaltic tubing part number 400110 To ensure proper performance use only tubing available from Affymetrix This tubing is manufactured to the requi
116. oting Problem Possible Cause Corrective Action No image when Power off or cable Check all connections and power scanning loose Loss of laser power Contact technical support Intermittent problems Loose cable Check all rear connections scanning Scanner fails with array Power failure Manually extract array Check all inside connections to scanner Turn scanner on restart software Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 115 Issues Relating to Scanner Operation In using the scanner you may encounter some issues or problems that may require your intervention Below is a list of these issues Table B 3 Issues that may affect the scanner Issue Explanation If communications are interrupted during a scan by a faulty cable connection or power being lost at the scanner for example AMDS will properly note the failure and present an alert that says Cannot connect to scanner or something similar However there are two issues to note first AMDS will report such a failure only after a network time out of about 30 seconds Second rarely if communications have been lost AMDS and the scanner may not be able to automatically restore communications once the problem is rectified and both may become unresponsive To restore proper operation verify that the scanner is on that communication cables are properly connected See the section Changing System Management Screens on page 52
117. r Troubleshooting Guide Continued Problem Possible Cause Corrective Action Carousel does not rotate AutoLoaderDx misses next array Door is open or ajar System is warming up array in heater Carousel not seated on D ring Alignment Pin not engaged in Carousel a Laser in scanner is warming up AMDS has Start grayed out in this case Array UP sensor not working call technical support Stuck array See the section Manually Removing a Lodged Array Cartridge on page 117 AutoLoaderDx freezes up Door is open or ajar Scanner overheats Heater Failure a TE failure TE hot fans vent blocked Call technical support Call technical support Autofocus routine fails to conclude Check for salt on chrome border Use Tough Spots to prevent leaks in the GeneChip array See the quick reference card p n 08 0076 or Using Tough Spots to Prevent Leaks on page 109 Salt buildup on array cartridge substrate The array does not descend into scanner Carousel not seated correctly Door is open or ajar a Heater is waiting until array is at temperature Scanner Error Messages The following error messages indicate a serious malfunction of the scanner Your arrays or the data generated from them may be at risk You should shut down the scanner and remove the carousel Do not continue to use the scanner in Automode Call Affymetrix Technical Support Table B 5 Scanner
118. r criteria in the row that is just below the audit log column headers You can filter the log according to Date Time Workflow step Log message type User Printing Audit Logs To print an audit log 1 Select the audit log for printing 2 Click Print Exporting and Burning Log Files to CD or DVD NOTE You can burn logs only to the workstation s internal CD DVD drive At any time while viewing either a system or audit log you can click Export to send the entire log file to the export queue The View Logs toolbar shows the total size and number of logs in the queue To export log files 1 For each system and audit file you want to export Select the file a Click Export The View Logs toolbar increases the number of exported files by 1 The entire unfiltered log file is exported To burn the log file to CD or DVD 1 Click Burn to export the current list to the workstation s CD DVD drive a All queued log files burn to the disc drive Whether you click the System Log Burn button or the Audit Log Burn button all exported log files regardless of log type burn to CD DVD Chapter 5 AMDS Administrative Features 47 Managing Assays The Assay Management function provides the capability to install repair deactivate assays or deactivate SSL certificates Installing Assays Assay Management NOTE If the assay communicates with a remote server and the certificate for that server has no
119. re from the list and click Perform The Confirm Step dialog box opens Enter your password and event reason AMDS enters the time and date information into the device log Replacing the Peristaltic Tubing Procedure 1 Open the module door See Figure A 21 on page 85 component number 2 and Figure A 22 Appendix A GeneChip Fluidics Station FS450Dx Figure A 21 Module door open showing peristaltic tubing Peristaltic Tubing 2 Open the white clamps to release tubing on both sides See Figure A 21 85 Figure A 22 releasing the peristaltic tubing gt a eee White Clamp Appendix A GeneChip Fluidics Station FS450Dx 86 l5 WARNING Do not remove the module Do not attempt to replace the tubing on a module where the module has been removed from the case of the fluidics station In this case rotating the pump may damage the motor driver circuitry 3 Pull tubing off while gently turning the peristaltic pump head Discard old tubing 4 Replace tubing with new peristaltic tubing supplied with the accessory kit as described below a Attach one end of the new tubing to the fitting on the right at the top of the pump enclosure b Insert the tubing into the clamp under the fitting without stretching the portion of the tubing between the fitting and the clamp There should be a small amount of slack in that portion of the tubing C Work the tubing into the pump head
120. red specifications to ensure proper fluid delivery and array performance You can obtain additional tubing by ordering from Affymetrix Setting the Peristaltic Tubing Maintenance Parameters You should set the peristaltic tubing maintenance parameters when you or the service engineer originally set up the fluidics station or after you have replaced the peristaltic tubing 1 Click the System Management Figure A 19 button on the Administrator pane Appendix A GeneChip Fluidics Station FS450Dx 84 Figure A 19 The Administrator Pane Administrator View Logs m Assay Management uu User Management System Management 2 The System Management screen displays The User Performed Service screen should be the default screen If not select In House Service User Service The User Performed Service screen displays Note the fluidics station maintenance area Figure A 20 Figure A 20 The user maintenance functions for the fluidics station Fluidics Station Configuration Station 1 v Bleach Interval Warning Limit n 0 d Time Elapsed Since Bleach Interval Alert Limit 100 d Last Bleach 105 d Last Change Tubing w lid Change Tubing Warning Limit n 0 d Change Tubing Alert Limit 100 d Procedure Change Tubing b 3 From the dropdown list select a station number The system displays the last bleach and peristaltic tube change 4 Select the Change Tubing procedu
121. ridge holder Under electrical to 100 C or higher a The fluidics station requires two people to lift and handle it safely Each person should firmly grasp the base of the instrument at the end opposite the other to lift Use OSHA standards for lifting techniques The instrument must be surrounded by adequate airspace Slots and openings in the instrument and the electronics compartment covers are for ventilation Do not block or cover them Never push an object into the instrument ventilation slots equipment damage or injury may result Do not set liquids on top of the instrument a The fluidics station is intended for indoor laboratory use in a controlled environment Caution Notices PA CAUTION You must have read and understood the contents of this manual before attempting to operate this fluidics station CAUTION The power supply cord is used as the main disconnect device Ensure that the socket outlet is located and installed near the equipment and is easily accessible When to Contact Affymetrix Under any of the following conditions unplug the instrument from the power source and contact technical Support When the power cord is damaged or frayed a If any liquid has been spilled into the instrument a If the instrument has been penetrated by water a If after service or calibration the instrument does not perform in accordance with the capabilities stated in the specifications If the instrument
122. rrays should be loaded into the carousel starting at position 71 Additional arrays need not be contiguous The scanner will always scan and check all 48 slots starting a position 71 Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 111 Loading the Carousel into the AutoLoaderDx 1 If you have previously removed the carousel from the AutoLoaderDx Load the carousel into the AutoLoaderDx by inserting the carousel into the AutoLoaderDx and turning the carousel until the alignment pin seats into the alignment hole Figure B 7 on page 111 2 Turn the carousel clockwise until the carousel mounting key flat seats gently into the AutoLoaderDx alignment key You may have to turn the carousel several times before it will seat into the alignment pin and alignment key When seated properly the carousel will be flush with the AutoLoaderDx housing Close the AutoLoaderDx door Figure B 9 on page 113 NOTE The seating of the key flat is confirmed by a gentle falling of the carousel into the key Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 112 Alignment Hole Carousel Mounting Key Flat Alignment Key in the Autoloader Alignment Pin Inserting Carousel into the AutoLoaderDx Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 113 Starting the Scanner 1 Press the I O button on the front pane
123. rtridge Front Probe array on glass substrate Using Tough Spots to Prevent Leaks Tough Spots are chemically inert polyvinyl labels that adhere to all plastics Affymetrix recommends using 3 8 inch circle diameter Tough Spots to prevent leakage from the array cartridge septa Before loading the array cartridge into the scanner follow this procedure to prevent the leaking of fluids from the array during scanning Even if you have already applied Tough Spots to the array prior to hybridization or after washing you must remove the old Tough Spots and apply new ones before you load them into the scanner Affymetrix recommends the use of Tough Spots obtained from Affymetrix P N 64 0158 or from USA Scientific Inc P O Box 3565 Ocala FL 34478 800 LAB TIPS P N 9185 0000 1 On the back of the array cartridge clean excess fluid from around septa Figure B 6 on page 110 Appendix B GeneChip Scanner 3000Dx with AutoLoaderDx 110 2 Carefully apply one Tough Spot over each of the two septa Press to ensure that the spots remain flat If a Tough Spot does not apply smoothly that is if you observe bumps bubbles tears or curled edges do not attempt to smooth them out Remove the spot and apply a new one Figure B 6 on page 110 Tough Spots Loading Arrays into the Carousel 1 Load your arrays into the carousel up to 48 Note that only one orientation is possible Figure B 7 on page 111 A
124. s may be covered by one or more of the following patents U S Patent Nos 6 114 122 6 287 850 6 391 623 6 422 249 and other U S or foreign patents Scanners Products may be covered by one or more of the following patents U S Patent Nos 5 578 832 5 631 734 5 834 758 5 936 324 5 981 956 6 025 601 6 141 096 6 171 793 6 185 030 6 201 639 6 207 960 6 218 803 6 225 625 6 252 236 6 335 824 6 403 320 6 407 858 6 472 671 6 490 533 6 650 411 6 643 015 6 813 567 7 682 782 7 689 022 and other U S or foreign patents Autoloaders Products may be covered by one or more of the following patents U S Patent Nos 6 511 277 6 604 902 6 705 754 7 108 472 and other U S or foreign patents Hybridization Oven Rotational Mixer Products may be covered by one or more of the following patents U S Patent Nos 6 050 719 6 386 749 6 705 754 and other U S or foreign patents Software Products may be covered by one or more of the following patents U S Patent Nos 5 733 729 5 795 716 5 974 164 6 066 454 6 090 555 6 185 561 6 188 783 6 223 127 6 228 593 6 229 911 6 242 180 6 308 170 6 361 937 6 420 108 6 484 183 6 505 125 6510 391 6 532 462 6 546 340 6 687 692 6 607 887 7 062 092 7 451 047 7 634 363 7 674 587 and other U S or foreign patents Limited License Notice Limited License Subject to the Affymetrix terms and conditions that govern your use of Affymetrix products Affymetrix grants you a non exclusive n
125. s station Cartridge Lever engages or releases the cartridge holder Needle Lever inserts the needles into the sample vials LCD screen displays messages during processes Lid Release Buttons one on each side on older fluidics station models New models open merely by lifting the lid Wash Bottles 2 hold wash buffers and tubing that draws buffer through system DI Water Bottle holds deionized water and tubing that draws water through system Waste Bottle collects waste from hybridizations and washes Sample or Vial Needles extend into the sample vials and draw fluid Barcode Label each module has an associated barcode to identify the module that is used by the worklist Figure A 2 The GeneChip Fluidics Station 450 and components 6 Needle Lever 3 amp 4 Wash block and Cartridge Holder 13 Barcode Label 7 LCD screen 8 Lid Release Button on older fluidics station models 9 Wash A Bottle 2 Module Door 5 Cartridge Lever 11 Waste Bottle 12 Sample Needles extended 1 Sample Holder Appendix A GeneChip Fluidics Station FS450Dx 69 Figure A 3 Location of the serial ports and ON OFF switch CommLink Out Connector to terminator or cable to next fluidics station CommLink In Connector Power Cable Lid Release Button ON OFF Note these buttons Switch may be present or Power Main absent depending on the model of th
126. se assays skip this step and proceed to fluidics For more information see Hybridization Oven Hybridizing Arrays in the Hybridization Oven on page 35 Chapter 2 Affymetrix GeneChip System 3000Dx v 2 System Overview 20 Figure 2 10 Hybridization Oven Button Hybridization Oven Fluidics Worklist Click Fluidics Figure 2 11 on page 20 to associate a test request with a fluidics station and module and to run the associated fluidics script The selected station and module will wash and stain the array For more information see Fluidics Washing and Staining Arrays in the Fluidics Station on page 38 See also GeneChip Fluidics Station FS450Dx on page 66 Figure 2 11 Fluidics Button Fluidics Scanner Worklist After the array has been processed on the fluidics station click Scanner Figure 2 12 on page 20 to view the Scanner Worklist AMDS automates control of the scanner and uses the assay information provided by the assay software module to manage the scanner settings for each type of array The software enables you to scan the arrays on the scanner AMDS then automatically grids the image computes the intensities and runs the analysis algorithm associated with the assay to generate a result For more information see Scanner Scanning Arrays on page 40 Also see GeneChip Scanner 3000Dx with AutoLoaderDx on page 101 Figure 2 12 Scanner Button Scanner Chapter 2 A
127. solution A Filling with WashA Empty fill with wash A mix by drain and fill repeat leave cell full A washes D F Wash with A by mixing using drain and fill procedure Flushing with Wash Flushing with wash solution B B washes D F Wash with B by mixing using the D F drain and fill procedure REMOVE SAMPLE VIAL Make sure sample vial is removed LOAD EMPTY VIAL IN LOC 1 Make sure empty vial is present Flushing with Wash Flushing with wash solution B Draining to Waste Drain waste needle 1 w Wash Flush needle 1 with Wash B Washing needle Wash needle with water REMOVE VIAL Prompt to remove vial Washing done Completion of washing READY System is ready Appendix A GeneChip Fluidics Station FS450Dx 96 The FS450Dx Instrument Specifications Fluidics Station Dimensions height depth width 40 2 x 41 0 x 71 1 cm or 15 13 16 x 16 1 8 x 28 inches Product Weight Approximately 80 pounds or 36 3 kg Power Input 100 to 240 V 3 A 300 watts or less Main supply voltage fluctuations not to exceed 10 of the nominal supply voltage Temperature Operating 15 to 30 C Storage non operating 10 to 60 C Humidity Operating 10 90 RH non condensing Storage non operating 10 to 95 RH Other Pollution degree 2 Installation category II Electrical Supply The electrical supply shall meet the input specified
128. solving 64 AMDS 8 quick reference guide 25 Array cartridge 29 handling 29 removing from AutoLoaderDx 116 scanning 40 scanning one array 41 Arrays loading cartridges 109 scanning 108 Assay deactivating 48 installation 47 scanning 40 Assay management panel selecting assays 48 AutoLoaderDx 101 carousel 110 China RoHS 124 configuring 113 declaration of conformity 119 dimensions 118 electrical safety 103 electrical supply 118 issues 114 laser safety 102 regulatory 123 safe operation 102 setting up 103 troubleshooting 113 114 weight 118 working environment 118 B Barcode reader 27 associate an array and fluidics station 69 Bleach cycle 78 Bleach interval alert limit 54 Bleach interval warning 54 Bubbles 75 c Cancelling test requests 32 Carousel loading 109 Cartridge septa 72 China RoHS AutoLoaderDx 124 fluidics station 99 Configuration panel 54 Creating test request 31 D Deactivate assay 48 Declaration of conformity AutoLoaderDx 119 Documentation fluidics station assay 69 Edit user 51 Error error while draining 92 missing fluid 89 92 sensor timeout 90 Errors operational and data input 64 resolving device related 61 test requests 63 F Fluidics station assay documentation 69 bleach protocol 78 care and maintenance 77 components 67 dimensions 96 error messages 91 home procedure 70 homing 70 installation category 96 modules 67 operating altitude 96 operating humidity
129. ssible use the barcode reader rather than entering data by hand Active Worklist Entering Editing or Canceling Test Requests Click on the Active Worklist button Figure 4 1 on page 31 in the Workflow pane to create edit and cancel test requests The Active Worklist contains all active test requests regardless of which step they are in the workflow After all steps ofthe workflow are complete you can approve or reject test request results from the Active Worklist Once approved rejected or canceled test requests appear on the Non Active Worklist Chapter 4 Test Request Processing 31 Active Worklist gt Entering Test Requests To create a test request 1 Click Active Worklist The Active Worklist displays Figure 4 2 on page 31 active test requests Active Worklist es eo one Mose Uri 2 Click Create a The Enter Test Request Screen displays Figure 4 3 on page 31 Youcan create more than one test request at a time Enter Test Request T8802 HG U133 Plur 20 v2 2 655507199 CytoScan HD v1 0 MSI0M tocan HD v1 0 HG 4133 Plus 2 0 v2 2 HG U133 Plus 2 0 v2 2 AM38 HG 1133 Plus 2 0 v2 2 AM30 Human SNP 6 0 v2 2 r CyoScan HD v1 0 3 Enter the Specimen ID Use your barcode reader to enter the Specimen ID barcode If your specimen doesn t have a barcode enter the name of the Specimen ID by hand in the Specimen ID field
130. t The Fluidics Station 450Dx differs from RUO version of the product in labeling color of the levers and the presence of a barcode next to the LCD screen for each module Lu IMPORTANT Make sure you familiarize yourself with the AMDS software interface before operating the Fluidics station See AMDS User Interface on page 17 Warnings and Precautions Installation and de installation of the system must be done by a trained Affymetrix representative The system warranty may be voided if used in a manner not specified by the manufacturer Exercise the normal precautions that are required for handling all laboratory reagents Wear gloves when using the fluidics station Exercise standard precautions when obtaining handling and disposing of potentially carcinogenic reagents Do not send your instrument elsewhere for service or attempt to service it yourself To protect your warranty and ensure safe operation the instrument should be serviced only by Affymetrix or its representatives If the instrument is not working correctly please contact your Affymetrix Technical Support representative Appendix A GeneChip Fluidics Station FS450Dx 67 Do not use the fluidics station in ways not specified by Affymetrix Doing so may impair the protections provided by the fluidics station load conditions the area behind the cartridge holder can have temperatures that rise n WARNING Do not place hands or fingers inside the cart
131. t been installed on AMDS you need to install the server certificate first See your assay software module manual to determine if you need to install the certificate See also Installing a Certificate on page 48 NOTE In most cases an Affymetrix field service engineer will install the certificate and assay In order to install an assay you must have the assay s installation bundle which is typically provided on a CD To install the assay 1 Click the Assay Management button Figure 5 1 on page 44 in the Administrator pane The Assay Management screen displays Figure 5 3 on page 47 2 Place the cd containing the assay software module installation bundle into the workstation s internal CD DVD drive 3 On the Assay Management toolbar click Install Assay The Assay Installation Dialog displays Figure 5 4 on page 48 4 Inthe Select the Manifest file box enter or browse to the manifest file The assay manufacturer provide the manifest file as part of the assay installation bundle 5 Select the users who should be permitted to run this assay a Click Select All to select all the users Click Deselect All to deselect all the users 6 When the Install button displays click Install Chapter 5 AMDS Administrative Features 48 Figure 5 4 The Assay Installation Function Assay Installation Select the Manifest file LIS name L Dx2User Danielle Tech Select
132. tation 70 Stopping a scan 42 System logoff 26 shutting down 26 T Technical support 11 Test requests additional information 33 cancelling 32 creating 31 deleting 32 editing 32 processing 30 35 registration 34 resolving errors 63 scanning 40 scanning one array 41 washing and staining 38 Tough Spots 108 Troubleshooting 61 AutoLoaderDx 113 fluidics station 86 instruments 64 U User management add user 50 edit user 51 Ww Washblock 73 Washing and staining 38
133. tem Overview 13 Hardware Cormpornents irese resit diiine aa E Pi E OO SP addo tetas 13 Standard Hardware Components 00 0 cece eee 13 Additional Optional Hardware Components 0 0 000000 cece eee 16 Optional Hybridization Oven 2 0 eee ee 16 Software Components sek ees s Rond a RAE oe X DOR RC OR Re Rl aba BA 17 AMDS Software Component 0 0 00 00 res 17 Assay SoftWare Modules 9 0 ocho Gi we xxv qur E ee we bE RR o C 4 17 AMDS User interface 2 2502060 Lb Sie ese RIS PRSE ees AE bbe Piebiues e 17 Workflow Pane 4 2 224242 228 taper ee be ee eh ee esas db edie se hese ee 18 Active WOFKIISt 2 4224 oi cea ede beh be one Ip uere ae ee ee ee eh dew ode 18 Registration Worklist 0 0 eee eee 19 Hybridization Oven Worklist 2 0 0 0 0 0 eee eee 19 Fluidics WOrkIIst va 2a24e2542anecennnees oh cules beeen Qaeda seas eos 20 Scanner WOrklist cs cr a eed ave ea epe deeds DABEI E ee haves 20 NoncActive Wotkllst x 4 o2ac 2anemomes baci ekad eda a aad EEEE aA Mad 21 Administrator PANE sas tu Su dc Ice iu E E eise EIE A D Pau 21 User and System Information Panes 22 User Details Pane exse 5x08 lee ede EE os ened ane bY RE E edge ue 22 Device Status Pane tete 1b T Seed b EPA ee ee A E ades 22 Alert Pane and Alert Details Pane 20 eee 23 Affymetrix GeneChip System 3000Dx v 2 Operation Basics 25 NrOdUCHON jc ces oc crea oe EnA ELTE E et ae ae ee GE ele A A E E 25 Start
134. that came with the cartridge kit for the appropriate wash buffer solutions or contact your Affymetrix technical support representative If you have not yet primed the fluidics station for the new assay prime the fluidics station now See the section Priming the Fluidics Station on page 75 In the Active Worklist pane click Fluidics The Fluidics Worklist displays Figure A 4 on page 71 Figure A 4 Fluidics Worklist Fluidics Worklist Total 9 If you using a barcode reader to associate a test request with a fluidics station and module do the following See Using the Barcode Reader with the Fluidics Station on page 69 a Load the array cartridge into the module washblock Do not engage the washload until prompted by the fluidics station LCD b Scan the barcode on the array cartridge c Scan the barcode on the fluidics station module If you are manually associating a test request with a fluidics station and module do the following a In the test request record that contains the desired Specimen ID place the cursor in the Station field and enter the station number b Place the cursor in the Module field and enter the module number c Place the array cartridge in the module washblock Figure A 5 on page 72 Do not engage the washblock until prompted by the fluidics station LCD The module must be the same as the module that you earlier associated with the array Select the test request rows that you wo
135. ting and Burning Log Files to CD or DVD l liissssss isses 46 Chapter 6 Appendix A Contents 5 Managing ASSAYS cc cea saarin anaon EEE aain eel a E eau al RURE ms Alans a EA A a diese Cab ee anes oe 47 Installing ASSAYS 0 anana aaa 47 Deactivating anm Assay iuo duod dor e Ye Ro e GEO MRE DS E E We adk 48 Repairing or Reactivating an Assay nannaa aaan 48 l stalling a Certificate esanei cree pia Recte deo Wad EEE E E E E a 48 Managing Users scannt ta aona a UR SER ood a a e a A MP E a 49 About UserRoles sae aae E EEE eS wee Fd died x etc ew amp e ANE 50 Adding a USEE Aono uaa nae ooo ea een A E E E E 50 Editing a User rc D E A ed e Ree a ee ee ee 51 Deactivating a User 2 ee eR eos pe EEA E pe RR Rn 51 Managing the System 0 02 eh 51 Changing System Management Screens 0 00000 eee 52 Managing Instrument Settings on the User Performed Service Screen 52 Viewing User Performed Service Logs lssissssess ee 56 Archiving and Purging Test Requests 57 Setting General Configurations eresse rien s 59 AMDS Troubleshooting exe sas e Re m e rece Re eoe 61 Jaitgeret acon MOTOR 61 Instrument Related Errors vac dw tse e y ED Rerd COR WV CR EYED 61 Device Status and Alert ICONS 2 0 0 ete 62 Viewing Alerts and Alert Details 2 0 0 0 00 eee 62 Individual Test Request Errors 2 0 rns 63 Operational and Data Input Errors ere 2l 64 Resolving Alerts aae sue arate 9 OE Ue R
136. trument Care Disconnect the power cord of Fluidics Station before replacing fuses a Use a surge protector on the power line to the fluidics station Always run a Shutdown protocol when the instrument will be off or unused overnight or longer This prevents salt crystals from forming within the fluidics system When not using the instrument leave the sample needles in the lowered position Each needle should extend into an empty vial This protects them from accidental damage Always use deionized water to prevent contamination of the lines Change buffers with freshly prepared buffer at each system startup The fluidics station should be positioned on a sturdy level bench away from extremes in temperature and away from moving air Fluidics Station Bleach Protocol Appendix A GeneChip Fluidics Station FS450Dx 78 This protocol is designed to eliminate any residual SAPE antibody complex that may be present in the fluidics station tubing and needles The protocol runs a bleach solution through the system followed by a rinse cycle with deionized DI water This protocol takes approximately one hour and forty minutes to complete Affymetrix recommends running this protocol weekly If you have AMDS administrator privileges you can set the Bleach Interval Warning Limit and Bleach Interval Alert Limit See the section Managing Fluidics Stations on page 53 To avoid carryover or cross contamination from the bleach protocol
137. uipments for measurement control and laboratory use Particular requirements for in vitro diagnostic medical equipment Safety requirements for electrical equipment for measurement control and laboratory use Particular requirements for automatic and semi automatic laboratory equipment for analysis and other purposes This device complies with Part 15 of FCC Rules Operation is subject to the following two conditions 1 This device may not cause harmful interference and 2 This device must accept any interference received including interference that may cause undesired operation This Class A digital apparatus meets all requirements of the Canadian Interference Causing Equipment Regulation Cet appareil num rique de la classe A respecte toutes les exigences du R glement sur le mat riel broullier du Canada Regulatory Agency Certification LE Compliant with directive 2002 96 EC WEEE Appendix A GeneChip Fluidics Station FS450Dx 99 China RoHS Restriction of Hazardous Substances Compliance Manufacturers of Electronic Information products EIPs that are sold to the People s Republic of China are required to provide information about lead cadmium mercury hexavalent chromium polybrominated biphenyls and polybrominated diphenyl ethers contained within In accordance with the Chinese RoHS Restriction of Hazardous Substances Table A 6 contains information identifying the specific hazardous
138. uld like to start processing on the fluidics station These rows should indicate Ready in the Status field Click Start to begin the fluidics protocol The LCD screen on the fluidics station and the AMDS Status field in the Fluidics Worklist indicates the status of the protocol as it progresses Follow the instructions on the fluidics station LCD screen See also the section Fluidics Station LCD Messages on page 94 for more LCD messages A selection of the available prompts is given below as examples u If prompted to LOAD VIALS Load the 1 5 mL vials into the sample holder of the fluidics station Appendix A GeneChip Fluidics Station FS450Dx 72 o If prompted to LOAD CARTRIDGE Since you earlier loaded an array cartridge into the fluidics station module you must now engage the washblock Flip the cartridge lever up to engage the cartridge septa needles into the septa Proper engagement of the washblock with the cartridge is indicated by a change in the message on the LCD Figure A 6 on page 72 Appendix A GeneChip Fluidics Station FS450Dx 73 IMPORTANT To minimize damage to the array the door closure forces are controlled If you cannot get proper engagement simply press on the washblock to complete the action Do not force anything Press on the washblock DO NOT FORCE UP THE CARTRIDGE LEVER 9 If prompted to LOAD VIALS 1 2 3 place the three 1 5 mL sampl
139. vice name a The device status a Last activity Check the device status icons to see if there are instrument errors In Figure 6 1 on page 62 for instance all devices have green status but the hard drive health has a yellow triangle indicating that the hard drive is rebuilding For more information see Device Status and Alert Icons on page 62 and Viewing Alerts and Alert Details on page 62 NOTE Occasionally an instrument issue occurs and no alert is evident in AMDS One example is a leaking fluidics module If you are not sure how to handle an issue and there is no alert with a recommended resolution turn off the instrument and contact Affymetrix support NOTE In some cases you may not be able to resolve an instrument problem You will be directed to contact Affymetrix support to resolve the problem You should not attempt to correct this kind of problem yourself Figure 6 1 Device Status Pane Hyb Oven 1 Fluidics Station 1 Fluidics Station 2 Fluidics Station 3 Fluidics Station 4 Fluidics Station 5 Fluidics Station 6 Fluidics Station Fluidics Station 8 Scanner Hard Drive Health Printer Status 9 9 9 9 9 9 9 9 Device Status T 49 9 C A 60 RPM Closed Module 3 Stopped Module 4 Stopped Module 2 Stopped Module 1 Stopped Module 1 Stopped Module 1 Stopped Module 1 Stopped Module 1 Stopped AutoLoader Door Unlocked Rebuilding 2 in 3 Minutes Ready
140. you are unable to resolve issues related to your GCS3000Dx v 2 system please contact Affymetrix technical support If you are experiencing fluidics station or scanner problems especially under any of the following conditions unplug the instrument from the power source and contact Affymetrix technical support When the power cord is damaged or frayed a If after service or calibration the instrument does not perform to the specifications stated in The FS450Dx Instrument Specifications on page 96 or GCS3000Dx Specifications on page 119 Lu IMPORTANT Make sure you have the model and serial number available when you make this call Affymetrix Inc 3420 Central Expressway Santa Clara CA 95051 USA www affymetrix com Email support affymetrix com Tel 1 888 362 2447 1 888 DNA CHIP Fax 1 408 731 5441 Emergo Europe Molenstraat 15 2513 BH The Hague The Netherlands Tel 31 70 345 8570 Fax 31 70 346 7299 Affymetrix UK Ltd Voyager Mercury Park Wycombe Lane Wooburn Green High Wycombe HP10 OHH United Kingdom Tel 44 0 1628 552550 Fax 44 0 1628 552585 France Tel 33 08 00 91 95 05 Germany Tel 49 01803 001334 Italy Tel 39 800 91 59 74 Email supporteurope affymetrix com Affymetrix Japan K K ORIX Hamamatsucho Bldg 7F 1 24 8 Hamamatsucho Minato ku Tokyo 105 0013 Japan Tel 81 3 6430 4030 Fax 81 3 6430 4021 Email supportjapan affymetrix com Chapter 1 Welcome to AMDS 1
141. you can view its status by clicking Active Worklist Data associated with that test request only appears on the Active Worklist and the test request s current stage in the workflow Click Active Worklist Figure 2 8 on page 19 to Chapter 2 Affymetrix GeneChip System 3000Dx v 2 System Overview 19 a View the current status of all active test requests Create new test requests View and approve test results You cannot edit information that is displayed in the Active Worklist rather AMDS automatically maintains and updates the list For more information see Active Worklist Entering Editing or Canceling Test Requests on page 30 Figure 2 8 Active Worklist Button Active Worklist Registration Worklist After you create the test request click Registration Worklist Figure 2 9 on page 19 to associate a test request with a single array cartridge and to add the target preparation reagent kit lot numbers if it supported by the assay software module For more information see Registration Registering Test Requests on page 34 Figure 2 9 Registration Button Registration Hybridization Oven Worklist Click Hybridization Worklist Figure 2 10 on page 20 to enter data related to oven hybridization and to process the array in the hybridization oven Some assays do not use the hybridization oven they perform hybridization on the fluidics station Test requests that are associated with the
142. ystem Change your password a Use the barcode reader Handle array cartridges IMPORTANT Before attempting any assay runs you must be familiar with the operation of the fluidics station see the appendix GeneChip Fluidics Station FS450Dx on page 66 and the operation of the scanner see the appendix GeneChip Scanner 3000Dx with AutoLoaderDx on page 101 Starting and Shutting Down the System Before you process test requests you need to start the workstation and follow instructions for starting the instrumentation Starting the Workstation Turn on the computer workstation to launch AMDS Ifthe option Turn on Laser has been selected the scanner laser will start to warm up when you launch AMDS a If you have administrator privileges see Configuring Scanner Settings on page 60 for instructions on how to have the scanner laser warm up when AMDS launches a AMDS will perform a system self test to confirm the operational status of the system and ensure that all components are connected and operating properly a AMDS will also perform some housekeeping tasks to ensure that all test requests are in known states and can be processed Once AMDS completes its self test the AMDS User Logon screen displays Figure 3 1 on page 26 Logging onto AMDS After you start the workstation and the User Logon screen displays Figure 3 1 on page 26 enter your User Name and Password and click Log On a The Affymetrix service en

Download Pdf Manuals

Related Search

Related Contents

Conducted Spurious Emission into VSWR の測定方法  AP エアスプレーガン 上CUP 400cc 取扱説明書  ドライブハロー HL20  Bedienungsanleitung - KB Metallverarbeitung GmbH  AcPC4610 User`s Manual  Manual de Uso Oxímetro 560  Bondex Premium Porcelanato Rápido  User Manual HPC-7140 - download.advantech.com  Fujitsu LIFEBOOK U904  Le Pays d`Auge, Pays d`art et d`histoire  

Copyright © All rights reserved. Failed to retrieve file