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Affy GeneChip Human Gene 1.0 ST Assay

1. 1 Click the Assay Management button The Assay Management window appears 2 Click the Install Certificate button The server certificate browse dialog box appears Figure 1 2 Figure 1 2 The Server Certificate browse dialog box note that the CD DVD drive is the default drive EE Please select a server certificate to ins Install from CD O Install from local disk drive 3 Select either the default drive Install from CD i e the internal drive D or Install from local disk drive 4 Browse for your desired xxxxx cer file where xxxxx is the name of the certificate that the installer of the RUO server provided to you Click the OK button or the Cancel button If successful you are notified by a message You have successfully added the server certificate xxxxx cer to the AMDS trusted certificate store Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 7 If the certificate installation fails AMDS notifies you with the particular algorithm error message The software prevents you from accessing the server and from transferring data without the proper certificate installed 7 Click the OK button on the message to return to the Assay Management screen Installing the Human Gene 1 0 ST v1 0 ASM The assay installation process is relatively simple It requires the selection of an assay manifest file and the selection of approved user access NOTE
2. Test Requests Reagent Information Specimen ID Registration Date A Reagent Kit Name PartNumber Manufacturer LotNumber Expiration Date H919800 E Ambion WT Expression Kit 10 rxn 4411973 Ambion 9532626 2022 01 01 H919801 2 Ambion WT Expression Kit 30 rxn 4411974 Ambion 3435002 2024 02 03 H919802 GeneChip Eukaryotic Poly A RNA Controls 10 900433 Affymetrix 5881875 2024 12 29 H919803 GeneChip Expression 3 Amplification Reagen 900454 Affymetrix 3639291 2022 09 17 H818804 GeneChip Expression 3 Amplification Reagen 900457 Affymetrix 513760 2024 07 14 H919805 GeneChip WT Terminal Labeling Kit 10 mn 900670 Affymetrix 2411889 2022 10 31 GeneChip WT Terminal Labeling Kit 30 rxn 300571 Affymetrix 4073376 2024 05 31 GeneChip Hybridizatio in Kit 30 r 90 Affymetrix 2077567 2022 04 01 NOTE Select one or more test requests on the Test Requests list on the left pane Data is entered only for the test requests that you have selected In the Human Gene 1 0 ST v1 0 Assay Home screen you can view the following reagent kit information u Reagent kit name o Ambion WT Expression Kit 10 rxn P N 4411973 o Ambion WT Expression Kit 30 rxn P N 4411974 o GeneChip Eukaryotic Poly A RNA Controls 100 rxn P N 900433 o GeneChip Expression 3 Amplification Reagent Hybridization Controls 30 rxn P N 900454 o GeneChip Expression 3 Amplification Reagent Hybr
3. H919805 Specimen Type Requestor Last Name Clark Requestor First Name Sydney Requesting Institution El Camino Hospital Request Date Additional info 1 Additional info 2 Additional info 3 Additional info 4 Additional info 5 If the selection contains one or more test requests that have either started or completed scanning when you click the Batch Edit button the application displays the Assay Batch Information screen with the statement Test Requests have passed scanning step Data cannot be changed Gridding Manually You can manually grid your results if an error arises in the automatic gridding function Before you attempt to grid manually you must be familiar with the gridding function referenced in the Affymetrix GeneChip System 3000Dx v 2 User Guide P N 08 0261 the Affymetrix GeneChip Command Console 1 0 User s Guide P N 702569 or the GeneChip System 3000Dx for EU User s Guide P N 08 0136 or other Affymetrix documentation The AMDS manual gridding procedure is based on the gridding procedure outlined in these manuals A gridding failure for a test request will trigger a manual grid alignment alert To remedy this gridding failure Click the alert that is visible on the right side of the page in the Alerts panel View the alert then click the Resolve button Enter your user ID and password Click OK The DatImageViewer window appears Manually adjust th
4. GeneChip Expression Wash Stain and Scan User Manual P N 702731 and Quick Reference Card QC Metrics for Gene and Gene Design Expression Arrays P N 702670 before you can use the information contained in this supplement to run the assay Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 5 Reagents Reagents for the GeneChip Human Gene 1 0 ST Array single array P N 511545 comprise the following reagent sub kits and associated part numbers u Ambion WT Expression Kit 10 rxn P N 4411973 Ambion WT Expression Kit 30 rxn P N 4411974 u GeneChip Eukaryotic Poly A RNA Controls 100 rxn P N 900433 u GeneChip Expression 3 Amplification Reagent Hybridization Controls 30 rxn P N 900454 u GeneChip Expression 3 Amplification Reagent Hybridization Controls 150 rxn P N 900457 a GeneChip WT Terminal Labeling Kit 10 rxn P N 900670 u GeneChip WT Terminal Labeling Kit 30 rxn P N 900671 u GeneChip Hybridization Wash amp Stain Kit 30 rxn P N 900720 Installing the Assay Software Module To create a Human Gene 1 0 ST v1 0 test request you must 1 Install a certificate 2 Install the Human Gene 1 0 ST v1 0 ASM 3 Enter the test request NOTE In most cases an Affymetrix field service technician will install the certificate and assay software module Installing a Certificate As a security measure AMDS requires that you or the Affymetrix field service technician inst
5. You must be logged in with either Laboratory Supervisor or with System Maintainer privileges to install an Assay Software Module 1 Click on the Assay Management button The Assay Management window appears 2 Click the Install Assay button The Assay Installation browse dialog box appears Figure 1 3 Figure 1 3 The Assay Installation browse dialog box Assay Installation Select the Manifest file LIS name ds2labsuper Select All Deselect All Cancel 3 Click the Browse button The Assay Installation browse dialog box appears Figure 1 4 Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 Figure 1 4 The Assay Installation browse dialog box note this figure shows internal CD drive D EB Locate Manifest File Install from CD O Install from local disk drive m DA HS AGCC Templates aS Human Gene 1 0 ST v1 0 Archive E Bin Cacheln CacheOut Data LibraryFiles SecureCom human_gene_1 0_st_v1 0 manifest 4 Select either the default drive Install from CD i e an internal CD drive D or Install from local disk drive i e the C drive 5 Browse for your desired xxxxx Manifest file In the present case it is the Human Gene 1 0 ST vl 0 Manifest file Typically you will access the manifest file from the D drive It should be in the folder similar to D Human Gene 1 0 ST v1 0 Browse for it and select it 6 Click the OK but
6. D430 024 and other U S or foreign patents Products are manufactured and sold under license from OGT under 5 700 637 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 Fluidics Stations Products may be protected 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 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 Copyright 2012 Affymetrix Inc All rights reserved Contents Chapter1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 4 IM OCUCUION Prem 4 Nomenclature s saia E E dee ane ns mar gets hud A aaa ate Boe Bs aban 4 Major Features of Human Gene 1 0 ST V1 0 A kk kk kk KK KK ae 4 REAGENS ofa 6co10 I bbebb heli died ded dd bt ede etae bed dd 5 Installing the Assay Software Module JW kk kk kk kk 0 kK KK KK KK KK KK KK KI KK KK KK KK eee 5 Installing e Certificat qu ee n n ete bdo ee eed el te y n REPERI MR ee eed oes 5 Installing the Human Gene 1 0 ST v1 0 ASM
7. WW kk kk kk kK KK eee 7 Creating the Test Request kk kk kk kk kk kK kK KK KK KK KK KK KK KK KK KK KK KK KK KK KK 11 Adding Additional Information to the Specimen kk kk kk kK KK cee ee 12 The Assay Information Screen Adding Reagent Information n saasaa aaan 14 Reagent Information Tab 2 iilis 15 Specimen Report Tab 45 44 5 524 1 eee were epe re EE DNE ER NE eee 17 Test Request Log Tab seii ep REP RR PD Dd b ob e eoe eed be pies 17 Batching Additional Test Request Information kk kk kK KK KK KK KIRI eee 19 Gilldding Mantally 4 e Lara o EE ekir ER den ized UE PESE Eid PUES A 20 Transfering Data sooner tex uere the Medd See te Res Ao ap m 21 Reviewing the Test Report kk kk kk kk kk hn 22 Ordering Information Ak kk kk kk kk eee KK KK KK KK 24 Technical SUPPORT lt cc a ax Skala kan cle tee ap an Saa sins at a AWA Bla toe pt dR QR Bn an hwa bl di av 24 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 Introduction This user s guide shows you how to create the GeneChip Human Gene 1 0 ST Assay Software Module v1 0 RUO assay test request This module is for the GeneChip Human Gene 1 0 ST Assay that is run on the GCS3000Dx v 2 system using the Affymetrix Molecular Diagnostic Software AMDS Affymetrix has designed this assay software to be compatible with the GCS3000Dx v 2 system and the GeneChip Human Gene 1 0 ST Array Reagent Kits Nomenclature The assay name i
8. field Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 14 a Specimen Size Unit manually entered or from a drop down menu u mL m uL a OZ mg ag inch s cm s mm a blank field Specimen Size Value manually entered floating point numeric value Method of Collection manually entered as freeform text Collection Date manually entered as an ISO 8601 format date Collection Time manually entered using either a 12 or 24 hour time scale e g 1 15 pm or 13 15 The software will display the time using 12 hour time scale e g 1 15 pm Requestor Last Name manually entered as freeform text Requestor First Name manually entered as freeform text Requesting Institution manually entered as freeform text Request Date manually entered as an ISO 8601 format date u Additional Info 1 5 Five Additional fields manually entered as freeform text 3 When you have completed adding the information click Save and Close or just Close to exit without saving When you click Close only the following events may occur u If you made no edits the screen will close If you made edits a pop up asking Would you like to save changes with Yes No and Cancel appears u Click Yes in the dialog box and the software collects an e signature and then saves and closes the screen Click No and the software discards changes and closes the screen u Click Cancel and the software returns to the S
9. 1 0 ST Assay vA Affymetrix Field Name Patient ID Patient Last Name Patient First Name Sex Date of Birth Specimen Type Specimen Size Unit Specimen Size Value Method of Collection Collection Date Collection Time Requestor Last Name Requestor First Name Requesting Institution Request Date Additional info 1 Additional info 2 Additional info 3 Additional info 4 Additional info 5 Specimen ID H919800 Bolded Value indicates new value to be saved Field Values 655507193 Wilson Lynn Female 2010 08 07 Blood mL 21 venipuncture 2011 01 15 4 43 00 PM Clark Sydney For Research Use Only Enter Date as YYYY MM DD Time as HH MM SS am pm Save and Close Add the following information This information includes u Patient ID manually entered as freeform text or read from a barcode Patient Last Name manually entered as freeform text Patient First Name manually entered as freeform text u Sex chosen from a drop down menu The menu includes the following choices Male Female u Unknown u blank field 13 a Date of Birth manually entered with defined format The format must be entered in an ISO 8601 format that is with 4 digit year first then month then day e g 2001 11 09 for November 9 2001 No other format is allowed Specimen Type chosen from a drop down menu Blood u Solid Tissue u Soft Tissue u Saliva u Buccal Swab Plasma blank
10. 131407 001 H919800 GRD 20120412 131407 001 H919800 LLOG 20120412_131407_001_H919800 ARR Qo 7 20120412 131407 001 H919800 AUDIT 2 View Worklist Comments and Errors The reports displays a Upload details o Upload URL where the files went o Upload Time o Source Machine Name Assay Details n Specimen ID n Array Barcode Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 23 u Uploaded files the list of the files that were transferred n ARR file AUDIT CEL file DAT file GRD file log file MDS file u Click the Close button to close the results screen without doing anything B 8 B E E p u Click the Print button to print the results to the default printer Click the View Worklist Comments and Errors button n The Audit Log Comments and Errors window opens Figure 1 18 This window displays any comments or errors that the user or AMDS application associated with that test request Figure 1 18 The Audit Log Comments and Errors window Audit Log Comments and Errors The n nice aice wan upload attempt was unsuccessful Id 232ada63 707c 4c2a b50b ccb5550c025c Gridding Alignment failed dx2labsuper Id 12942ebd 1430 4ed3 9f17 da3d0c2e164a Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 24 Ordering Information Table 1 1 lists the Human Gene 1 0 ST v1 0 reagents and arrays
11. TG Affymetrix User s Guide GeneChip Gene 1 0 ST Assay Software Module Version 1 0 For research use only Trademarks Affymetrix Axiom Command Console CytoScan DMET GeneAtlas GeneChip GeneChip compatible GeneTitan Genotyping Console myDesign NetAffx OncoScan Powered by Affymetrix PrimeView Procarta and QuantiGene are trademarks or registered 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 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 this Affymetrix product in combination with a product not provided licensed or specifically recommended by Affymetrix for such use Patents 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 6 551 817 6 733 977 7 629 164 7 790 389 and
12. all a SSL server certificate on your local workstation in order for your workstation to communicate with the server This is required for the transfer of the Human Gene 1 0 ST v1 0 test request data to the server You should have the certificate installed before 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 or reinstall a certificate If a proper certificate has not been installed you can still install the assay and process test requests however you will not have permission to access the server and you cannot transfer test request data to the server If you cannot access the server and have already installed a certificate contact Affymetrix technical support NOTE You must be logged in with either Laboratory Supervisor or System Maintainer privileges to install a certificate Procedure for Installing a Certificate The Active Worklist Administrator panel contains the Assay Management button and provides the starting point for installing a certificate Figure 1 1 Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 6 Figure 1 1 The Active Worklist Administrator Panel Attymetrix Molecular Diagnostic Software Worktlow Fluidics
13. an Smith Linda Stanford Hospital H919802 G55507196 Chan Andy Clark Sydney El Camino Hospital H919803 G55507194 Burwell Kane Smith Linda Stanford Hospital H919804 G55507192 Collingsworth Taylor Clark Sydney El Camino Hospital H919805 G55507191 Henriques Addison Clark Sydney El Camino Hospital Click the Specimen Report tab to view all specimen IDs associated with that assay type You can view the Specimen ID a Patient_ID a Patient Last Name Patient First Name Requestor Last Name Requestor First Name Requesting Institution Request Date Test Request Log Tab Click the Test Request Log tab Figure 1 15 to view all the test requests associated with that assay type Each test request will include information regarding the following u Date of the log entry Time of the log entry User when the log entry was created Type of log entry Subsystem associated with log entry Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 18 u Short Message associated with the log entry Long Message related to the selected short message Assay Home Human Gene 1 0 ST v1 0 GeneChip Human Gene 1 0 ST Assay For Research Use Only Xwe Affymetr x Specimen Report Test RequestLog Reagent Information Test Requests Test Request Log Specimen ID y Date Time User Type Subsystem Short Message H919800 412 2012 1 20 PM System Workflow WebService State Change to Cre
14. and associated part numbers Table 1 1 Name P N Supplier Ambion WT Expression Kit 10 rxn 4411973 Ambion Ambion WT Expression Kit 30 rxn 4411974 Ambion GeneChip Eukaryotic Poly A RNA Controls 100 rxn 900433 Affymetrix GeneChip Expression 3 Amplification Reagent Hybridization Controls 30 rxn 900454 Affymetrix GeneChip Expression 3 Amplification Reagent Hybridization Controls 150 rxn 900457 Affymetrix GeneChip WT Terminal Labeling Kit 10 rxn 900670 Affymetrix GeneChip WT Terminal Labeling Kit 30 rxn 900671 Affymetrix GeneChip Hybridization Wash amp Stain Kit 30 rxn 900720 Affymetrix GeneChip Human Gene 1 0 ST Array 2 arrays 901085 Affymetrix GeneChip Human Gene 1 0 ST Array 6 arrays 901086 Affymetrix GeneChip Human Gene 1 0 ST Array 30 arrays 901087 Affymetrix Technical Support 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 Affymetrix UK Ltd Voyager Mercury Park Wycombe Lane Wooburn Green High Wycombe HP10 OHH United Kingdom www affymetrix com Email supporteurope affymetrix com UK 0800 328 0056 France 08 00 91 95 05 Germany 01803 001334 Italy 800 91 59 74 Other 44 1628 552550 Fax 44 0 1628 552598 Affymetrix Japan K K ORIX Hamamatsucho Bldg 7F 1 24 8 Hamamatsucho Minato ku Tokyo 105 0013 Japan Email supportjapan affymetrix com Te
15. atedState H919801 4 12 2012 1 24 PM e329b08f a98c Workflow GUI Successfully saved test request infc H919802 4 12 2012 1 24 PM e329b08fa98c Workflow GUI State Changed to ReadyForAnalys H919803 4 12 2012 1 27 PI dx2labsuper E Signature GUI E signature added for save on Edit Ha19804 4 M esee eem SES H319805 m GUI enged to ReadyForAnalys lt Long Message Saved these Name Value pairs Patient IDJG55507195 Patient Last Name Golston Patient First Name Jordan Sex Male Date of Birth 1956 08 26 Specimen Type Blood Specimen Size Unit mL Specimen Size Value 4 8 Method of Collection venipuncture Collection Datel Collection Time Requestor Last Name Smith Requestor First Name Linda Requesting Institution Stanford Hospital Request Date Additional info 1 Additional info 2 Additional info 3 Additional info 4 Additional info 5 Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 19 Batching Additional Test Request Information If you want to enter or edit the same information for multiple test requests at the same time you can use the Batch Edit feature NOTE You cannot associate any additional information with test requests after scanning has started You cannot save your edits and if you attempt to save the software displays an error message 1 In the Active Worklist or any of the worklist windows select yo
16. e grid Click the Save button SY Ur mo SS Close the DatImage Viewer Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 21 Transferring Data AMDS automatically transfers the completed assay data to the URL that you set up when you originally installed your assay The descriptor labels and data that AMDS transfers to the non AMDS system include u The following file types o ARR file AUDIT CEL file DAT file GRD file log file MDS file The MD 5 file is a checksum file You can use a utility such as FastSum Windows or md5sum Linux to confirm that AMDS has transferred all the files correctly All Specimen Information descriptor labels and their corresponding data fields which may be filled in or not EH EH E E EH E All tracked Reagent Information descriptor labels and their corresponding data fields which may be filled in or not The AMDS confirms that the data has completed transfer successfully by the following two criteria u the assay module detects no exceptions upon transferring a the assay module confirms that every file listed as transferred indeed exists on the server Once AMDS transfers the files to the server AMDS will place all the associated files in a folder named Human Gene 1 0 ST v1 0 This folder resides on the server All data files are intermingled Upon transfer the software assigns file names test request creation date and time 3 digits _ specim
17. ectories and Copy Installation Files Completed Verify Installation files Completed Create Assay Group Completed Apply Security setting Completed Install Web Services Completed Update System Settings Completed Current Status Installation completed for assay Human_Gene_1 0_ST_v1 0 If AMDS detects no errors it enables the Finish button 20 Click the Finish button to conclude the assay installation procedure and return to the Assay Management screen Setup is done You may now begin to use the assay software module Creating the Test Request You must be a Laboratory Supervisor Technician or a Technologist in order to create a test request 1 If you are not already in the Active Worklist window select Active Worklist from the Workflow panel on the left Figure 1 10 The Active Worklist panel opens Active Worklist Affymetrix Molecular Diagnostic Software Workflow Hybridization Oven Fluidics 2 Click the Create button on the toolbar of the Active Worklist The Enter Test Request Screen appears Figure 1 11 11 Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 12 Figure 1 11 The Enter Test Request window Enter Test Request H919800 PEE ee 3 Enter one or more Specimen ID and Assay Name combinations The current Assay Name for the GeneChip Human Gene 1 0 ST v1 0 ASM is H
18. enID original extension DAT CEL etc This makes it easy to determine which files are associated with a particular test request NOTE Upon successful data transfer AMDS deletes from the local AMDS hard drive the dat and cel files for the transferred test requests Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 22 Reviewing the Test Report When you have completed all the remaining assay steps Registration Hybridization Wash Stain Scanning etc the test request moves to the Non Active Worklist with a hyperlinked date time stamp in the Review Results field of the Test Request record To view the test result report you must be in the Non Active Worklist window 1 Click the date time hyperlink for the desired test request record The Test Results dialog box appears Figure 1 17 Figure 1 17 The Test Results View dialog box for the test report Test Result View Human Gene 1 0 ST v1 0 GeneChip Human Gene 1 0 ST Assay For Research Use Only Affymetrix Test Report GeneChip Human Gene 1 0 ST Assay For Research Use Only Upload URL dtsd5pfrbfl dx2_ruo_files AMDS TEST1 Human_Gene_1 0_ST_w1 0 Upload Time 2012 04 12 1 48 PM Source Machine Name AMDS TEST1 Assay Details Specimen ID 919800 Array Barcode 51154500413526052915401476193335 Uploaded Files 20120412_131407_001_H919800 MD5 20120412_131407_001_H919800 DAT 20120412 131407 001 H919800 CEL 20120412
19. idization Controls 150 rxn P N 900457 o GeneChip WT Terminal Labeling Kit 10 rxn P N 900670 o GeneChip WT Terminal Labeling Kit 30 rxn P N 900671 o GeneChip Hybridization Wash amp Stain Kit 30 rxn P N 900720 Reagent kit part number information Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 16 Reagent kit manufacturer information Reagent lot number Reagent expiration date The Reagent Kit Name Manufacturer Part Number Lot No and Expiration Date are not required to run the assay AMDS provides the ability to transfer the Reagent Kit Name Manufacturer Part Number Lot No and Expiration Date to the server along with other test request information 1 For any reagent with a manufacturer of Affymetrix select the test requests in the test request list on the left side of the Reagent Information screen Scan the barcodes from the reagents you used The software will enter the corresponding lot number and expiration date into the appropriate fields Remember you cannot make any edits to a test request after the array associated with that particular test request has started scanning on the GCS3000Dx v 2 scanner 2 Click the Save button 3 When you click Close only the following events may occur a If you made no edits the screen will close a If you made edits a pop up Would you like to save changes with Yes No and Cancel buttons appears u Click Yes in the dia
20. l 81 3 6430 4020 Fax 81 3 6430 4021 For complete contact information and specific regional support contact information please go to www affymetrix com browse contactUs jsp
21. log box and the software saves and closes the screen u Click No and the software discards the edits and returns to the Reagent Information screen Click Cancel and the software returns to the Reagent Information screen with edits preserved NOTE You can also enter the reagent kit information manually by selecting test requests in the left side of the screen then placing the cursor in to the lot number and expiration date fields for the appropriate kits and typing in the correct information This method should be used for all reagents manufactured by companies other than Affymetrix Inc The Human Gene 1 0 ST v1 0 remembers the association between a reagent kit and expiration date Scenarios are as follows 1 Enter a lot number and expiration date for the first time click Save u AMDS saves the data 2 Enter alot number already associated with another test request AMDS auto populates the expiration date that you had previously used u Click Save and the data is saved for all associated test requests 3 Enter a lot number already associated with another test request AMDS auto populates the expiration date that you had previously used Modify expiration date and click Save The software will display a pop up with the following message or words to this effect Do you want to save this expiration date for all other test requests with this lot number u Click OK or Cancel OK saves this information for all test requests Ca
22. ncel returns to the screen with edits preserved Special Note Regarding the Changing of Expiration Dates If you change the expiration date for a previously entered lot number see step 3 above and choose to save this change for all the test requests with this lot number the application displays the following message You have changed the expiration date for reagent kit name gt Lot lot number from old date to new date This affects count Test Requests Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 17 The application remembers the new expiration date and updates all the test requests with those lot number s which have not yet started scanning with the correct expiration date s If you click Cancel the software returns to the Reagent Information Screen with all edits preserved Specimen Report Tab Click the Specimen Report tab Figure 1 14 to view all the specimen IDs associated with that assay type in this case the Human Gene 1 0 ST v1 0 Figure 1 14 The Specimen Report tab Assay Home Human Gene 1 0 ST v1 0 GeneChip Human Gene 1 0 ST Assay For Research Use Only Affymetrix Specimen Report Test RequestLog Reagent Information Test Requests SpecimenlD PatientlD Patient Last Name Patient First Name Requestor Last Name Requestor First Name Requesting Institution H813800 G55507193 Wilson Lynn Clark Sydney El Camino Hospital H919801 G55507195 Golston Jord
23. pair an assay are 1 Activating a disabled assay 2 Updating the server information for assays requiring a server 3 Returning the assay to a newly installed state Please do not repair this assay if there are test requests associated with this assay in the In Progress state on any worklist To stop the repair click Cancel To continue with the repair click Continue User Credentials User Name ds2labsuper Password Event Reason Repair Reason 18 Any AMDS user with valid AMDS credentials and with the right permissions can repair or reinstall the assay You can include a reason but this is optional 19 Click the Continue button or the Cancel button If you clicked Continue an Assay Installation status window appears and displays the progress of the assay installation Figure 1 9 u If you clicked Install and if AMDS accepts your user ID and password the system checks for the appropriate firewall parameters The system also checks the proper server credentials and displays an error message if it detects the wrong credentials If the system detects the proper firewall setup it accepts the assay installation and returns to the Assay Management screen Setup is done Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 Assay Installation Human Gene 1 0 ST v1 0 Installation Status Check Installation files Completed Create Dir
24. pecimen ID additional information screen with edits preserved The Assay Information Screen Adding Reagent Information The Assay Information screen or the Assay Home screen provides you with a summary of all the specimen information test request logs and pertinent reagent information for particular assay type The Assay Home screen has the following tabs sub screens Reagent Information Specimen Report u Test Request Log In any worklist window in the Assay Name field click on the Assay Name The Assay Home aka Assay Information window appears Figure 1 13 Reagent Information screen is the default tab Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 15 Reagent Information Tab Click the Reagent Information tab Figure 1 13 to view current reagent information NOTE If you select specimen IDs from the list on the left then scan the reagent kit barcode the software parses the reagent information and enters the lot number and expiration date into the correct fields for all selected test requests without manual intervention Figure 1 13 The Reagent Information tab Assay Home Human Gene 1 0 ST v1 0 GeneChip Human Gene 1 0 ST Assay For Research Use Only Affymetrix Bolded Reagent Kit Name indicates multiple old values exist Bolded Data indicates new value to be saved Enter Expiration Date as Y YYY MM DD Specimen Report Test RequestLog Reagent Information
25. rver usually your workstation user password or network user credentials 13 Confirm your password NOTE Your NA Device Server Username and Password are not the user name and password that you used to log into AMDS You must enter your user name and password that you use to access the server 14 Confirm that the firewall is on and that your workstation is connected to the network 15 Click the Install button or the Cancel button u Ifthe system does not pass your system s firewall settings the following error message is displayed Figure 1 7 Figure 1 7 Error Message Remote Device Settings Unable to connect to Firewall Abort will terminate assay installation Ignore will install the assay but the system will not have permission to communicate with the remote machine Retry will attempt to connect again 16 Click the Abort button to exit the assay installation procedure u or click the Retry button to attempt another try u or click the Ignore button to continue Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 10 x NOTE If you select Ignore the AMDS will still install the assay but you will not have permission to communicate with any remote server 17 If the same assay already exists in the system a message appears asking if you would like to repair the assay Figure 1 8 This assay is already installed Would you like to repair it Reasons to re
26. s GeneChip Human Gene 1 0 ST Assay The assay display name is Human Gene 1 0 ST v1 0 The term ASM refers to Assay Software Module Major Features of Human Gene 1 0 ST v1 0 The major features of the Human Gene 1 0 ST v1 0 are four screens that augment assay record keeping This user guide will also discuss the use of these screens in setting up the assay These screens include 1 Additional Information screen 2 Assay Home screen or Assay Landing screen 3 Batch Edit screen 4 Report screen In addition the Human Gene 1 0 ST v1 0 under the control of the AMDS application can transfer all specimen information to the server It is not the purpose of this short user s guide to instruct you on how to run the assay This user s guide will show you how to create the RUO test request To complete the assay run you will still need to follow the standard AMDS assay protocols and process it through the workflow to register hybridize wash stain and scan the array as part of the array cartridge the details of which are discussed in the Affymetrix Molecular Diagnostic Software User Guide P N 08 0261 You must be thoroughly familiar with the information contained in the Affymetrix Molecular Diagnostic Software User Guide the Affymetrix Molecular Diagnostic Software Quick Reference Card P N 08 0262 GeneChip WT Terminal Labeling and Hybridization User Manual P N 702808 The Ambion WT Expression Kit P N 4425209
27. ton The Assay Installation browse screen appears Figure 1 5 Figure 1 5 The Assay Installation browse screen for the Human Gene 1 0 ST v1 0 Assay Installation Select the Manifest file D Human_Gene_1 O_ST_v1 0H uman_G ene 1 0 5 T D Manifest LIS name Human Gene 1 U ST v1 0 Configure User Access dxZlabsuper Selecta Deselect all 7 Choose those users who will have access to this assay either by selecting individual users or by clicking the Select All button or if you desire to start the selection over click the Deselect All button Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 9 8 Click the Install button or the Cancel button 9 If you clicked the Install button the Data Transfer Server credentials dialog box window appears Figure 1 6 Figure 1 6 The Data Transfer Server Credentials dialog box Assay Installation Remote Device Settings N Device URL N Device Server Username N Device Server Password Confirm Password 10 Locate and enter the NA Device URL i e the secure URL server where AMDS will send the completed assay data as an example https dx2webdavserver RUO 11 Enter the NA Device Server Username This is your user name for the server usually your workstation user name or network user credentials 12 Enter the NA Device Server Password This is your password for the se
28. uman Gene 1 0 ST v1 0 4 Once you have made the entries click the Submit button and the Enter Test Request screen closes The software displays the Active Worklist window with the newly created test request s on the screen NOTE After you have submitted the test request the procedures for Registration Hybridization Fluidics Station processing and Scanning are the same as those steps outlined in the Affymetrix Molecular Diagnostic Software User s Guide P N 08 0261 Refer to that document for further instructions Adding Additional Information to the Specimen After you add a specimen and return to the Active Worklist you can add certain types of pertinent information about the specimen You can also add this information later here or in other worklists This information is not necessary in order to run the assay Hi IMPORTANT You cannot associate any additional information with test requests after scanning has started You will not be able to save your edits If you attempt to save the software displays an error message Saving and editing specimen information requires an e signature upon saving 1 Click the desired Specimen ID field The Additional Information dialog box opens Figure 1 12 Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 Figure 1 12 The Specimen ID Additional Information dialog box Additional Information Human Gene 1 0 ST v1 0 GeneChip Human Gene
29. ur test requests 2 Click the Batch Edit button u The Assay Batch Information dialog box appears Figure 1 16 The left column lists the selected Specimen IDs 3 Enter or change in the right dialog box Sex of the test request subject Specimen Type Requestor Last Name Requestor First Name Requesting Institution Request Date Additional Info 1 5 five user defined fields Click the Save and Close button to save your changes and close the window 5 Click the Close button If you did not make any edits the Assay Batch screen closes If you made any edits a Yes No Cancel window appears u Click Yes No or Cancel u Yes saves this information u No discards all changes Cancel returns you to the Assay Batch screen with edits preserved NOTE You must save this information before you begin the scanning step This is to ensure the safety of the data Do not attempt to add or edit this information after scanning Chapter 1 GeneChip Human Gene 1 0 ST Assay Software Module Version 1 0 20 Figure 1 16 The Assay Batch Information dialog box Assay Batch Information Human Gene 1 0 ST v1 0 GeneChip Human Gene 1 0 ST Assay For Research Use Only An Affymetrix Test Requests in Assay Batch Bolded Field Name indicates multiple old values exist Bolded Value indicates new value to be saved Specimen ID Enter Date as YYYY MM DD Time as HH MM SS am pm H919800 H919802 Field Name Field Value H919804 a

Affy GeneChip Human Gene 1.0 ST Assay

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