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Applied Biosystems AutoCaller™ Software User Guide (PN 4385543)

1. 3 At the prompts click Yes and OK to delete the sample set from the AutoCaller software database Note If a study is using the sample set information the software displays an error message and does not delete the sample set 4 Click Close to close the Sample Set Management window Create a study using a sample set Once you create page 105 and import page 106 a sample set file into the AutoCaller software you can create a study using the sample set IMPORTANT You must create and import the sample set file into the AutoCaller software database before you create the study Create a study 1 From the main window toolbar select Tools Manage Studies using a sample set s Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences Notes 112 Applied Biosystems AutoCaller Software User Guide Appendix A Manage Sample Set Files A Create a study using a sample set 2 In the Study Management window click 3 Add a new study to the database us Study Management Name Date Created Sample Set Platform Assays Comments 08 June Genotyping D6 16 2008 Generic Sample Set Plate 7 First test of the new instrument Al 2007 Samples 06 16 2008 Generic Sample Set Plate 8 Lymphoma Study 06 17 2008 Generic Sample Set Plate lo Work done by Smith Lab 3 In the Stud
2. 0000 e eee 96 Appendix A Manage Sample Set Files lt e cece eee eee 103 Appendix overview 0000 eee 104 Create a sample set file ERT R RTE A 9 A eee 105 Import a sample set fille 2 0 0 0 l l 106 Manage sample sets n u anuanua rr 109 Create a study using a sample set een 112 Appendix B Manage xml Files eell eee 117 Appendix overview spea Z ea reatu p Mt Re ERI eot N ele eee A EFE RO doo eds 118 Export a study in xml format naana ees 119 Import xml files into a study ee 121 Appendix C Software Warranty Information 125 Computer configuration hr 126 Limited product warranty XA R 9 RR sarean wenns tenes 126 OS SAY T css hes ile eaa oed et reece aaa Sica masons 129 Index 4 05 bbe 0 a rd had et EE ao ce eae S d ea 131 iv Applied Biosystems AutoCaller Software User Guide Preface How to use this guide Purpose of this guide Audience Assumptions Text conventions User attention words The Applied Biosystems AutoCaller Software User Guide provides step by step instructions for using the Applied Biosystems AutoCaller Software This guide is intended for novice and experienced AutoCaller software users at the following User Levels Administrator Scientist Production This guide uses conventions and terminology that assume a working knowledge of the Microsoft Windows operati
3. N 14476 N A17111 Sample NA17112 N A17113 N A17114 NA17115 Sample Sample Sample Sample Sample Sample Sample Sample Sample Sample Sample Sample Sample Sample Sample 3 Omit the sample a Click the sample to be omitted The right side of the Data Explorer window displays information about the sample Sample Name Study Sample Set Population Gender Source Is Control Notes 10AE137 Lymphoma Study Generic Sample Set Default False Applied Biosystems AutoCaller Software User Guide 79 m Chapter 4 View and Edit Data Edit data b Right click and select Omit wells associated with sample name amp O Samples fap 10AE137 Sample i 104E258 aand L EL EH i 10AE315 Sample Include all wells associated with 10AE137 i 10AJ1 Sample 10AJ129 Sample i 1043136 Sample s 10AJ137 Sample 10AJ139 Sample 10AJ61 Sample c Atthe prompt click Yes to omit all wells for the sample Select an Option 9 This will include all wells in study 08 June Genotyping associated with Sample 10AE137 Cancel g Are you sure you want to do this d Click OK in the message box The wells for this sample are omitted from any analysis In the Analyze window the selected well s are less intensely shaded and the Omitted check box in the Data Table pane is checked The statistics in the Statistics tab are calculated without the values fr
4. a Change a value for a criterion Note Applied Biosystems recommends accepting the default values for the analysis criteria b Enable Disable the analysis criteria When you enable an analysis criterion the AutoCaller software applies the criterion to the study When you disable an analysis criterion the software ignores it Note The types of analysis criteria Name column and the Auto Codes are predefined in the AutoCaller software and cannot be edited For more information see About the automation settings on page 22 5 Click Save Il Edit Study 4a Basic Study Information Automatior Settings 4b Please choose settings approprial e for the platform and ir struments to be used in this study The default entries in the value ci lumn of the table below are for the 7900 instrument These parameters may be innapr priate when using instru ments other than the 7900 Default values For Fluorescent int nsity automation settin s Min Rox Max ROX Wells NTC Avg Max Non speci ic VIC Non specific FAN Weak VIC Weak FAM have not been defined for the OpenAn ay platform hence thes automation settings are disabled by default when creatind a Study For use on the DpenarrayPlatform Name Value Enabled Auto Code Min Genotype Conf 0 95 v Min ROX 200 v Min Genotyped 90 rz rezo Ma
5. For example to sort the data by sample name click Sample Name The assays are sorted by sample name in alpha numerical order To search for a sample a Right click the Sample Name column heading then click Search for Sample b In the Search for Sample dialog box enter the sample name then click OK The software highlights the first row that the sample is found in Note The Sample Name field is case sensitive Search for Sample 1 Sample Name OK Cancel Toexport the data click Export Table Data to File enter a file name and type then click Save To print the Data Table pane a Right click in the table and select Print Well Data b When prompted click OK in the Print dialog box Notes 66 Applied Biosystems AutoCaller Software User Guide Chapter 4 View and Edit Data View data Statistics tab The Statistics tab displays calculated statistics for the selected assay based on the category you select Category Description Allele Frequencies Displays the total number of times as a percentage that Allele 1 and Allele 2 occur in the samples for the selected reaction plate or multiplate Genotype Distribution Displays the total number of times as a percentage each possible genotype occurs in the samples for the selected reaction plate or multiplate Hardy Weinberg Displays the Hardy Weinberg Equilibrium HWE for any target Equilibrium populations identified when
6. From the Analyze window toolbar click Search for assays to open the Search for Assays dialog box From the Choose Study drop down menu select the study in which you want to search for assays Optional In the Assay Name field enter the name or ID number of the assay to find To search for more than one assay at a time click Open to open a dialog box where you can enter or paste more than one assay name You can enter an asterisk as a wild card For example if you enter 245 the search will return all assays with names that include a 245 sequence C__232456789_20 C__332456789_20 and so on If you do not specify an assay name or ID number the software returns all assays in the study Optional In the Assay Collection drop down menu define the assay collection Select the assay collection in which you want to search for assays or Select Define a new collection to define a new assay collection for use as a search criterion See page 48 for instructions Optional In the Plate Barcode field enter the barcode for the reaction plate Note Entering a barcode is useful when you want to see all the assays run on a single reaction plate 58 Applied Biosystems AutoCaller Software User Guide Chapter 4 View and Edit Data A Search a study for assays 6 Optional In the Criteria pane specify any of the following criteria to narrow the set of assays returned by the search Fiel
7. txt For more information see the SDS Online Help 5 In the Barcode field enter a name for the reaction plate or enter or scan the barcode 6 Click OK to close the New Document window and open the SDS software main window New Document Assay Allelic Discrimination 2 Container 384 Wells Clear Plate Em _ 3 Template Blank Template Eh Browse Barcode 123456788 5 Save Settings As My Default OK Cancel 7 Enter the assay ID E a Inthe Setup tab click Add Marker then Select the assay name or ID number or Click New enter the assay name or ID number then assign the detectors Note In the SDS software the term marker is used instead of assay ID Both terms refer to the assay name or ID number You can enter the Applied Biosystems assay identification number for example C 34816113 20 ora name of your own choosing Notes 8 Applied Biosystems AutoCaller Software User Guide Chapter 2 Preparation Tasks 0 Set up an SDS file b Click Done to return to the SDS software main window Marker Manager Markers Allele X Allele X Base Allele Y Allele Y Ba AIF Assay ID Color Modificatio Creation D New Import Import AIF Export Delete Edit N Detector Manager Copy To Plate Document Done 8 Label the NTC wells correctly a In the plate layout highlight the NTC wells b In the Setup tab
8. Choose an Auto Analysis option When a file is successfully imported the Imports all run data associated with the assays directly into a study You can use the software to search studies for assays then view and edit the assay run data For more information see Chapter 4 on page 55 Imports the assay names or ID numbers into the Assay Management window For more information see Edit assay information on page 41 From the main window toolbar select File K Load TaqMan OpenArray File to Database to open the Load Setup dialog box for importing OpenArray files Tools Help New Analysis Window Load SDS File to Database Load XML File to Database Load TaqMan Opendrray to Database Load EDS File to Database Exit AutoCaller software automatically calls the genotypes for each assay in the file In the Load Setup dialog box Deselect the Conduct Auto analysis check box to track which assays are new All assays from the file are given the status NEW for more information see Assay Selection pane on page 60 Select the Conduct Auto analysis check box to automatically apply Auto Codes page 22 to each assay in the file From the Choose Study drop down menu select the study you want the Open Array file imported into Note You can import the same OpenArray file into more than one study Click Browse to navigate to and select the file or folder you want to import The file or folder name is displayed in the Cho
9. TC Code Status DNA Plate Priority Code Chromosome Comments Chapter 5 Publish Data Creating a comparison report Cie 08 June Genotyping Any TC Code Any Status MULTI v 6 Click Browse then navigate to and select a destination folder 7 Click Report The AutoCaller software Displays the results in the Report window Exports the data as two txt files 8 Click Close to close the Report window 9 Open the destination folder to confirm that the export was successful The AutoCaller software produces two files The comparison txt file contains the results of the comparison The mismatches txt file contains a summary of discrepancies The txt file names include the report type comparison or mismatches the date and time the name of Study 1 and the name of Study 2 10 Open the txt files in a spreadsheet or simple text application Generate a Wild 1 From the main window toolbar select Tools r Generate Reports Type Sample Comparison Hep Data Explorer Repo rt Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences Notes Applied Biosystems AutoCaller Software User Guide 99 Notes Chapter 5 Publish Data Creating a comparison report 2 Inthe Report window select Wild Type Sample Comparison then click Next ler zu A From the Choose S
10. An assay collection is a group of two or more assays You can create an assay collection by choosing the assays one by one or by importing an assay collection from a text file txt The file should contain each assay name on a separate line 1 Select Tools r Manage Assay Collections Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences Name the new assay collection In the Manage Assay Collections dialog box enter a name in Name field Assay collection names can contain only letters numbers underscores and spaces 48 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information vam Manage assay collections 3 Select assays for the collection Either Click the name of the assay in the All Available Assays list and then click gt gt Repeat for all assays to be added to the collection Optional To quickly find an assay enter the first few letters of the assay name in the lt filter items here gt field above the All Available Assays list The list scrolls to display assays that begin with the letters you entered or Click Import In the dialog box that opens locate the file containing the assay collection and click Open I Assay Collection Management m An assay collection is a user defined set of assays that can be saved and used for A be AutoCaller s s
11. Select the source DNA plate name from the drop down menu DNA plate name user defined MULTI NoDNA Plate Note Applied Biosystems recommends that you select MULTI If you select MULTI the software exports all data for the selected assay s once for the multiplate If you select No DNA Plate the software exports all data for the selected assay s twice once for the multiplate and once for the individual plates Priority Code Select a priority code from the drop down menu Chromosome Select a chromosome from the drop down menu Comments Click the Comments field then enter any comments that appear in the Assay Management window or the Comments tab of the Analyze window Enter the comments exactly as they appear in the Assay Management or Analyze window or enter an asterisk as a wild card For more information on each criterion see About the search criteria on page 57 Note If you do not specify any criteria the software returns all assays with the name or ID number you entered in step 4 If you did not enter an assay name or ID number the software returns all assays in the study Notes Applied Biosystems AutoCaller Software User Guide 101 Chapter 5 Publish Data Creating a comparison report 8 From the Choose Control Sample drop down menu select a control sample wild type that you want to compare the study to Report Select Report Criteria Select Co
12. Statistics Codes Comments Assay Info Name Value Assay Name de ABCxy1 plate C DMA set C Platform Plate Is this a redo No DNA Plates 1 Chromosome NA Status AUTO PASS Well Address Allele 1 Allele 2 9 8722 9 6922 Predicted Geno Gender No Gender No Gender Genotype ROX Confidence 22 3 083 33 22 3 255 42 Population 1 Default 1 Default 10 04 22 10 1222 10 422 10 12 22 Genotype 00 1 Sample Name lal A12 Iai A13 Iai Ald Data Table 2 Aig pane l S page 65 Als 10 49 22 1 Default 1pefauit 1pefaukt 1 Default 1 Default No Gender No Gender No Gender No Gender No Gender 22 3 031 16 3 2 908 74 S 2 413 09 2 847 35 2 112 21 A22 A23 L NA17210 A24 Assay Selection pane Notes 10 21 22 10 58 22 10 322 lpefauk 1 Defaut 1 Default No Gender No Gender No Gender 2 805 35 2 335 89 2 756 81 x Export Table Data to File Assay Selection M pane page 60 Statistics tab page 67 Codes tab page 68 Comments tab page 68 Assay Info tab page 69 Status menu page 70 The Assay Selection pane displays the assays returned by the search and includes the following information Column Description Assay Name The assay name or ID number Plate Barcode page 71 The name or barcode of the reaction plate in which the assay was run T
13. You can a Select deselect the Hide study check box When you hide a study the study will not appear in any of the software drop down menus For example the study will not appear in the Choose Study drop down menu when you search for assays or select report criteria b Select deselect the Freeze study check box When you freeze a study the study cannot be edited Note Users at the Administrator and Scientist User Levels can unfreeze any study at any time Notes Applied Biosystems AutoCaller Software User Guide 35 NEN Chapter 3 Manage Studies and Assay Information Manage studies c If a study does not include data that is an SDS file has not yet been imported into the study you can also edit the study name platform sample set and population IMPORTANT If a study includes data you cannot edit the study name platform sample set or population 4a Edit Study Basic Study Setup Enter Study Name Preliminary Screening Choose Platform Plate Choose Sample Set Feline Lymphoma Study v rStudy Management i Hide study _ Freeze study r Choose Target Populations Tabby Siamese Calico Comments I Clear Save Cancel 5 Save your changes Click Save then click OK at the prompts 6 Click Close to close the Study Management window Notes 4b 36 Applied Biosystems Auto
14. effective date Warranty claims Notes Applied Biosystems warrants that for a period of ninety 90 days from the date the warranty period begins its Applied Biosystems AutoCaller Software will perform substantially in accordance with the functions and features described in its accompanying documentation when properly installed on the instrument system for which it is designated and that for a period of ninety 90 days from the date the warranty period begins the tapes diskettes or other media bearing the software product will be free of defects in materials and workmanship under normal use If buyer believes that it has discovered a failure of the software to satisfy the foregoing warranty and if buyer notifies Applied Biosystems of such failure in writing during the ninety 90 day warranty period and if Applied Biosystems is able to reliably reproduce such failure then Applied Biosystems at its sole option will either i provide any software corrections or bug fixes of the identified failure if and when they become commercially available to buyer free of charge or ii notify buyer that Applied Biosystems will accept a return of the software from the buyer and upon such return and removal of the software from buyer s systems terminate the license to use the software and refund the buyer s purchase price for the software If there is a defect in the media covered by the above warranty and the media is returned to Applied B
15. study name gt in the SDS file the AutoCaller software can automatically import the SDS file into the correct study However you can omit this step and manually import the SDS file into any study When you manually import an SDS file you can import the same SDS file into more than one study See Import SDS files on page 24 c Click OK to return to the SDS software main window 10 Save and close the SDS file Notes 10 Applied Biosystems AutoCaller Software User Guide Chapter 2 Preparation Tasks o Set up an SDS file 11 Run your reaction plate on the 7900HT instrument to collect data Note Alternatively you can perform thermal cycling on a GeneAmp PCR System 9700 then use the 7900HT instrument to read the data This option is best for users performing high throughput experiments To set up an existing SDS file If you have already created and run an SDS file follow this procedure to ensure the SDS file is compatible with the AutoCaller software 1 Start the SDS software then open an existing SDS file IMPORTANT The AutoCaller software is intended for SNP genotyping experiments only Be sure to open an Allelic Discrimination AD plate document 2 Label the NTC wells correctly a In the plate layout highlight the NTC wells b In the Setup tab enter NTC in the Sample Name field IMPORTANT You must label all NTC wells NTC If you label the NTC wells as water blank and so on the AutoCal
16. 0 Assays on this Plate Assay Name MNOeF78 PQRgh9 STUij10 VWXKITI Plate Location T Comments SONS b Right click and select Delete You can also click 3 Delete E amp Studies 6 08 06 Drug Resistance amp C3 Plates plate A Plate i plate B Plate plate C Plate plate D P amp C3 Assays t ABCxyl Assay GHIab45 Assay JKLlcd Assay Delete Notes Applied Biosystems AutoCaller Software User Guide 53 wu Chapter 3 Manage Studies and Assay Information Delete assays and plates c Atthe prompt click Yes to delete the plate from the study Select an Option 4 Chick OK in the message box then click E3 Close to close the Data Explorer window The plate is deleted from the study Notes 54 Applied Biosystems AutoCaller Software User Guide Chapter 4 View and Edit Data This chapter covers Chapter oveni N s solu d nado a positura ue Hare d q DUC ROMS bisa too BA 56 B Search a study forassays 2 i 26cces ddusans bees Seder E eu EE EEEE 57 MAUI a ay omy E TEE 60 BN Ot date c ie dee E S EA A E E E E N 73 Applied Biosystems AutoCaller Software User Guide 55 74 Chapter 4 View and Edit Data Chapter overview Chapter overview This chapter explains how to search a study in the Applied Biosystems AutoCaller Software database for assays then view and edit data in the studies IMPORTANT Any edits you make to the
17. 34275590 10 MULTI MULTI 94 100 0 1 063829787 0 0 0 0 10 Column Description Oligo Name The assay name or ID number S1 DNA Plate For Study 1 S1 DNA Plate and Study 2 S2 DNA Plate the name or barcode of the source DNA plate that is the DNA plate that was S2 DNA Plate used to seed the reaction plate DNA plate name The software displays the source DNA plate name if the user included the name in the file or in the sample set file e MULTI The software assigns the name MULTI whenever there is more than one plate in the study with the same assay e No DNA Plate The software displays No DNA Plate for any reaction plates that do not have a name or a multiplate assignment Wells The number of wells in the reaction plate that contain matching samples assays 96 Matched The percentage of samples in Study 1 with genotypes that match the sample genotypes in Study 2 96 Mismatched The percentage of samples in Study 1 with genotypes that do not match the sample genotypes in Study 2 96 UDT The percentage of samples in Study 1 with undetermined genotypes Remaining columns The remaining columns list every possible combination of genotyping comparisons The legend is as follows e S1 Study 1 e S2 Study 2 s 00 Undetermined genotype e 11 Homozygous VIC dye e 12 Heterozygous e 22 Homozygous FAM dye For each assay the software lists the number of samples that falls into each comp
18. 439 Applied User Guide E Bibystems Introduction 3 Applied Biosystems AutoCaller Software SNP Genotyping Analysis Tool Preparation Tasks Manage Studies and Assay Information View and Edit Data e Publish Data Copyright 2008 Applied Biosystems All rights reserved For Research Use Only Not for use in diagnostic procedures Information in this document is subject to change without notice Applied Biosystems assumes no responsibility for any errors that may appear in this document APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE WHETHER IN CONTRACT TORT WARRANTY OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL INCIDENTAL INDIRECT PUNITIVE MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT INCLUDING BUT NOT LIMITED TO THE USE THEREOF Notice to Purchaser License Disclaimer Purchase of this software product alone does not imply any license under any process instrument or other apparatus system composition reagent or kit rights under patent claims owned or otherwise controlled by Applera Corporation either expressly or by estoppel Trademarks Applied Biosystems AB Design GeneAmp and VIC are registered trademarks and AutoCaller FAM ROX StepOne and StepOnePlus are trademarks
19. Platform PLATE Plate Format 8 a rows X 12 columns well Num wel Addr Sample Population Assay SNP Assay 1 1 4 622 462 A SNP Assay 1 1 515 4 809 485 SNP Assay 1 E 4 717 54 S SNP Assay 1 57 T 4 547 244 SNP Assay 1 2 4 773 978 SNP Assay 1 4 380 898 SNP Assay 1 j 271 4 121 215 SNP Assay 1 a 4 218 219 SNP Assay 1 A 22 3 85178 SNP Assay 1 al h 4 466 398 SNP Assay 1 y 22 4 343 316 SNP Assay 1 i k 3 645 33 SNP Assay 1 0 0 042 5 136 298 SNP Assay 1 0 0 4 508 463 SNP Assay 1 0 0 3 926 328 SNP Assay 1 3 0 4 234 847 SNP Assay 1 0 D 4 916 575 SNP Assay 1 0 036 0112 454 555 Skip this plate 7 When the File Progress field in the Loading dialog box displays Done a Review the information for each assay Column Description Assay Name The assay name or ID number Plate The name or barcode of the reaction plate in which the assay was run The name or barcode is entered by the user in the file page 7 DNA Plate The name or barcode of the source DNA plate that was used to seed the reaction plate DNA plate name The software displays the source DNA plate name if the user included the name in the file page 7 or in the sample set file page 105 e No DNA Plate The software displays No DNA Plate for any reaction plates that do not have a name or multi
20. Priority Code Actual Allele 1 Actual Allele 2 Display Allele 1 Display Allele 2 C 33490361 10 1 ABCB10 C 25761435 20 1 ABCB10 C 32340905 10 1 ABCB10 C 25634362 20 1 ABCB10 C 25634369 20 C 25634377 20 9 C 27531774 20 10 C 15853280 10 11 C 15853281 20 169533 20 169534 20 169539 20 25982477 10 25985082 10 47 C 25985104 20 OO R PP o 2 3 4 5 C 32340910 10 1 ABCB10 6 7 8 1 ABCB10 1 ABCB10 1 ALDH4A1 1 ALDH4A1 1 ALDH4A1 1 ALDH4A1 1 ALDH4A1 1 ALDH4A1 1 ALDH4A1 1 ALDH4A1 1 ALDH4A1 QO O0O0 O02m O00 000 dO GO dO O EO KOG GO dO R dO O dG dO dOd dO Od RO K Od G Applied Biosystems AutoCaller Software User Guide 4 Save the spreadsheet as a text txt file C 25634362 20 C 25634369 20 C 25634377 20 C 27531774 20 C 15853280 10 C 15853281 20 C 169533 20 C 169534 20 C 169539 20 C 25982477 10 C 25985082 10 C 25985104 20 C 22271516 20 C 25599727 20 C 9578046 10 C 25472931 20 C 30480743 10 C 7477307 30 C 566822 10 C 1917952 20 C 32558900 10 C 32558987 10 C 27859819 10 s Kaa aM Ka K Ka K Ka Ke Ka Ke Ka b Ka Ke a K ph Ka K Ka K Ka K ba t E DME Autocaller Assay Info File test txt Notepad Priority Code c All PANAANAPANANNANPANNAOAN APADPANADAAADAPANDAANADNAPAPNAAD Chapter 3 Manage Studies and Assay Information Edit assay information Alt PANAANAPANANNANPANNADANN ANPADPANDAADAAPANDANAANAPNENAD Actual Allele 1 Ac
21. UNDO feature for edits to the data Required user To perform the procedures in this section log in to the AutoCaller software at the level Administrator or Scientist User Level Edit the There are two ways to edit genotypes allele calls genotypes Use the Plot View pane below Use the Data Table pane page 74 Edit genotypes in the Plot View pane 1 Inthe Assay Selection pane select the desired assay You can select Asingle assay to edit the assay for an individual reaction plate or Amultiplate to edit the assay across reaction plates Look for MULTI in the Plate Barcode column There may be several multiplates the software creates a multiplate for any assay that was run on more than one reaction plate 2 In the Plot View pane draw a box around the samples points to edit Note When you draw a box around the points in the Plot View pane the corresponding samples in the Data Table pane are highlighted 3 Right click anywhere in the Plot View pane then select the appropriate option from the pop up menu 1 Homozygous VIC dye e 12 Heterozygous 22 Homozygous FAM dye e UDT Undetermined genotype Notes Applied Biosystems AutoCaller Software User Guide 73 wm Chapter 4 View and Edit Data Edit data Genotype Cartesian v Hints Change Settings Assay ABCxy1 DHA Plate DHA_set_A View Genotype Type Cartesian Zoom Print Plot Change Genotype to 11 Change Ge
22. a new assay collection for use as a search criterion See page 48 for instructions Optional In the Plate Barcode field enter the barcode for the reaction plate Note Entering a barcode is useful when you want to export data for all assays run on a single reaction plate 90 Applied Biosystems AutoCaller Software User Guide Chapter 5 Publish Data Creating a report from a study 7 Optional In the Criteria pane specify any of the following criteria to narrow the set of assays exported Field To specify this criterion Date Loaded Click I Choose Date Assays Were Loaded then select the date the assay was imported into the AutoCaller software database TC Code Select the Auto Code from the drop down menu Status Select the analysis status from the drop down menu DNA Plate Select the source DNA plate name from the drop down menu DNA plate name user defined MULTI NoDNA Plate Note Applied Biosystems recommends that you select MULTI If you select MULTI the software exports all data for the selected assay s once for the multiplate If you select No DNA Plate the software exports all data for the selected assay s twice once for the multiplate and once for the individual plates Priority Code Select a priority code from the drop down menu Chromosome Select a chromosome from the drop down menu Comments Click the Comments field then enter any comments that appear
23. analysis criteria For a list of Auto Codes and the corresponding analysis criteria see page 22 b Review the statistics information Stats Ifthe Assays Errored field displays 0 the SDS file s were imported successfully Ifthe Assays Errored field displays 70 some or all of the SDS file s were not imported See Importing errors on page 32 c Optional Click Export to export and archive the information in the Loading dialog box d Click Close I Loading SDS File A302X8X2 sds 6a Project Assay Hame Plate Dna Plate Wells Status Assay Codes Project Assay Hame Plate Dna Plate Wells Status Assay Codes TestFiles E LLY22 10 A302X8X2 1 NGS D 64 SUCCESS TC20 TC15 6b Finished anig NEM Total Assays Read 1 Assays Imported 1 Assays Errored 0 Plates Read 1 File Progress Export 6c Folder Progress 6d On import the AutoCaller software automatically analyzes the data in the SDS files To search for assays and view edit the data see Chapter 4 on page 55 Notes 26 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information ww Import files Import OpenArray NT Imager Genotyping System files When you import OpenArray files created for allelic discrimination plates in the OpenArray NT Imager Genotyping System into the AutoCaller software database the software Importan 1 OpenArray file Notes
24. assay are deleted from the AutoCaller software database Select an Option 3 All data from assay GHIab45 will be deleted Are you sure you want to delete all data from assay GHIab45 Cancel window Click OK in the message box then click E3 Close to close the Data Explorer The assay is deleted from the study and from the AutoCaller software database 1 Select Tools K Data Explorer from a study He Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences 52 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information Delete assays and plates 2 In the Data Explorer window click to open a study and view the associated plates and assays B AutoCaller Data Explorer As Use the Data Explorer to browse the contents of the database and remove Plates and Assays from studies Removable items can be removed with a Right click gt gt Delete or using the trash can icon E O Studies 08 June Genotyping t CUES plate B Plate plate C Plate plate D Plate H O Assays H O Samples i C3 All 2007 Samples tH C3 Assays 3 Delete the plate a Click the plate to be deleted The right side of the Data Explorer window displays the assays associated with the plate Plate plate_B Study 08 June Genotyping Date Loaded 2008 06 16 11 24 16
25. been made for the selected assay For more information on comments see Comments tab on page 68 Notes Applied Biosystems AutoCaller Software User Guide 81 wu Chapter 4 View and Edit Data Edit data Notes 82 Applied Biosystems AutoCaller Software User Guide Chapter 5 Publish Data This chapter covers E Chapter Oveni N Sieb neqoe a possideas dU R sas Saks Be 84 BH Crea ngareport from a study cs 0 RR A R der kete R3 DRE RUP IESETETI SS 85 R Creating a comparison report e 93 Applied Biosystems AutoCaller Software User Guide 83 Chapter 5 Publish Data Chapter overview Chapter overview This chapter explains how to generate reports from a study in the Applied Biosystems AutoCaller Software This chapter also explains how to generate comparison reports for downstream analysis Workflow Preparation Tasks Chapter 2 wv Manage Studies and Assay Information Chapter 3 b d View and Edit Data Chapter 4 b d Publish Data Chapter 5 Review the report types Create reports from a study Create comparison reports BR ODM Use reports in publications and or downstream analysis Required user To perform the procedures in this chapter log in to the AutoCaller software at any User levels Level For information on User Levels see About user levels on page 3 Report types AutoCaller software creates two types of reports Study r
26. can be successfully accessed by the AutoCaller software see Set up an SDS file on page 7 Text txt files created with a simple text application and formatted for use with the AutoCaller software EDS files created on the Applied Biosystems StepOne StepOnePlus and 7500 and 7500 Fast Real Time PCR Systems Files exported from the OpenArray SNP Genotyping Analysis software Files in xml format created with the AutoCaller software Applied Biosystems AutoCaller Software User Guide Chapter 1 Introduction About user levels About user levels Your AutoCaller software Administrator is responsible for managing users in the AutoCaller software When creating a user the Administrator must assign the user a User Level By assigning a User Level the Administrator can control the tasks each user is allowed to perform in the AutoCaller Software User level tasks There are three predefined User Levels in the AutoCaller software Users at each User Level can perform the tasks listed below User Level Allowed Tasks Administrator s Install the AutoCaller software e Manage users e Manage studies includes deleting studies Manage assay information Manage assay collections View and edit data Publish data Manage sample sets Manage xml files Scientist Manage studies does not include deleting studies e Manage assay information e Manage assay collections e View and edit
27. enter NTC in the Sample Name field IMPORTANT You must label all NTC wells NTC If you label the NTC wells as water blank and so on the AutoCaller software does not recognize them as NTC wells Notes Applied Biosystems AutoCaller Software User Guide 9 Chapter 2 Preparation Tasks Set up an SDS file 9 Optional Enter study information You can enter this information into each SDS file by typing or by copying and pasting a Select Tools Document Info b In the Plate Comments field enter the following information studyName lt study name gt amp SourceDNABC lt DNA plate name gt where study name gt is the AutoCaller study name that the SDS file will be imported into DNA plate name gt is the name of the source DNA plate the DNA plate used to seed the reaction plate For example if your source DNA plate is named SourceX and you want to put this data into a study named Population_Study you enter study Name Population_Study amp sourceDNABC SourceX 3 Document Information Plate Description Operator Barcode 123456788 File Name Untitled 1 This name will appear on reports Instrument Unknown Assay Allelic Discrimination Last Modified Acquisition started Acquisition ended Data collected on Unknown Plate Format 384 Wells Clear Plate Plate Comments studyName Population StudyssourceDNABC Sourcex 9b The comments you enter here will appear on reports pg prt If you enter the
28. erian rli keel bt Bee ba bee aaa eee et IM EE 19 Import fll8s oves eer Er REIS UE ER RC weed ux RU EA eae Kate tds 24 Import SDS files ees Rx RR RR AREA EX EUR KR RR ROUEN SRS 24 Import OpenArray NT Imager Genotyping System Thies anaana naaa 27 Import EDS fIIess s So eR RERO ead ede ceed erg ade vee Rex 29 Manage Studies serer kx keke E TAK eee es Ladd Eade EA a EE RUE Rn 34 Edit assay information so Rg 9 6 RCR R 0 Ra eee 41 Import assay information from a text Tle ee eee 41 Edit assay information in the Assay Management window 45 Manage assay collections K 9 tinai RR KR RRR RRR nnn 48 Delete assays and plates 0 eee 51 Applied Biosystems AutoCaller Software User Guide iii Chapter 4 View and Edit Data ccs is a Ra eae es ee eee ee dee eee ek 55 Chapter overview 0 0 eee 56 Search a study for assays 2 0 T SRTR el nee 57 View data 2rd Led eR INE et ee Ca eae Gee ae D RUE lcs 60 Edit data Eb pened a ave ee NE oe inet wore See le wD ae 73 Chapter 5 Publish Datla sorridono nianiar bes oe ees yale wees cen 83 Chapter overview 0000 ete 84 Creating a report from a study 6 06 9 R 9 0 0c eee res 85 Contents of the study reports x e e e e eee 85 How to create a study report xx e eee eee 89 Creating a comparison report 0 eee 93 Contents of the comparison reports eee eee 93 How to create a comparison report
29. file is an SDS software document that stores data for a single reaction plate SDS files are also called plate documents When you perform an experiment on an Applied Biosystems 7900HT Fast Real Time PCR System you 1 Create an SDS file in the SDS software The SDS file contains information about each well in the reaction plate including the sample names and assay IDs 2 Run the reaction plate on the 7900HT instrument The data from the run is collected by the SDS software and stored in the SDS file After the run you can import the SDS file into the AutoCaller software database The AutoCaller software analyzes the SDS file data upon import use the AutoCaller software to view and edit the data Using SDS files To ensure that the SDS file is imported correctly into the AutoCaller software database with the set up the SDS file so that it includes the following information software nnc Correct information for the no template control NTC wells IMPORTANT You must label all NTC wells NTC If you label the NTC wells as water blank and so on the AutoCaller software does not recognize them as NTC wells Reaction plate name or barcode Optional AutoCaller software study information Applied Biosystems recommends that you include the above information when you first create an SDS file You can add this information to an existing SDS file However if you do not include this information before you import the SDS file
30. for computers with altered configuration 126 training information on vii U user attention words described v user level administrator 129 production level 130 scientist 130 tasks 3 V validation run definition 130 W WARNING description ix warranty claims 126 exceptions 127 for computers with altered configuration 126 limitations 127 period 126 warranty period effective date 126 wild type sample comparison report 95 wildcards in searching 58 workflow software 4 workstation safety x 133 Index X XML files exporting 119 importing 121 134 Applied Biosystems AutoCaller Software User Guide www appliedbiosystems com Worldwide Sales and Support Applied Biosystems vast distribution and service network composed of highly trained support and applications personnel reaches 150 countries on six continents For sales office locations and technical support please call our local office or refer to our Web site at www appliedbiosystems com Applied Biosystems is committed to providing the world s leading technology and information for life scientists Headquarters 850 Lincoln Centre Drive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free In North America 1 800 345 5224 Fax 1 650 638 5884 09 2008 Applied Biosystems Part Number 4385543 Rev C
31. from the drop down menu Comments Click the Comments field then enter any comments that appear in the Assay Management window or the Comments tab of the Analyze window Enter the comments exactly as they appear in the Assay Management or Analyze window or enter an asterisk as a wild card For more information on each criterion see About the search criteria on EJ page 57 Note If you do not specify any criteria the software exports data for all assays with the name or ID number you entered in step 3b If you did not enter an assay name or ID number the software exports data for all assays in the study 4 Select the report criteria for Study 2 a From the Database 2 drop down menu select ACDB b From the Choose Study drop down menu select Study 2 Study 2 is the study you want to compare Study 1 to c Repeat steps 3b through 3e for Study 2 Notes 98 Applied Biosystems AutoCaller Software User Guide Report Select Study 1 Criteria Database Database 1 Study Choose Study Names Assay Name Assay Collection Plate Barcode Criteria Date Loaded TC Code Status DNA Plate Priority Code Chromosome Comments 5 Click Next 3e 08 June Genotyping Any TC Code Any Status MULTI Select Study 2 Criteria Database Database 2 Study Choose Study Names Assay Name Assay Collection Plate Barcode Criteria Date Loaded
32. gender or source information in the txt file If you do not include population information the AutoCaller software calculates statistics allele frequency genotype frequency and so on for all samples A B C D 2 1 DME 3 2 DME 03 DME 04 3 NA10859 NA10859 F Conell 4 NA14474 African American F Coriell 5 NA14476 African American F Coriell 6 NA17102 African American M Coriell 7 NA17103 African American M Coriell 8 NA17104 African American M Coriell 9 NA17105 African American M Coriell 10 NA17106 African American M Coriell 11 NA17107 African American M Coriell 12 NA17108 African American M Coriell 13 NA17109 African American M Coriell 14 NA17110 African American F Coriell 4 15 NA17111 African American M Coriell 16 NA17112 African American F Coriell 17 NA17113 African American F Coriell 18 NA17114 African American M Coriell 19 NA17115 African American M Coriell 20 NA17116 African American F Coriell 21 NA17117 African American M Coriell 22 NA17118 African American F Coriell 23 NA17119 African American F Coriell 24 NA17120 African American F Coriell Notes Applied Biosystems AutoCaller Software User Guide 105 N Appendix A Manage Sample Set Files mm Import a sample set file 5 Save the spreadsheet as a text txt file DME DME 03 DME 04 NA10859 NA10859 F Coriell NA14474 African American F Coriell NA14476 African American F coriell 4 NA17102 African American M Coriell
33. in the Assay Management window or the Comments tab of the Analyze window Enter the comments exactly as they appear in the Assay Management or Analyze window or enter an asterisk as a wild card For more information on each criterion see About the search criteria on page 57 Note If you do not specify any criteria the software exports data for all assays with the name or ID number you entered in step 4 If you did not enter an assay name or ID number the software exports data for all assays in the study Notes Applied Biosystems AutoCaller Software User Guide 91 minn Chapter 5 Publish Data Creating a report from a study Select Export Criteria Study Choose Study 08 June Genotyping Names Assay Name 23 Assay Collection Plate Barcode Criteria Date Loaded TC Code Any TC Code Status Any Status DNA Plate Any DNA Plate Priority Code Chromosome Comments 8 For the Sample Assay Report only Select a sample from the Choose Sample drop down menu Note If you select All Samples the software generates a separate report for each sample with information for each assay selected in the search Select Report Criteria Select Sample Study Choose Sample All Samples Al Samples 8 Choose Study 08 June Genotyping INA17227 INA17263 Names NA17207 INA17102 Assay Name INA17208 J INA17201 Assay Collection INA17262 Plate Bar
34. in the file option comments step 3 on page 24 but the SDS file does not include a study name No plate barcode specified for The SDS file does not include the reaction plate barcode lt SDS file gt For more information see Set up an SDS file on page 7 Notes Applied Biosystems AutoCaller Software User Guide 33 ww Chapter 3 Manage Studies and Assay Information Manage studies Manage studies The Study Management window displays a list of all studies in the AutoCaller software database You can use the Study Management window to Adda study as described in Create studies on page 19 View study information below Edita study Change basic study information page 35 Change analysis criteria page 37 Reassign genotypes for multiplate assays with NEW status page 39 Export a study in xml format as described in Appendix B View study View the Study Management window to determine if all the expected data was imported information into a study 1 From the main window toolbar select Tools Manage Studies Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences 2 In the Study Management window check the study information for accuracy The Study Management window includes the following information Column Description Name The name of the st
35. information to an existing EDS file or you can enter it when you load the file into AutoCaller software Note The following information only includes instructions for the AutoCaller software specific information you must include when designing an experiment in StepOne and 7500 Software v2 0 See the appropriate Getting Started Guide for detailed information on designing genotyping experiments In the Experiment Properties screen be sure to Click the Barcode field and enter a name for the reaction plate or enter or scan the barcode Click Genotyping for Experiment Type Optional In the Comments field enter the following information study Name lt study name gt amp SourceDNABC lt DNA plate name gt where lt study name gt is the AutoCaller study name that the SDS file will be imported into lt DNA plate name gt is the name of the source DNA plate that is the name of the DNA plate used to seed the reaction plate For example if your source DNA plate is named SourceX and you want to put this data into a study named Population_Study you enter study Name Population_Study amp sourceDNABC SourceX If you enter the lt study name gt in the EDS file the AutoCaller software can automatically import the EDS file into the correct study However you can omit this step and manually import the EDS file into any study When you manually import an EDS file you can import the same EDS file into more than one study In the Samples
36. into AutoCaller software the AutoCaller software displays an error message and does not import the SDS file Set up an SDS file You can set up A new SDS file page 7 Anexisting SDS file page 11 These procedures include only the steps required to set up an SDS file for import into the AutoCaller software These procedures do not include all of the setup steps for complete procedures see the Applied Biosystems 7900HT Fast Real Time PCR System Allelic Discrimination Getting Started Guide To set up a new SDS file 1 Start the SDS software then select File New to open the New Document dialog box Notes Applied Biosystems AutoCaller Software User Guide 7 Chapter 2 Preparation Tasks Set up an SDS file 2 From the Assay drop down menu select Allelic Discrimination IMPORTANT The AutoCaller software is intended for SNP genotyping experiments only Be sure to create an Allelic Discrimination AD plate document 3 From the Container drop down menu select the appropriate reaction plate Note The TaqMan DME Array is not a supported SNP genotyping application Do not select the 384 Wells TaqMan Low Density Array option from the drop down menu 4 Enter the sample names by selecting the appropriate template from the Template drop down menu Note Alternatively enter the sample names manually in the Setup tab of the SDS software main window or import the sample names via a tab delimited text file
37. into the AutoCaller software database the software Imports all run data associated with the assays directly into a study You can use the software to search studies for assays then view and edit the assay run data For more information see Chapter 4 on page 55 Imports the assay names ID numbers into the Assay Management window For more information see Edit assay information on page 41 Required user To perform the procedures in this section you must log in to the AutoCaller software at levels he Administrator or Scientist User Level Import an 1 From the main window toolbar select File Load XML to Database to open the xml file Load Setup dialog box for importing xml files Tools Help New Analysis Window Load SDS File to Database Load XML File to Database Load TaqMan Open rray to Database Load EDS File to Database Exit 2 Deselect the Conduct Auto analysis check box Note To ensure that all xml files are imported into the AutoCaller software database exactly as they were exported the software does not conduct auto analysis that is the software does not call the genotypes for xml files on import The software does not perform auto analysis even if you select the Conduct Auto analysis check box However you should deselect the Conduct Auto analysis check box so that all assays from the xml file are given the status NEW for more information see Status menu on page 70 3 From the Ch
38. level definition 130 p value analysis criterion 23 definition 130 R repetitive motion safety x reports assay and sample report 87 assay and well report 86 assay comparison 93 assay report 85 creating a comparison report 96 creating a study report 89 definition of comparison report 93 definition of study report 85 sample assay report 88 sample genotype report 88 wild type sample comparison 95 S safety conventions ix ergonomic x repetitive motion x workstation x sample assay report contents 88 sample genotype report contents 88 sample set files definition 104 importing 106 sample sets deleting 111 editing 109 samples omitting from analysis 79 searching for in Data Table 66 scale changing in plot 63 scientist user level definition 130 SDS files creating 7 definition 130 editing existing 11 errors during importing 32 importing 24 27 29 searching table of criteria 57 using wildcards 58 sigma separation analysis criterion 23 definition 130 Applied Biosystems AutoCaller Software User Guide Index software features 2 warranty 126 workflow 4 Statistics tab changing statistics displayed 67 contents 67 studies creating 19 editing 35 editing analysis criteria 37 exporting to XML file 119 importing from XML file 121 reassigning genotypes 39 searching for 57 study reports creating 89 definition 85 study definition 130 T Technical Support contacting vii technical support
39. overview Chapter overview This chapter explains how to create a study in the Applied Biosystems AutoCaller Software then import data files into the study This chapter also explains how to manage studies and assays once they have been imported into the AutoCaller software database Workflow Preparation Tasks Chapter 2 WwW Manage Studies and Assay Information Chapter 3 Create a study and set the analysis criteria Import data files into a study Manage studies Edit assay information Edit assay collections O gus cQ NS Delete assays and plates wv View and Edit Data Chapter 4 wv Publish Data Chapter 5 Required user To perform the procedures in this chapter log in to the AutoCaller software at the level Administrator or Scientist User Level For information on User Levels see About user levels on page 3 Notes 18 Applied Biosystems AutoCaller Software User Guide Create studies Chapter 3 Manage Studies and Assay Information 3 Create studies In AutoCaller software a study consists of a set of DNA samples run against a number of different TaqMan genotyping assays You can create multiple studies in the AutoCaller software database organizing data based on projects or experiments For example you may want to create a validation study that includes all of your validation runs and create separate studies for other experiments Create a study 1 2 Inthe Study Manageme
40. page 22 The AutoCaller software automatically assigns Auto Codes to assays when the SDS file is imported Users at the Administrator or Scientist User Level can also assign add or remove Auto Codes manually Note If an Auto Code is manually added or removed by a user the user s name and the date and time the change was made are recorded in the AutoCaller software database To view codes in the Codes tab click the Codes tab The Auto Codes assigned to the assay are displayed in the panel on the right hand side If there is more than one Auto Code assigned to the assay you can move the Auto Code up or down in the list Select the Auto Code then click the up or down arrow Statistics Codes Comments Assay Info TC1 Automatically passed L TC2 2 Good Clusters ites Homozygous Vic TC4 Homozygous Fam TCS Heterozygous TCG Weak Amp Both TC Weak Vic TC8 Weak Fam TC8 Non specific Vic CTF Fant eee YN um a Description To add or remove an Auto Code see Edit data on page 73 Note You must belong to the Administrator or Scientist User Level to add or remove Auto Codes The Comments tab provides space for you to record information about the assay For example you may want to record why you manually failed an assay or you may want to leave notes for other users To view or add comments in the Comments tab click the Comments tab To add comments for the selected assay enter
41. see page 51 From the main window toolbar select Tools K Manage Assays Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences Applied Biosystems AutoCaller Software User Guide 45 mida Chapter 3 Manage Studies and Assay Information Edit assay information 2 Select the assay to clear In the Assay Management window a Select the assay s for which you want to clear information Note Press Ctrl click or Shift click to select multiple assays b Click Clear data for the selected assays Any edits done below will immediately be saved to the database Name Chromosome Priority Code Actual Allele 1 Actual Allele 2 Display Allele 1 Display Allele 2 Comment 2a eee a L E E Pico 1 S E EJ C 8878782 10 x MAOB G c G c a g a Close J 3 Confirm that the information has been cleared for the selected assay Any edits done below will immediately be saved to the database Name Chromosome Priority Code Actual Allele 1 Actual Allele 2 Display Allele 1 Display Allele 2 Comment ay LBs a Close Notes 46 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information vu Edit assay information Delete an assay You can delete an assay which d
42. selected study the Sample Assay Report shows the genotype information for a single sample across assays as described below For example if you select SampleX when specifying the export criteria page 91 the report lists the assays that SampleX was run in and shows how SampleX was genotyped in each of the assays Report Notes A 1 Autocaller Version 3 2 0 2 Assay Name 3 C 26334975 20 4 C 26334975 20 5 C Plate Barcode Genotype A302GL4M A302GL4H 12 12 Column Description Assay Name The assay name or ID number Plate Barcode The name or barcode of the reaction plate in which the assay was run Genotype The genotype for the selected sample 11 12 22 or 00 Note If a user defined the genotype in the Assay Manager see Edit assay information on page 41 the genotype for the selected sample is AA TT and so on 88 Applied Biosystems AutoCaller Software User Guide Chapter 5 Publish Data Creating a report from a study How to create a study report For each AutoCaller Software report type the AutoCaller software exports the data from the AutoCaller software database to a text file txt You can open the text file in a spreadsheet application such as Microsoft Excel software or simple text application such as Microsoft Notepad software Note The report provides information only for the assays in the study that meet the export cr
43. settings 22 C call definition 129 Cartesian coordinates Applied Biosystems AutoCaller Software User Guide Index definition 129 viewing 62 CAUTION description ix Codes tab contents 68 editing the Auto Codes 75 colors changing in plot 63 comments adding to a study 20 adding to an assay 68 deleting 80 Comments tab contents 68 comparison reports creating 96 definition 93 comparison text file contents 94 computer configuration requirement 126 technical support for altered configuration 126 confidence value definition 129 conventions for describing menu commands v IMPORTANTS v Notes v text v user attention words v conventions safety ix creating assay collections 48 comparison reports 96 EDS files 14 reports 84 SDS files 7 studies 19 study reports 89 D DANGER description ix data files compatible 2 Data Table contents 65 exporting to a text file 66 printing 66 searching for samples 66 deleting 131 Index assay collection 50 assays 47 assays froma study 51 comments 80 sample sets 111 documentation related vi E editing analysis criteria for a study 37 analysis status 76 assay collection 49 assay information 45 Auto Codes 75 existing EDS files 14 existing SDS files 11 sample sets 109 studies 35 EDS files about 13 creating 14 definition 129 editing existing 14 importing 29 ergonomics safety x experiment definition 129 exporting contents of Loadin
44. the information you want to record then click B Save to database Note When you save a comment the software displays your user name and the date and time you made the comment Additionally the software displays 9 in the Comments tab to indicate that comments have been made for the selected assay Statistics Codes 9 Comments Assay Info Enter comments here autocaller 2007 04 22 14 55 Notes 68 Applied Biosystems AutoCaller Software User Guide Assay Info tab Notes Chapter 4 View and Edit Data View data To delete all comments for the selected assay see Edit data on page 73 IMPORTANT You must belong to the Administrator or Scientist User Level to delete comments The Assay Info tab provides the following information for the selected assay Row Name Description Assay Name The assay name or ID number Plate Barcode The name or barcode of the reaction plate in which the assay was run The name or barcode is entered by the user in the SDS file page 7 DNA Plate Barcode The name or barcode of the source DNA plate that is the DNA plate that was used to seed the reaction plate e DNA plate name The software displays the source DNA plate name if the user included the name in the file page 7 or in the sample set file page 105 e MULTI The software assigns the name MULTI whenever there is more than one plate in
45. the study was created Create studies on page 19 The HWE can help you determine How to call two cluster plots Whether or not an assay is following normal Mendelian rules Averages and Displays the average signal level and standard deviation for each Standard Deviations cluster Normalized Averages Displays the Rn NTC value for each cluster MaxL Metrics Displays statistics from genotyping called by the software These values are used in the auto analysis criteria To view statistics in the Statistics tab 1 Click the Statistics tab default 2 Select a category from the drop down menu Allele Frequencies Genotype Distribution Hardy Weinberg Equilibrium Averages and Standard Deviations Normalized Averages MaxL Metrics The display in the Statistics tab changes depending on the category you select For example if you select Allele Frequencies the Statistics tab displays the table below 1 2 Statistics Codes Comments Assay Info allele Frequencies Population Allele 1 Allele 2 Global 0 80 0 20 Default 0 80 0 20 96 Genotyped 100 00 Notes Applied Biosystems AutoCaller Software User Guide 67 Chapter 4 View and Edit Data View data Codes tab Comments tab The Codes tab displays the Auto Codes assigned to the assay based on the analysis criteria you selected for the study see About the automation settings on
46. the study with the same assay For more information see Select a multiplate on page 71 e No DNA Plate The software displays No DNA Plate for any reaction plates that do not have a name or multiplate assignment Platform The consumable used in the experiment e Plate indicates a 96 or 384 well reaction plate e OpenArray indicates the data was collected on the OpenArray NT Imager Genotyping System DNA Plates For multiplate studies the number of reaction plates imported via the SDS file for the assay Chromosome The chromosome assigned to the assay Allele 1 The base assigned to allele 1 of the assay A C G T or if a user selected a base for Actual Allele 1 in the Assay Management window For more information see Edit assay information on page 41 Allele 2 The base assigned to allele 2 of the assay A C G T or if a user selected a base for Actual Allele 2 in the Assay Management window For more information see Edit assay information on page 41 SNP Comments Comments entered by a user in the Assay Management window For more information see page 41 Priority Code The priority code assigned by a user to the assay in the Assay Management window Priority codes are defined by the user and can be used to facilitate searches for example a gene name can be used as a priority code For more information see Edit assay information on page 41 Load Date The date
47. then browse to and select a destination folder b Click Export A list of assays scrolls by as the export progresses When the export is finished the software displays the number of assays plates and wells that were exported c Click Close to close the Export Study window Applied Biosystems AutoCaller Software User Guide 119 Fog Appendix B Manage xml Files mA Export a study in xml format Export Study Example Study E3 Specify output directory C Program Files Applied BiosystemslAutocaller TestReports Export 3a 3b f Export Progress Writting Samples 4 Exporting Assays jl Exporting Assay E LLY22 10 Finished exporting Assays Exported 1 Plates Exported 1 Wells Exported 64 Close 4 Open the destination folder to confirm that the export was successful The AutoCaller software produces two files An xml file containing all data from the study A txt file containing a summary of the export The file names include the report type export and export log the database name the study name and the date and time the report was exported 5 To view the export summary open the txt file in a spreadsheet or simple text application Notes 120 Applied Biosystems AutoCaller Software User Guide Appendix B Manage xml Files lala m Import xml files into a study Import xml files into a study When you import xml files
48. 1 Introduction About the Applied Biosystems AutoCaller Software About the Applied Biosystems AutoCaller Software Applied Biosystems AutoCaller Software is a SNP genotyping analysis tool and client server program that you can use to efficiently analyze edit and compare TaqMan SNP Genotyping Assays run on an the following Applied Biosystems Real Time PCR Instruments 7900HT Fast Real Time PCR System 77500 Real Time PCR System with 7500 software 77500 Fast Real Time PCR System with 7500 software StepOne Real Time PCR System StepOnePlus Real Time PCR System OpenArray NT Imager Genotyping System Features AutoCaller software allows you to Import SNP genotyping experiment data from SDS EDS and XML files then manage the data in a database Search the database for assays using specific search criteria Easily view data in a variety of ways plots statistics status codes and so on Edit data your edits are saved to the database Overlay data from multiple plates Export data to Perform downstream secondary analysis software tools Share with other laboratories that use the AutoCaller software Compatible data You can use AutoCaller software with the following data files files Notes SDS files for allelic discrimination plates only created with the SDS Software for the Applied Biosystems 7900HT Fast Real Time PCR System When you set up your SDS files you must include information that
49. 105 NA17106 NA17107 NA17108 NA17109 NA17110 NA17111 NA17112 NA17113 3 C 26334975 20 11 11 12 11 12 12 12 12 12 12 12 12 22 11 12 4 C 26334975 20 11 11 12 11 12 12 12 12 12 12 12 12 22 11 12 5 C 26334975 20 11 11 12 11 12 12 12 12 12 12 12 12 22 11 12 6 Column Description AssayName The assay name or ID number sample name The genotype for each sample 11 12 22 or 00 Note If a user defined the genotypes in the Assay Manager see Edit assay information on page 41 the sample name is AA TT and so on Notes Applied Biosystems AutoCaller Software User Guide 87 Chapter 5 Publish Data Creating a report from a study Sample Genotype For the selected study the Sample Genotype Report shows the percentage of assays that each sample is genotyped for as described below Report A 1 Autocaller Version 3 2 0 3 NA17130 4 NA17188 5 NA17262 6 NA17128 7 NA17254 8 NA14476 9 NA17123 10 NA17106 END Sample Name Percent Genotyped 100 100 100 100 100 100 100 100 Column Description DNA Sample Name The name of the sample Percent Genotyped The percentage of assays that each sample is genotyped for For example if SampleX was run in 10 assays and was genotyped in 9 of the 10 assays the Percent Genotyped column displays 90 This is useful for DNA QC statistics a low percentage might indicate a low quality sample Sample Assay For the
50. 3 NA17103 African American M coriell NA17104 African American N coriell NA17105 African American M Coriell NA17106 African American M Coriell NA17107 African American M coriell NA17108 African American N coriell NA17109 African American M coriell NA17110 African American F Coriell NA17111 African American M Coriell NA17112 African American F coriell NA17113 African American F coriell NA17114 African American M Coriell NA17115 African American M coriell NA17116 African American F Coriell NA17117 African American M Coriell NA17118 African American F coriell NA17119 African American F coriell NA17120 African American F Coriell NA17121 African American F coriell NA17122 African American F Coriell NA17123 African American F Coriell NA17124 African American F Coriell v Import a sample set file 1 From the main window toolbar select Tools Manage Sample Sets EJ Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences 2 In the Sample Set Management window click Add a new sample set to the database m Sample Set Management Name Date Created 3t Samples eneric Sample Set 12 21 2006 Notes 106 Applied Biosystems AutoCaller Software User Guide Appendix A Manage Sample Set Files A Import a sample set file 3 In the Re
51. 7 NTC Avg Max 2 v TC18 Non specific VIC 2 iz TCS Non specific FAM I 2 T l rc10 Weak VIC HI T TO TC6 Weak FAM 1 v TC8 TC6 Min Sigma Separation 10 v TC15 Min P value per Population 0 05 v TC21 i 4c lt Back Finish Cancel 5 At the prompts click OK to save the new study 6 Click Close to close the Study Management window Notes Applied Biosystems AutoCaller Software User Guide 21 mila Chapter 3 Manage Studies and Assay Information Create studies About the Use the Automation Settings dialog box displayed when you create or edit a study to set automation the analysis criteria that you want applied to the current study when you import your SDS settings files into the study IMPORTANT Analysis criteria are study specific The criteria are applied only to the current study and are not applied to any other studies in the AutoCaller software database If you do not change the analysis criteria for a study the software uses the default criteria listed on page 22 The Automation Settings dialog box displays the following Column Description Name The name of each analysis criterion that you can apply to your study For a description of each criterion see page 22 Value The cut off value defined for each analysis criterion You can edit the value for each criterion Note Applied Biosystems recommends accepting the default values for t
52. Assign Genotypes to reassign genotypes and codes based on the included wells e Click Repeat Auto Analysis to reassign only codes based on the included wells To include omitted wells 1 Inthe Plot View pane draw a box around the samples points to include 2 Right click anywhere in the Plot View pane then select Include Selected Wells from the pop up menu The selected well s are reshaded the Omitted check box in the Data Table pane is unchecked and the statistics in the Statistics tab are immediately recalculated Notes Applied Biosystems AutoCaller Software User Guide 77 mln Chapter 4 View and Edit Data l Edit data Omit wells in the Data Table pane 1 Inthe Assay Selection pane select the desired assay You can select A single assay to edit the assay for an individual reaction plate or Amultiplate to edit the assay across reaction plates Look for MULTI in the Plate Barcode column There may be several multiplates the software creates a multiplate for any assay that was run on more than one reaction plate 2 In the Data Table pane right click and select Omit Selected Wells The selected well s become less intensely shaded and the Omitted check box in the Data Table pane is checked The statistics in the Statistics tab are immediately recalculated without including the values from the omitted wells The wells remain omitted from any further analysis After omitting well
53. C20 TC15 e To search for assays and view edit data see Chapter 4 on page 55 Notes Applied Biosystems AutoCaller Software User Guide 123 rou Appendix B Manage xml Files m Import xml files into a study Notes 124 Applied Biosystems AutoCaller Software User Guide Appendix C software Warranty Information This appendix covers m Computer Configurations 23 ni 625 sex Fan Z GG PA 39 06 RT R RA ATA case s 126 B Limited product Warranty esses see e pett EE EYE CREER Ges 60a 126 Applied Biosystems AutoCaller Software User Guide 125 Fas Appendix C Software Warranty Information Computer configuration Computer configuration Applied Biosystems supplies or recommends certain configurations of computer hardware software and peripherals for use with its instrumentation Applied Biosystems reserves the right to decline support for or impose extra charges for supporting nonstandard computer configurations or components that have not been supplied or recommended by Applied Biosystems Applied Biosystems also reserves the right to require that computer hardware and software be restored to the standard configuration prior to providing service or technical support For systems that have built in computers or processing units installing unauthorized hardware or software may void the Warranty or Service Plan Limited product warranty Limited warranty Warranty period
54. C20 TC17 TC18 TC9 TC10 TC7 TC6 TC8 TC6 TC15 TC21 JE EST EST EST EST EST ESTIST ISTIS 4c 5 At the prompts click OK to save the new study 6 Click Close to close the Study Management window Notes Applied Biosystems AutoCaller Software User Guide 115 mila Appendix A Manage Sample Set Files lad Create a study using a sample set Notes 116 Applied Biosystems AutoCaller Software User Guide Appendix B Manage xml Files This appendix covers B Appendix OVeIVieW jua dad RUE dekh 88 0 Up bad tho Rad domope Hada Aes 118 B Exporta study m xml format 5 45 seek Gd ween Re ER Ges A R wens Hes 119 B Import xml files into a sud 121 Applied Biosystems AutoCaller Software User Guide 117 lala Appendix B Manage xml Files m Appendix overview Appendix overview This appendix explains how to manage xml files Workflow Manage xml Files Appendix B 1 Export a study in xml format 2 Import xml files into a study About xml files You can use the Applied Biosystems AutoCaller Software to export an entire study in xml format Studies that have been exported in xml format can then be imported back into the AutoCaller software The xml files are useful when you want to share studies with other laboratories that use the AutoCaller software Required user To perform th
55. Caller Software User Guide Chapter 3 Manage Studies and Assay Information wu Manage studies Change analysis criteria IMPORTANT If you change the analysis criteria for a study the software applies the new criteria only to new files imported into the study The analysis criteria are not changed for data already in the study IMPORTANT Analysis criteria are study specific The criteria are applied only to the current study and are not applied to any other studies in the AutoCaller software database 1 From the main window toolbar select Tools Manage Studies Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences 2 In the Study Management window a Select the study to edit b Click 7 Edit an existing study us Study Management Name Date Created Sample Set Platform Assays Comments n Dp June Genotyping 06 16 2008 _ _ Generic Sample Set plate First test of the new instrument All 2007 Samples 06 16 2008 Generic Sample Set Plate a Lymphoma Study 06 17 2008 Generic Sample Set Work done by Smith Lab I 3 In the Edit Study dialog box select the Automation Settings tab Notes Applied Biosystems AutoCaller Software User Guide 37 Notes Chapter 3 Manage Studies and Assay Information Manage studies 4 Edit the information You can
56. Cluster Colors Graph Scale ELT Automatic 3 Manual Choose Scale x Max 6 x Min d y Max 10 d y Min 0 0 Ly D To zoom in out To zoom in draw a box around the data you want to see more closely right click in the box then select Zoom from the pop up menu Assay C_11711420_30 DHA Plate Ho DNA Plate View Genotype Type Cartesian Print Plot skesseeedesskssedseesl C 7 d l l l t h 9 4 meer de 2 0 E oe T Ra s Change Genotype to 11 acest L i h A Change Genotype to 12 i M L i 18 Change Genotype to 22 H ask H H 1 4 Change Genotype to UDT Dk 12 Omit selected Wells Fa Include selected Wells 40 4 4 ear aae dea E E AE S L S T EEE TE NUN D c C E A rrr eee es y QE PPP e I PCR lc ID STER UPPER Ce T 02 0 0 0 1 0 2 0 3 0 4 0 5 06 0 7 os 0 9 10 To return to the original view double click anywhere in the plot To print the Plot View pane a Right click in the plot and select Print Plot Notes 64 Applied Biosystems AutoCaller Software User Guide Chapter 4 View and Edit Data A View data b When prompted click OK in the Print dialog box To view a second copy of the Plot View pane click 2 Open New Graph Panel A Graph Panel window appears displaying the same plot as shown in the Plot View pane You can change the plot controls as needed to view different informa
57. Guide 129 Glossary polar coordinates Production p value Rn Scientist SDS file sigma separation study validation run 130 A two dimensional coordinate system in which each point on a plane is expressed as an angle and a radius In AutoCaller software genotyping results displayed in polar coordinates plots the angle on the Y axis and log radius on the X axis When genotyping results are plotted in polar coordinates the radius is a single value that correlates well with genotype User Level in the Applied Biosystems AutoCaller Software Users at the Production User Level can View data Publish data Note User Levels are assigned by the users with the Administrator User Level Assays for which the samples have a p value 0 05 are 95 likely to have genotype frequencies that do not conform to Hardy Weinberg Equilibrium HWE expectations That is there are too few homozygotes or too few heterozygotes See normalized reporter User Level in the Applied Biosystems AutoCaller Software Users at the Scientist User Level can Manage studies does not include deleting studies Manage assay information View and edit data Publish data Manage sample sets Manage xml files Note All User Levels are assigned by the users at the Administrator User Level A file created in the SDS software that represents a single reaction plate Data from an SDS file can be imported into the Applied Bios
58. ME 03 NA17214 193 11 0 996325911 1 831281185 0 810485959 4 C 26334975 20 A302GLAM DME 03 NA10859 194 11 0 999481466 1 760317087 0 908820927 5 C 26334975 20 A302GL4M DME 03 NA17216 195 11 0 999920814 1 772682667 0 857936502 6 C 26334975 20 A302GL4M DME 03 NA17261 196 11 0 999978968 1 766975403 0 857633114 7 C 26334975 20 A302GL4M DME 03 NA17239 200 11 0 990026172 1 883795619 0 909038603 8 C 26334975 20 A302GL4M DME 03 NA17207 202 11 0 991726793 1 874718428 0 887204111 9 C 26334975 20 A302GLAM DME 03 NA17226 204 11 0 991134626 1 874757767 0 919510245 10 C 26334975 20 A302GL4M DME 03 NA17117 205 11 0 996626938 1 832411647 0 832931161 11 C 26334975 20 A302GL4M DME 03 NA17102 208 11 0 995311366 1 84733665 0 870146632 12 C 26334975 20 A302GLAM DME 03 NA17242 217 11 0 999038801 1 730233788 0 824412346 Column Description assay name The assay name or ID number plate barcode The name or barcode of the reaction plate in which the assay was run 86 Applied Biosystems AutoCaller Software User Guide Chapter 5 Publish Data minn Creating a report from a study Column Description dna_plate The name or barcode of the source DNA plate that is the DNA plate that was used to seed the reaction plate e DNA plate name The software displays the source DNA plate name if the user included the name in the file or in the sample set file e MULTI The software assigns the name MULTI when
59. a View data Column Description Population Population information if population information was included in your sample set filet If no population information was included Default is displayed in the sample s Population field Gender Gender information if gender information was included in your sample set file If no gender information was included No Gender is displayed in the sample s Gender field t To use sample sets you must first create sample set files then import the files into the AutoCaller software database Sample set files contain information about each sample in a reaction plate For more information on sample set files see Appendix A on page 103 Sample Name Row Column Allele 1 Allele 2 Predicted Genotype Genotype ROX Confidence Population Gender INA17235 O16 14 2 2212 12 1 691 3 1 Default No Gender l INA17205 017 1 76 0 88 11 11 1 804 03 1 Default No Gender NA10859 018 1 64 0 81 11 11 1 630 25 0 99 Default No Gender NA17102 P13 1 85 0 87 11 11 1 481 31 1 Default No Gender INA17127 P14 0 71 2 9922 11 1 770 08 1 Default No Gender NA17132 PIS 1 63 0 86 11 11 1 492 72 0 99 Default No Gender INA17120 P16 1 35 2 2212 12 1 508 9 1 Default No Gender INA17231 P17 1 75 0 87 11 11 2 066 32 1 Default No Gender E NTC P18 0 38 0 48 NTC NTC 1 330 75 0 Default No Gender Export Table Data to File To view data in the Data Table pane To sort data click a column heading
60. ad a sample set file dialog box browse to and select a sample set file txt then click Read Read a sample set file Look In ca TestFiles M amp a Ej aez DME Data paired plates 7 21380090_corrected sds 7 21380106_corrected sds E 21380108_corrected sds E A302X8X2 sds cDMEH D01 Sample Set txt export log RESTEST DME data test 2007 04 23 12 07 txt E export RESTEST DME data test 2007 04 23 12 07 xml File Name DME sample set txt Files of Type al Files Read Cancel 4 Inthe Load New Sample Set dialog box review the sample set information for accuracy If needed you can edit the sample set information as follows Column Description To edit Sample Name The name of the sample N A You cannot edit the sample names Population The population from which the sample is Double click the Population field for a sample then from enter the new population name Gender The gender from which the sample is Click the Gender field for a sample then select a from gender from the drop down menu Source The source of the DNA sample that is Double click the Source field for a sample then enter a where the DNA came from new source Note Any edits you make are imported into the AutoCaller software database However they are not saved to the original sample set file txt file Notes Applied Biosystems AutoCaller Softw
61. age 68 Applied Biosystems AutoCaller Software User Guide 75 w Chapter 4 View and Edit Data r Edit data Edit the analysis To change the analysis status status Inthe Assay Selection pane select the assay to edit click the Status cell for the assay you want to change then select a status from the drop down menu Assay Selection Assay Name Plate Barcode DNA Plate Status C 26334975 20 A302GL4M DME 03 K MANUAL FAIL C 26334975 20 A302GL4H DME 04 C 26334975 20 MULTI C 26334975 20 MULTI REDO HOLD NEW REPLICATE REDONE AUTO PASS AUTO FAIL 3 assay s were Found that meet your search criteria Inthe Status menu select an analysis status from the drop down menu AUTO PASS Status Gender notype No Gender No Gender No Gender No Gender No Gender No Gender 11 1 JAUTO PASS Note AUTO PASS and AUTO FAIL are automatically assigned by the AutoCaller software Users cannot manually set these options For more information on the analysis status options see Status menu on page 70 Omit wells from There are three ways to omit wells from analysis the analysis Use the Plot View pane below Use the Data Table pane page 78 Use the Data Explorer window to omit all wells for a given sample page 79 Omit wells in the Plot View pane 1 In the Assay Selection pane select the desired assay You can select Asingle assay t
62. all assays in the study c Optional In the Assay Collection drop down menu select the assay collection for which you want to export data d Optional In the Plate Barcode field enter the barcode for the reaction plate Note Entering a barcode is useful when you want to export data for all assays run on a single reaction plate Notes Applied Biosystems AutoCaller Software User Guide 97 Chapter 5 Publish Data Creating a comparison report e Optional In the Criteria pane specify any of the following criteria to narrow the set of assays exported Field To specify this criterion Date Loaded Click _ i3 Choose Date Assays Were Loaded then select the date the assay was imported into the AutoCaller software database TC Code Select the Auto Code from the drop down menu Status Select the analysis status from the drop down menu DNA Plate Select the source DNA plate name from the drop down menu DNA plate name user defined MULTI e No DNA Plate Note Applied Biosystems recommends that you select MULTI If you select MULTI the software exports all data for the selected assay s once for the multiplate If you select No DNA Plate the software exports all data for the selected assay s twice once for the multiplate and once for the individual plates Priority Code Select a priority code from the drop down menu Chromosome Select a chromosome
63. analysis criteria for a study page 37 the software applies the new criteria to all the multiplates in the study as part of the re genotyping 5 Click Close to close the Study Management window Notes 40 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information ww Edit assay information j Edit assay information About editing When you import an SDS EDS or OpenArray file into the AutoCaller software assay information database all of the assay names and ID numbers in the file are automatically added to the Assay Management window You can then manually add or edit basic information for each assay in the Assay Management window The workflow for adding information to an assay 1 Create and import a text file that contains basic information for the assays below or Edit each assay individually in the Assay Management window View or edit assay information on page 45 This may be more time consuming 2 Use the Assay Management window to View and edit assay information page 45 Clear assay information page 45 Delete an assay from the AutoCaller software database page 47 Note The Assay Management window allows you to manage basic information about any assay in the AutoCaller software database for example you can change chromosome or allele assignments The Assay Management window does not allow you to search for assays or view edit run data To perform
64. and Replicates screen be sure to include negative controls Follow the instructions in Import EDS files on page 29 to import the file into AutoCaller software 14 Applied Biosystems AutoCaller Software User Guide gem ci B Log In to the AutoCaller software Login 1 Double click DA AutoCaller software shortcut icon to start the AutoCaller software The software displays a DOS command window the splash screen then the AutoCaller Login dialog box 2 Complete the AutoCaller Login dialog box a In the User name and Password fields enter the user name and password provided by your AutoCaller software Administrator b From the User Mode drop down menu select the name of the database Be default this is ACDB E AutoCaller Login AutoCaller Version 1 1 3 Click OK to open the AutoCaller software By default the AutoCaller software displays the Analyze window Assay Selection Assay Name Plate Bar DNA Plate Status Instrument Format Seatisties codes Comments assay Info bei Frequencies z Population Allele 1 Allele 2 Genotyped NIA Status Sample Name yal Address iks Allele 2 Predicted Ge Genotype ROX Confidence Population Gender IMPORTANT The remaining procedures in this guide assume that you have logged into the AutoCaller software Notes Applied Biosystems AutoCaller Software User G
65. are User Guide 107 A Notes Appendix A Manage Sample Set Files Import a sample set file 5 Click Load to import the sample set file into the AutoCaller software database E Load New Sample Set Feline Lymphoma Study DNA Barcode List Trixie 001 DNA Sample List Sample Name Population Gender Source 4 Tigger_003 Tabby M ACDB Milo 004 Siamese M ACDS Theo_001 Calico M ACDB Oscar 001 Tabby M acos Oscar_002 Tabby M JACDB 5 Cs 6 When the sample set file is imported Load completed successfully appears in the Load New Sample Set dialog box Click Close to close the Load New Sample Set dialog box 7 The new sample set appears in the Sample Set Management window Click Close to close the Sample Set Management window 108 Applied Biosystems AutoCaller Software User Guide Appendix A Manage Sample Set Files A Manage sample sets Manage sample sets The Sample Set Management window displays a list of all sample sets in the AutoCaller software database You can use the Sample Set Management window to View or edit a 1 sample set 3 4 Notes Add a sample set as described in Import a sample set file on page 106 View or edit a sample set below Delete a sample set from the database page 111 From the main window toolbar select Tools Manage Sample Sets Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Us
66. arison category For example column S2 00 S1 11 lists the number of samples for each assay that have undetermined genotypes in Study 2 and homozygous VIC dye genotypes in Study 1 In the comparison txt file illustrated above assay C 29712728 10 contains 0 samples that meet this criteria 94 Applied Biosystems AutoCaller Software User Guide Chapter 5 Publish Data minn Creating a comparison report Mismatches txt file A B C D E F G H 1 Assay Name DNA Name DNA Plate S1 Well Num S1 Genotype Prod DNA Plate Prod Well Num Prod Genotype 2 C 33171049 10 NA17214 null 289 11 null 289 22 3 C 33171049 10 NA10859 null 290 11 null 290 22 4 C 33171049 10 NA17216 null 291 11 null 291 22 5 C 33171049 10 NA17261 null 292 11 null 292 22 6 C 33171049 10 NA17227 null 293 11 null 293 22 7 C 33171049 10 NA17263 null 294 11 null 294 22 8 C 33171049 10 NA17137 null 295 11 null 295 22 9 C 33171049 10 NA17239 null 296 11 null 296 22 Column Description Assay Name The assay name or ID number DNA Name The sample name or ID number DNA Plate For Study 1 DNA Plate and Study 2 Prod DNA Plate the name or barcode of the source DNA plate that is the DNA plate that was Prod DNA Plate used to seed the reaction plate e DNA plate name The software displays the source DNA plate name if the user included the name in the file or in the sample set file MULTI The software assigns the name MULTI whene
67. assay was run twice on the same sample set Assign REDO to an assay as a way to flag assays for further inspection You can search for assays with the REDO status in the Search for Assays dialog box Assign MANUAL PASS to indicate that the assay was passed by a user and not by the software This is useful if e The assay failed one or more analysis criteria selected for the study but you were able to pass the assay after manually calling genotypes The assay was imported with the NEW status that is no analysis criteria were selected for the study Assign MANUAL FAIL to indicate that the assay was failed by a user and not by the software This status is useful if The assay passed all analysis criteria selected for the study but you want to fail the assay anyway e You want to confirm an AUTO FAIL call that is you reviewed the AUTO FAIL call and confirmed the data do not pass The assay was imported with the NEW status that is no analysis criteria were selected for the study Notes 70 Applied Biosystems AutoCaller Software User Guide Chapter 4 View and Edit Data A View data For information on analysis criteria see About the automation settings on page 22 Use the Status menu shown below to view the analysis status assigned to an assay To manually assign an analysis status see Edit data on page 73 Status AUTO PASS z IMPORTANT You must belong to t
68. ate Description Operator 3b 1 Barcode 123456789 File Name Untitled 1 This name will appear on reports Instrument Unknown Assay Allelic Discrimination Last Modified Acquisition started Acquisition ended Data collected on Unknown Plate Format 384 Wells Clear Plate Plate Comments studyName Population 3 tudyssourceDNABC Sourcey MHums 3c The comments you enter here will appear on reports S Print Cancel 4 Save and close the SDS file Notes 12 Applied Biosystems AutoCaller Software User Guide Chapter 2 Preparation Tasks LO Set up an OpenArray file Set up an OpenArray file About OpenArray data Export OpenArray data AutoCaller software can read files created by the Applied Biosystems OpenArray SNP Genotyping Analysis software To export OpenArray SNP Genotyping Analysis software data for use in AutoCaller Software Start the OpenArray SNP Genotyping Analysis software Open the project containing the data of interest 2 3 Select File Export To Applied Biosystems AutoCaller 4 Select a location for the file and click Save Set up an EDS file About EDS files Using EDS files with the AutoCaller software Notes An EDS file is a file created by the Applied Biosystems StepOne StepOnePlus 7500 or 7500 Fast Real Time PCR system An EDS file stores data for a single reaction plate When you perform an ex
69. ault No Gender H16 1 47 0 75 11 1 818 02 1 Default No Gender P17 1 47 0 74 11 1 630 59 1 Default No Gender 7 1 47 0 77 11 1 669 91 1 Default No Gender f l Notes 74 Applied Biosystems AutoCaller Software User Guide Notes Edit the Auto Codes Chapter 4 View and Edit Data Edit data Vu In the Assay Selection pane select the desired assay then click the Codes tab The Auto Codes assigned to the assay are displayed in the list on the right hand side To add an Auto Code to the assay 1 Select the appropriate Auto Code from the list on the left side 2 Click Add assay code s You can select one code at a time Statistics Codes 9 Comments 5 Assay Info U TC7 Weak Vic TC1 3 Good Clusters TC2 2 Good Clusters 2 TC3 Homozygous Vic TC4 Homozygous Fam TCS Heterozygous TCG Weak Amp Both TCO Non specific Vic Description To remove an Auto Code from the assay 1 Select the appropriate Auto Code from the list on the right side 2 Click Remove assay code s Statistics Codes 9 Comments Assay Info TC1 3 Good Clusters TC7 Weak Vic TC2 2 Good Clusters TC3 Homozygous Vic oe gt P TC4 Homozygous Fam TCS Heterozygous TCS Weak Amp Both TCO Non specific Vic TC10 Non specific Fam E lt Description Weak Fam For more information on the Auto Codes see Codes tab on p
70. code Criteria Date Loaded TC Code Any TC Code Status Any Status DNA Plate Any DNA Plate Priority Code Chromosome Comments 9 Click Next 10 Click Browse then navigate to and select a destination folder Notes 92 Applied Biosystems AutoCaller Software User Guide Chapter 5 Publish Data min Creating a comparison report 11 Click Report The AutoCaller software Displays the results in the Report window Exports the data as a text txt file and saves the file to the selected destination folder 12 Click Close to close the Report window 13 Open the destination folder to confirm that the export was successful The txt file name includes the report type the date and time the report was exported and the study name For Sample Assay Reports the file name also includes the sample name 14 Open the txt file in a spreadsheet or simple text application Creating a comparison report The AutoCaller software can generate two types of Comparison Reports Assay Comparison Report below Wild Type Sample Comparison Report page 95 These reports are called comparison reports because they compare information from one study to either another study or a single sample in the study To create a comparison report see How to create a comparison report on page 96 Contents of the comparison reports Assay The Assay Comparison Report compares genotypes between identical samples
71. d To specify this criterion Date Loaded Click 3 Choose Date Assays Were Loaded then select the date the assay was imported into the AutoCaller software database TC Code Select the Auto Code from the drop down menu Status Select the analysis status from the drop down menu DNA Plate Select the source DNA plate name from the drop down menu e lt DNA plate name gt user defined MULTI No DNA Plate Priority Code Select a priority code from the drop down menu Chromosome Select a chromosome from the drop down menu Comments Click the Comments field then enter any comments that appear in the Assay Management window page 41 or the Comments tab of the Analyze window page 68 Enter the comments exactly as they appear in the Assay Management or Analyze window or enter an asterisk as a wild card Note If you do not specify any criteria the software returns all assays with the name or ID number you entered in step 3 If you did not enter an assay name or ID number the software returns all assays in the study 7T Click Search The assays returned by the search are displayed in the Assay Selection pane of the Analyze window Search for Assays Study Choose Study SL 2 Names Assay Name bat ba L 3 Assay Collection l 4 Plate Barcode 5 Criteria Date Loaded TC Code Any TC Code v Status Any Status v DNA Plate Any DNA Plate v 6 Priority Code Chr
72. data Publish data e Manage sample sets e Manage xml files Production e Manage assay collections e View data e Publish data t For information on installing the AutoCaller software managing users and backing up and restoring the AutoCaller software database see the Quick Reference Card Applied Biosystems AutoCaller Software Tasks for Users at the Administrator User Level Notes Applied Biosystems AutoCaller Software User Guide 3 Chapter 1 Introduction Workflow Workflow This user guide explains how to perform tasks with the AutoCaller software following the workflow below Preparation Tasks Chapter 2 1 Set up files for import into the AutoCaller software SDS Files EDS Files OpenArray Files 2 Log in to the AutoCaller software and optionally change your password ww Manage Studies and Assay Information Chapter 3 Create a study and set the analysis criteria Import data files into a study Manage studies Edit assay information Edit assay collections oar Wn Delete assays and plates ww View and Edit Data Chapter 4 1 Search a study for assays 2 View data 3 Edit data ww Publish Data Chapter 5 Review the report types Create reports from a study Create comparison reports A WO N a Use reports in publications and or downstream analysis Notes 4 Appli
73. data are saved to the AutoCaller software database Your edits are tracked with your user name and the date and time you made the edits Workflow Preparation Tasks Chapter 2 ww Manage Studies and Assay Information Chapter 3 b d View and Edit Data Chapter 4 1 Search a study for assays 2 View data 3 Edit data b d Publish Data Chapter 5 Required user To perform the procedures in this chapter log in to the AutoCaller software as a member levels ofthe required User Level The required User Level is indicated at the beginning each section in this chapter For information on User Levels see About user levels on page 3 Notes 56 Applied Biosystems AutoCaller Software User Guide Chapter 4 View and Edit Data Search a study for assays Search a study for assays Required user To perform the procedures in this section log in to the AutoCaller software at any User level Level About the search In the Search for Assays dialog box you can optionally select any of the following search criteria criteria to either narrow or broaden your search Criterion Description Assay Name The assay name or ID number Assay Collection A name given to a group of two or more assays Plate Barcode The name or barcode of the reaction plate in which the assay was run Date Loaded The date the assay was imported into the AutoCaller software database TC Code The Auto Code automatical
74. documentation For more information see Safety alert words on page ix How to obtain more information Documentation vi AutoCaller software documentation Portable document format PDF versions of this guide and the Quick Reference Card Applied Biosystems AutoCaller Software Tasks for Users at the Administrator User Level PN 4387768 are available on the AutoCaller software installation CD and from the Help menu in AutoCaller software Note To open the user documentation included on the AutoCaller software installation CD use the Adobe Acrobat Reader software available from www adobe com Related documentation Document PN Applied Biosystems 7900HT Fast Real Time PCR System Allelic Discrimination 4364015 Getting Started Guide GeneAmp PCR System 9700 Base Module User s Manual 4303481 SDS Software Online Help N A Applied Biosystems StepOne and StepOnePlus Real Time PCR Systems 4376786 Getting Started Guide for Genotyping Experiments StepOne and StepOnePlus Software Online Help N A Applied Biosystems 7500 7500 Fast Real Time PCR System Getting Started 4387784 Guide for Genotyping Experiments StepOne and StepOnePlus Software Online Help N A OpenArray NT Imager Genotyping System User Guide 4400385 OpenArray NT Imager Genotyping Software Online Help N A Note For additional documentation see How to obtain support on page vii Applied Biosystems AutoCaller Softwa
75. e Note Applied Biosystems recommends accepting the default values for the analysis criteria b If you want the software to Apply a criterion to the study select the Enabled check box Ignore a criterion deselect the Enabled check box Note The types of analysis criteria Name column and the Auto Codes are predefined in the AutoCaller software and cannot be edited For more information see About the automation settings on page 22 c Click Finish Notes 114 Applied Biosystems AutoCaller Software User Guide Appendix A Manage Sample Set Files N Create a study using a sample set mm Please choose settings appropriate for the platform and instruments to be used in this study The default entries in the value column of the table below are For the 7900 instrument These parameters may be innapropriate when using instruments other than the 7900 Default values For Fluorescent intensity automation settings Min Rox Max ROX Wells NTC Avg Max Non specific VIC Non specific FAM Weak VIC Weak FAM have not been defined For the Opendrray platform hence these automation settings are disabled by default when creating a Study For use on the OpenArrayPlatform Name Value _ Auto Code Min Genotype Confidence Min ROX Min Genotyped Max ROX Wells NTC Avg Max Non specific VIC Non specific FAM Weak VIC Weak FAM Min Sigma Separation Min P value per Population T
76. e Load XML File to Database Load TaqMan Open rray to Database Load EDS File to Database Exit 2 Choose an Auto Analysis option When a file is successfully imported the AutoCaller software automatically calls the genotypes for each assay in the file In the Load Setup dialog box Deselect the Conduct Auto analysis check box to track which assays are new All assays from the file are given the status NEW for more information see Assay Selection pane on page 60 Select the Conduct Auto analysis check box to automatically apply Auto Codes page 22 to each assay in the EDS file 3 From the Choose Study drop down menu select one of the following Notes Applied Biosystems AutoCaller Software User Guide 29 wa Chapter 3 Manage Studies and Assay Information Import files Select Use study indicated in the file to import the EDS file into the study name gt indicated in the EDS file see Set up an SDS file on page 7 This option allows you to import multiple EDS files into multiple studies at the same time For example if you select a folder in step 4 below the AutoCaller software automatically imports each EDS file into the study name gt indicated in that EDS file even if all of the EDS files indicate different studies Note If you select Use study indicated in the file and the EDS file does not include a study name the AutoCaller software displays an error message and does not import the EDS f
77. e Assay Collections Change Password Generate Reports Preferences 2 In the Data Explorer window click to open a study and view the associated plates and assays AutoCaller Data Explorer DER As Use the Data Explorer to browse the contents of the database and remove Plates and Assays from studies Removable items can be removed with a Right click Delete or using the trash can icon E O Studies 08 June Genotyping t CARES plate B Plate plate C Plate plate D Plate H C3 Assays H 3 Samples H C3 All 2007 Samples H C3 Assays Notes Applied Biosystems AutoCaller Software User Guide 51 Delete a plate Notes Chapter 3 Manage Studies and Assay Information Delete assays and plates 3 Delete the assay a Click the assay to be deleted The right side of the Data Explorer window displays the plates associated with the assay VWXKITI 08 June Genotyping Assay Name Study Chromosome Alleles DisplayAlleles Comments Plates in this Study on which this Assay appears Plate plate B plate D b Right click and select Delete You can also click 3 Delete E C3 Studies 6 08 06 Drug Resistance C Plates amp C3 Assays ABCxyl Assay DEFzw23 Asea i GHlab45 A JKLcd6 Assay i MNOef78 Assay i PQRgh9 Assay c Atthe prompt click Yes to delete the assay from the study Any results for runs containing this
78. e User Guide Appendix A Manage Sample Set Files uw Manage sample sets rg Read a tab delimited sample information file Look In TestFiles M S L ze C3 DME Data paired plates E 21380090 corrected sds 6b E 21380106 corrected sds E 21380108 corrected sds E A302K8x2 sds E ceDMEH 001 Sample Set txt L B export log RESTEST DME data test 2007 04 23 12 07 txt E export RESTEST DME data test 2007 04 23 12 07 xml File Name DME sample set txt Files of Type All Files X 6c 7 Click Close to save your changes and close the Edit Existing Sample Set dialog box 8 Click Close to close the Sample Set Management window Delete a You can only delete sample sets that are not being used by any studies in the database sample set a 1 From the main window toolbar select Tools gt Manage Sample Sets Ea Help Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences 2 Inthe Sample Set Management window a Select the sample set you want to delete b Click Delete an existing sample set Notes Applied Biosystems AutoCaller Software User Guide 111 A Appendix A Manage Sample Set Files Create a study using a sample set Sample Set Management Date Created 3t DNA Plates 3t Samples 0 Generic Sample Set 03 11 2007
79. e procedures in this chapter log in to the AutoCaller software as a member levels with the required User Level The required User Level is indicated at the beginning each section in this chapter For information on User Levels see About user levels on page 3 Notes 118 Applied Biosystems AutoCaller Software User Guide Export a study in xml format Required user Export a study Notes Appendix B Manage xml Files Export a study in xml format B To perform the procedures in this section log in to the AutoCaller software at any User levels Level 1 From the main window toolbar select Tools Manage Studies Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences In the Study Management window select the study you want to export then click amp Export the selected study Note The AutoCaller software does not export any assays in the study that have a status of NEW us Study Management Date Created 06 16 2008 Name Sample Set Generic Sample Set 08 June Genotyping Platform Assays Plate m7 Comments First test of the new instrument All 2007 Samples Lymphoma Study 06 16 2008 06 17 2008 Generic Sample Set Generic Sample Set Plate i8 Work done by Smith Lab 3 Complete the Export Study dialog box a Click Specify output directory
80. earch and reporting Features Use this window to name and define the contents kand of your Assay Collections Choose a Collection Name 2 Add a new Collectio All Available Assays Assays in the collection ABCxy1 DEFzw23 GHIab45 JKLcd MNOeF78 3 sTuijt Import VWXHI 6 4 Verify that the assays in the Assays in the Collection list are correct 5 If needed follow the instructions in Edit an assay collection to add or remove assays 6 Click Save to save the assay collection then Close to close the dialog box At the prompt click Yes Edit an assay 1 Select Tools gt Manage Assay Collections collection Heb Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences 2 In the Choose a Collection list click the name of the collection to be edited Notes Applied Biosystems AutoCaller Software User Guide 49 wa Chapter 3 Manage Studies and Assay Information Manage assay collections Delete an assay 1 collection Notes To add an assay to the collection click the name of the assay in the All Available Assays list and then click gt gt To quickly find an assay enter the first few letters of the assay name in the filter items here gt field above the All Available Assays list The list scrolls to display assays that begin with the letters you entered To add a
81. ed Biosystems AutoCaller Software User Guide Chapter 2 Preparation Tasks This chapter covers Nu Chapter s where adora packs S gba d edd deas bad Saude Bed 6 NH Setup ai SDS Mle osuses osceebbtbee RR SORP ero tE EC E e EERU 7 B Setup an OpenArray file sssssssssseeeee eee 13 E SctupanEDS file nad R3 Vend Ro e Rand PARA EEG VE 13 E Log Into the AutoCaller software cssssseeeeeee e eee e eee 15 Applied Biosystems AutoCaller Software User Guide 5 Chapter 2 Preparation Tasks Chapter overview Chapter overview This chapter explains how to set up your SDS files for use with the Applied Biosystems AutoCaller Software and how to log in to the AutoCaller software and change your password Workflow Preparation Tasks Chapter 2 1 Set up files for import into the AutoCaller software SDS Files EDS Files OpenArray Files 2 Log in to the AutoCaller software and optionally change your password wv Manage Studies and Assay Information Chapter 3 b d View and Edit Data Chapter 4 b d Publish Data Chapter 5 Required user All User Levels in the AutoCaller software are allowed to perform the procedures in this levels chapter For information on User Levels see About user levels on page 3 Notes 6 Applied Biosystems AutoCaller Software User Guide Chapter 2 Preparation Tasks LO Set up an SDS file Set up an SDS file About SDS files An SDS
82. ed the reaction plate DNA plate name The software displays the source DNA plate name if the user included the name in the file page 7 or in the sample set file page 105 e No DNA Plate The software displays No DNA Plate for any reaction plates that do not have a name or multiplate assigned Wells The number of wells per assay Status SUCCESS or ERROR e f SUCCESS is displayed for all assays the software imported the xml file s successfully e f ERROR is displayed for one or more assays the software does not import the xml file s Assay Codes The Auto Code s automatically or manually assigned to an assay as defined by the analysis criteria For a list of Auto Codes and the corresponding analysis criteria see page 22 b Optional Click Export to export and archive the information in the Loading dialog box c Click Close Notes 122 Applied Biosystems AutoCaller Software User Guide Appendix B Manage xml Files Nu Import xml files into a study BB Loading XML File export RESTEST DME data test 2007 04 23 12 07 xml null C 34418888 10 A302G99M 4 DME 04 96 SUCCESS TC1 TC15 null C 34418888 10 A302GL4R 4 DME 03 96 SUCCESS TC1 TC15 null C 34446548 10 A3028UMU 4 DME 04 96 SUCCESS TC1 TC15 null C 34446548 10 23029540 4 DME 03 96 SUCCESS TC1 TC15 null C 2220259 20 A30269a6 4 DME 04 96 SUCCESS TC20 TC20 TC15 null C 2220259 20 A302GHTI 4 DME 03 96 SUCCESS TC20 T
83. edicted Genot Genotype ROX Confidence Population Gender INA17235 CIS 0 76 10 82 22 22 1 695 58 1 Default No Gender L INA17120 c16 0 54 8 1822 22 2 627 66 0 95 Default No Gender INA17206 isti 0 77 10 74 22 22 1 473 37 1 Default No Gender INA17112 icis 0 7 10 4422 22 2 070 42 1 Default No Gender INA17213 c19 0 75 10 91 22 22 1 478 81 1 Default No Gender NA17225 c21 0 76 10 68 22 22 1 525 19 1 Default No Gender INA17259 C22 0 65 10 9522 22 1 711 65 1 Default No Gender INA17253 C23 0 71 10 45 22 22 1 700 11 1ppefault No Gender INA17245 C24 0 82 9 8622 22 1 949 71 1 Default No Gender INA10859 D2 0 87 9 4222 22 2 805 25 0 99 Default No Gender 3 INA17130 D4 0 8 10 2522 22 2 712 42 1 Default No Gender INAL7122 DS 0 78 10 4 22 22 2 420 7 1 Default No Gender INA17212 D6 0 89 9 722 22 2 856 3 0 99 Default No Gender C Notes Export Table Data to File 72 Applied Biosystems AutoCaller Software User Guide Chapter 4 View and Edit Data Edit data Edit data You can edit data in the AutoCaller software as follows Edit genotypes allele calls below Edit Auto Codes page 75 Edit the analysis status page 76 Omit wells from the analysis page 76 Delete comments page 80 IMPORTANT Any edits you make to the data are saved to the AutoCaller software database Your edits are tracked with your user name and the date and time you made the edits There is no
84. eful when you want to see if the same DNA is an outlier in numerous assays Assay C 26334975 20 Dna Plate DME 04 View Genotype 1 1 1 i i 1 i i i 1 ebad T T MEENE T H HT HT T E dien T HT EE 4 et 2 To change the color of the data displayed a Click Change Settings to open the Change Cluster Plot Settings dialog box b Click the Cluster Colors tab default then select the desired colors from the drop down menus c Click Apply to save your changes b ge Cluster Plot Settings Cluster Colors Graph Scale Cluster 11 Cluster 12 Cluster 22 Undetermined wc Low Rox Highlight Apply Cancel J To change the scale of the data displayed a Click Change Settings to open the Change Cluster Plot Settings dialog box b Click the Graph Scale tab c Select one of the following Automatic Automatically scales the plot to the data Notes Applied Biosystems AutoCaller Software User Guide 63 mla Chapter 4 View and Edit Data View data e Manual Allows you to define the minimum and maximum values for the x and y axes d If you selected Manual enter the desired values for the x and y axes Note If data are outside the range you enter the data does not appear in the plot Applied Biosystems recommends the following values x Max 6 x Min 1 y Max 10 or 12 y Min 0 e Click Apply to save your changes b Change Cluster Plot Settings
85. eports described on page 85 contain information from a single study Comparison reports described on page 93 compare information from one study to either another study or a single sample in the study Both types of reports are text files Notes 84 Applied Biosystems AutoCaller Software User Guide Chapter 5 Publish Data minn Creating a report from a study Creating a report from a study The AutoCaller software provides the following report types for data from a study Assay Report below Assay amp Well Report page 86 Assay amp Sample Report page 87 Sample Genotype Report page 88 Sample Assay Report page 88 These reports are called study reports because they contain information from a single study To create a study report see How to create a study report on page 89 Contents of the study reports Assay Report Forthe selected study the Assay Report contains summary information for each assay as Autocaller Version 3 2 0 assay name C 26334975 20 C 26334975 20 C 26334975 20 Notes described below B c D E F G H I J K L M plate barcode dna plate plate location status chromosome allele1 allele2 percent genotyped sigma separation MAF Default Minor Allele Default codes comments A302GL4M DME_03 1 AUTO PASS N A N A NA 100 14 88541059 0 244680851 2 TC1 TC4 TC9 null A302GL4H DME_04 1 AUTO PASS N A N A N A 98 94 11 26291715 0 247311828 2TC1 Enter comment
86. er Software Users at the Administrator User Level can Install the AutoCaller software Manage users Manage studies includes deleting studies Manage assay information and assay collections View and edit data Publish data Manage sample sets Manage xml files Note All User Levels are assigned by the users at the Administrator User Level The genotype assigned to a sample 11 Homozygous VIC dye e 2 Heterozygous 22 Homozygous FAM dye 00 Undetermined genotype A two dimensional coordinate system in which each point on a plane 1s expressed as a distance from the two axes In AutoCaller software genotyping results displayed in Cartesian coordinates plots Rn for the VIC dye on the X axis and Rn for the FAM dye is on the Y axis The likelihood that the point belongs to the cluster the cluster is defined by the software A file created by either the 7500 Software v2 0 or greater or StepOne Software The EDS file represents a single reaction plate Data from the EDS files can be imported into the Applied Biosystems AutoCaller Software database The entire process of performing a run on a real time PCR instrument including file setup run and analysis Minor allele frequency The minor allele is the least frequent of the two alleles Fluorescence signal from the reporter dye normalized to the fluorescence signal of the passive reference Applied Biosystems AutoCaller Software User
87. ers Manage Assay Collections Change Password Generate Reports Preferences In the Sample Set Management window select the sample set you want to edit then click f Edit an existing sample set Sample Set Management Date Created DNA Plates Samples Ser E a aE Generic Sample Set 03 11 2007 0 478 In the Edit Existing Sample Set dialog box check the sample set information for accuracy To add a new reaction plate to the sample set a In the DNA Plate field enter the DNA plate name user defined b Click Add Applied Biosystems AutoCaller Software User Guide 109 A A Appendix A Manage Sample Set Files Manage sample sets 5 To edit the sample set information Column Description To edit Sample Name The name of the sample N A You cannot edit the sample names Population The population from which the sample is Double click the Population field for a sample then from enter the new population name Gender The gender from which the sample is Click the Gender field for a sample then select a from gender from the drop down menu Source The source of the DNA sample that is Double click the Source field for a sample then enter a where the DNA came from new source Edit Existing Sample Set DME Dna Barcode List pME 03 DME 04 3t DNA Plates 2 DNA Plate 4 Dna Sample List Any edits done belo
88. ever there is more than one plate in the study with the same assay No DNA Plate The software displays No DNA Plate for any reaction plates that do not have a name or a multiplate assignment sample name The name of the sample on which the assay is being run well number The reaction plate well in which the assay sample is located genotype The genotype for each sample 11 12 22 or 00 Note If a user selected a base in the Assay Management window the genotype for each sample is AA TT and so on For more information see Edit assay information on page 41 confidence The confidence value for each sample point The confidence value indicates the likelihood that the point belongs to the cluster the cluster is defined by the software allele 1 Rn normalized reporter value of the VIC dye signal allele 2 Rn normalized reporter value of the FAM dye signal Assay amp Sample For the selected study the Assay amp Sample Report lists the genotype for each sample for Report each assay as described below The Assay amp Sample Report is useful for exporting genotypes for downstream analysis however it is not recommended if no sample sets are defined If no sample sets are defined use the Assay amp Well Report described on page 86 instead B c D E F G H J K L M N o P 1 Autocaller Version 3 2 0 2 AssayName NA10859 NA14474 NA14476 NA17102 NA17103 NA17104 NA17
89. g 112 Applied Biosystems AutoCaller Software User Guide 103 Appendix A Manage Sample Set Files Appendix overview Appendix overview Workflow About sample set files Required user Notes levels This appendix explains how to create sample set files txt format import the files into the Applied Biosystems AutoCaller Software database and manage the sample sets in the AutoCaller software This appendix also explains how to create a study using sample sets Manage Sample Set Files Appendix A 1 Create a sample set file for multiplate studies 2 Import the sample set file into the AutoCaller software database 3 Manage the sample set file in the AutoCaller software 4 Create a study using the sample set file Sample set files are text txt files that contain information about each sample in a reaction plate You create sample set files in a text application then import the files into the AutoCaller software database When you import the files the AutoCaller software updates the sample information for any SDS file that included sample information for the reaction plate Sample set files allow you to Track individual reactions plates by sample which can help you identify under performing plates Calculate statistics and alter displays based on population and gender information To perform the procedures in this appendix you must log in to the AutoCaller software at the Administ
90. g dialog box 26 28 32 Data Table 66 OpenArray data 13 results from a study See creating reports studies to XML file 119 G genotypes editing in Data Table pane 74 78 editing in Plot View pane 73 regenotyping NEW assays for a multiplate 39 H hazard symbols See safety symbols on instruments IMPORTANT description ix importing assay collection 49 assay information text file 43 EDS files 29 errors during 32 OpenArray files 27 sample set files 106 SDS files 24 27 29 132 studies from XML file 121 L Loading dialog box exporting contents to a text file 26 28 32 logging in 15 M MAF See minor allele frequency magnifying plot area 64 minor allele frequency definition 129 mismatches text file contents 95 MSDSs obtaining vii multiplate creating a sample set file 105 definition 71 editing genotypes for 73 74 regenotyping NEW assays 39 selecting 71 N normalized reporter definition 129 O omitting samples and associated wells 79 wells from analysis 76 OpenArray files about 13 importing 27 P password changing 16 plot changing colors 63 changing coordinates 62 changing data displayed 62 changing scale 63 empty after rescaling 64 printing 64 zooming in 64 zooming out 64 Plot View pane contents 62 opening additional plots 65 polar coordinates definition 130 viewing 62 printing Data Table 66 Applied Biosystems AutoCaller Software User Guide plots 64 production level user
91. gn genotypes after omitting wells page 76 in the Analyze window or for multiplates by clicking the Re genotype multiplates in selected study in the Study Management window page 39 Predicted Genotype Displays data by genotype as automatically assigned by the AutoCaller software when the file is imported Population Displays data by population This option is only available if population information was included in the sample set file and a target population was selected when the study was created step 3d on page 20 Gender Displays data by gender This option is only available if gender information was included in the sample set file IMPORTANT Sample set files contain information about each sample in a reaction plate For more information on sample set files see Appendix A on page 103 To change the coordinates used to display the plot select the coordinates from the drop down menu Cartesian v Cartesian Polar Cartesian A plot of VIC dye Rn versus FAM dye Rn in Cartesian coordinates Polar A plot of VIC dye Rn versus FAM dye Rn in polar coordinates 62 Applied Biosystems AutoCaller Software User Guide Chapter 4 View and Edit Data View data um n To display hints check Hints check box When the Hints check box is selected the software displays information for each sample point in the plot when you move your mouse over the point This is us
92. he analysis criteria Enabled Check boxes that you select or deselect to determine whether or not the AutoCaller software applies the analysis criteria to your study Auto Code The code automatically or manually assigned to an assay Each code corresponds to a particular analysis criterion For example if your search returns an assay that lists the Auto Code TC20 then that assay did not pass the Min Genotyped analysis criterion Auto Codes and the corresponding analysis criteria are shown in the table below Note You can search for assays based on an Auto Code s For more information see Search a study for assays on page 57 Note The AutoCaller software automatically assigns Auto Codes to assays when a file is imported Users at the Administrator or Scientist User Level can also assign add or remove Auto Codes manually for more information see Edit data on page 73 Predefined analysis criteria and auto codes Criterion Auto Code Description Min Genotype Confidence N A Minimum confidence value The confidence value indicates the likelihood that the point belongs to the cluster the cluster is defined by the software Samples with values less than the specified minimum are genotyped as UDT undetermined or 00 Min ROX N A Minimum ROX dye value Samples with values less than the specified minimum are flagged as Low ROX ROX dye is a component of the TaqMan maste
93. he Administrator or Scientist User Level to manually assign an analysis status Open a second Open a second window to compare two runs from the same study or from different window studies There are two ways to open a second window From the main window toolbar select File K New Analysis Window Tools Help New Analysis Window Load SDS File to Database Load XML File to Database Load TaqMan Open rray to Database Load EDS File to Database Exit Start the AutoCaller software twice so that you have two instances of the software running You can either open The same study in each instance or A different study in each instance This option allows you to easily navigate between studies Selecta The AutoCaller software creates an extra plate a multiplate abbreviated as MULTI in multiplate he Assay Selection pane that contains all the reaction plates within a study for a single assay Each reaction plate is treated as an individual plate for importing and genotyping allele calling but all the plates can be viewed together and edited as a multiplate to save time Select a multiplate when you want to compare Duplicate runs the same assays run on the same samples Amultiplate experiment an experiment with more than 384 samples To select a multiplate 1 In the Assay Selection pane look for MULTI in the Plate Barcode column There may be several multiplates the software creates a multiplate for any a
94. he name or barcode is entered by the user in the file The software adds MULTI to the barcode for example MULTI A302GL4M whenever there is more than one plate in the study with the same assay For more information see Select a multiplate on 60 Applied Biosystems AutoCaller Software User Guide Chapter 4 View and Edit Data View data Column Description DNA Plate The name or barcode of the source DNA plate that is the DNA plate that was used to seed the reaction plate DNA plate name gt The software displays the source DNA plate name if the user included the name in the file or in the sample set file page 105 e MULTI The software assigns the name MULTI whenever there is more than one plate in the study with the same assay e No DNA Plate The software displays No DNA Plate for any reaction plates that do not have a name or multiplate assigned Status The analysis status of the assay Instrument The instrument where this assay was run Format The format of the data e a rows X b columns The number of rows a and columns b in the reaction plate e OpenArray Reaction plates imported from OpenArray data To view data in the Assay Selection pane 1 To select an assay click anywhere in the assay row The remaining panes and tabs in the Analyze window display additional information for the selected assay You can select only one as
95. ile Select the study you want the EDS file imported into Note You can import the same EDS file into more than one study 4 Click Browse to navigate to and select the file or folder to import The file or folder name is displayed in the Choose File field Note If you select a folder all files in the folder are imported 5 Click Load to import the selected file or folder into the AutoCaller software The Loading dialog box appears while the file is being imported 9 Load Setup 2 Conduct Auto analysis Choose Study Example Study 3 Choose File led Biosystems Autocaller TestFiles A302X8x2 sds Browse 4 Load Cancel If the EDS file is missing information the Plate Preview dialog box opens Any field with missing information is shown in pink Notes 30 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information vam Import files 6 Click in the pink fields and enter the missing information You can also use the right click commands Fill Down Copy Paste and Delete When all fields are complete click Continue or Click Skip This lI Plate preview Plate to omit the plate Please review your data Fields highlighted pink are invalid Correct invalid fields to continue File pon Plate Barcode 12346 DNA Plate Barcode No DNA Plate Study Name Basic Test Instrument StepOnePlus Chemistry Taqman
96. ile the Loading dialog box includes the following information The Status column displays ERROR along with a description of the error The Assays Errored field displays the number of assays with importing errors Loading SDS File A302X8X2 sds Project Assay Name Plate Dna Plate Wells Status Assay Codes Project Assay Hame Plate Dna Plate Wells Status Assay Codes TestFiles E LLY22 10 A302X0X2 1 NGS D 64 ERROR Ho study found with the name GTMM Cycle Tests Finished reading Total Assays Read Assays Imported File Progress Folder Progress The following errors may occur during import Error Cause Errors for All Types of Files No study found with the name You selected the Use study indicated in the file option study name but the study does not exist in the AutoCaller software Notes 32 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information ww Import files Error Cause Duplicate Plate You selected a file plate that was already imported into the study Note If you want to import a duplicate file plate into a study see REDO on page 70 Unknown sample If you selected a sample set other than Generic Sample Set a sample is included in the file that is not in the sample set list Errors Specific to SDS Files lt study name gt not found in plate You selected the Use study indicated
97. in the SDS file Chromosome The chromosome assigned to the assay Priority Code The priority code assigned to the assay Priority codes defined by the user can be used to facilitate searches For example you may want to use the gene name as a priority code Actual Allele 1 The actual alleles present in the sample Actual Allele 2 Display Allele 1 The alleles you want to display in your published reports A By default reports use the actual allele names Enter alternative io ia names for the alleles in the Display Allele columns For example you might use A T in the Actual Allele 1 and 2 columns but in the Display Allele 1 and 2 columns Comment Comments about the assay to add to the database 3 On the following lines enter information for each assay You can list the assays in any order but you must follow these parameters Enter one assay per line Enter the assay name or ID number exactly as it appears in the file IMPORTANT When you import a file into the AutoCaller software database all ofthe assay name or ID numbers that are in the file are added to the Assay Management window To ensure that any assay information you import into the Assay Management window is associated with the correct assay enter the assay name or ID number exactly as it appears in the file Optional Enter the remaining information listed in step 2 above A B C D E F G 1 Assay ID Chromosome
98. in the folder are imported 5 Click Load to import the selected file or folder into the AutoCaller software The Loading dialog box appears while the file is being imported is Load Setup 2 4 v Conduct Auto analysis Choose Study Example Study ys 3 Choose File ed Biosystems Autocaller TestFiles A302X8X2 sds Browse 4 mm Load Cancel Notes Applied Biosystems AutoCaller Software User Guide 25 Chapter 3 Manage Studies and Assay Information Import files 6 When the File Progress field in the Loading dialog box displays Done a Review the information for each assay Column Description Assay Name The assay name or ID number Plate The name or barcode of the reaction plate in which the assay was run The name or barcode is entered by the user in the SDS file page 7 DNA Plate The name or barcode of the source DNA plate that was used to seed the reaction plate DNA plate name gt The software displays the source DNA plate name if the user included the name in the file page 7 or in the sample set file page 105 e No DNA Plate The software displays No DNA Plate for any reaction plates that do not have a name or multiplate assigned Wells The number of wells in the reaction plate containing sample assay Status SUCCESS or ERROR Assay Codes The Auto Code s automatically or manually assigned to an assay as defined by the
99. ion Clear assay information from Notes the Assay Management window 1 1 From the main window toolbar select Tools Manage Assays Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences In the Assay Management window locate the assay of interest then view the assay information You can edit the assay information in any column except Name To edit assay information To edit a Do this Chromosome Click the Chromosome field for an assay then select a chromosome from the drop down menu Priority Code Double click the Priority Code field for an assay then enter a code Note You can enter any text in the Priority Code field Actual Allele 1 Click the field for an assay then select an option from the drop down menu You can select one of the following doaz e The base for the SNP A C G or T Display Allele 1 e Plus sign Indicates the presence of a mutation or indicates an insertion Display Allele 2 e Minus sign Indicates the absence of a mutation or indicates a deletion Comment Double click the Comments field then enter comments This feature clears assay information from the Assay Management window only It does not delete the assay or any run data for the assay from the AutoCaller software database To delete an assay from the database
100. iosystems within the ninety 90 day warranty period Applied Biosystems will replace the defective media Applied Biosystems does not warrant that the software will meet buyer s requirements or conform exactly to its documentation or that operation of the software will be uninterrupted or error free Any applicable warranty period under these sections begins on the earlier of the date of installation or ninety 90 days from the date of shipment for software installed by Applied Biosystems personnel For all software installed by the buyer or anyone other than Applied Biosystems the applicable warranty period begins the date the software is delivered to the buyer Warranty claims must be made within the applicable warranty period 126 Applied Biosystems AutoCaller Software User Guide Appendix C Software Warranty Information w Limited product warranty Warranty The above warranties do not apply to defects resulting from misuse neglect or accident exceptions including without limitation operation outside of the environmental or use specifications or not in conformance with the instructions for the instrument system software or accessories improper or inadequate maintenance by the user installation of software or interfacing or use in combination with software or products not supplied or authorized by Applied Biosystems and modification or repair of the product not authorized by Applied Biosystems The foregoing prov
101. isions set forth Applied Biosystems sole and exclusive representations warranties and obligations with respect to its products and Applied Biosystems makes no other warranty of any kind whatsoever expressed or implied including without limitation warranties of merchantability and fitness for a particular purpose whether arising from a statute or otherwise in law or from a course of dealing or usage of trade all of which are expressly disclaimed Warranty The remedies provided herein are the buyer s sole and exclusive remedies Without limitations limiting the generality of the foregoing in no event shall Applied Biosystems be liable whether in contract tort warranty or under any statute including without limitation any trade practice unfair competition or other statute of similar import or on any other basis for direct indirect punitive incidental multiple consequential or special damages sustained by the buyer or any other person or entity whether or not foreseeable and whether or not Applied Biosystems is advised of the possibility of such damages including without limitation damages arising from or related to loss of use loss of data failure or interruption in the operation of any equipment or software delay in repair or replacement or for loss of revenue or profits loss of good will loss of business or other financial loss or personal injury or property damage No agent employee or representative of Applied Bi
102. iteria you specify 1 From the main window toolbar select Tools gt Generate Reports Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences 2 Inthe Report window a Select the appropriate report Assay Report Assay amp Well Report Assay amp Sample Report Sample Genotype Report Sample Assay Report b Click Next E Report zu S Choose Report Type Assay Report The Simple Assa Example Assay Name hatch the given selection criteria ha Separation Minor Allele Frequency Minor Allele Codes Comments 3 From the Choose Study drop down menu select a study Notes Applied Biosystems AutoCaller Software User Guide 89 Notes Chapter 5 Publish Data Creating a report from a study 4 Optional In the Assay Name field enter the name or ID number of the assay for which you want to export data You can use an asterisk as a wild card For example if you enter 245 the software exports data for all assays with names that include a 245 sequence C__232456789_20 C__332456789_20 and so on If you do not specify the assay name or ID number the software exports data for all assays in the study Optional In the Assay Collection dropdown menu select The assay collection in which you want to export data Define a new collection to define
103. ler software does not recognize them as NTC wells 3 Enter barcode and optional study information You can enter this information into each SDS file by typing or by copying and pasting a Select Tools Document Info b In the Barcode field enter a name for the reaction plate or enter or scan the barcode c Optional In the Plate Comments field enter the following information studyName lt study name gt amp SourceDNABC lt DNA plate name gt where study name gt is the AutoCaller study name that the SDS file will be imported into Notes Applied Biosystems AutoCaller Software User Guide 11 wu Chapter 2 Preparation Tasks 4 Set up an SDS file DNA plate name gt is the name of the source DNA plate that is the name of the DNA plate used to seed the reaction plate For example if your source DNA plate is named SourceX and you want to put this data into a study named Population_Study you enter study Name Population_Study amp sourceDNABC SourceX Note If you enter the study name gt in the SDS file the AutoCaller software can automatically import the SDS file into the correct study However you can omit this step and manually import the SDS file into any study When you manually import an SDS file you can import the same SDS file into more than one study See Import SDS files on page 24 d Click OK to return to the SDS software main window 3 Document Information Pl
104. lied Biosystems AutoCaller Software User Guide 95 a Chapter 5 Publish Data Creating a comparison report A B C D E F G H l J K L M N 1 Autocaller Version 3 2 0 2 AssayName NA17108 NA10859 NA14474 NA14476 NA17102 NA17103 NA17104 NA17105 NA17106 NA17107 NA17108 NA17109 NA17110 3 C 26334975 20 1 0 0 1 0 1 1 1 1 1 1 1 0 4 C 26334975 20 1 0 0 1 0 1 1 1 1 1 1 1 0 5 C 26334975 20 1 0 0 1 0 1 1 1 1 1 1 1 0 6 Totals 3 0 0 3 0 3 3 3 3 3 3 3 0 7 Percentage 100 0 0 100 0 100 100 100 100 100 100 100 0 8 Column Tow Description AssayName The assay name or ID number sample ID Wild type score for each sample 1 The sample is like the wild type 0 The sample is different from the wild type N A No genotype called for the sample Totals The total number of assays where the sample genotype is identical to the wild type Percentage The number of times as a percentage the sample is like the wild type How to create a comparison report The software exports data from the Comparison Reports as text txt files You can open the exported data in a spreadsheet application such as Microsoft Excel software or simple text application such as Microsoft Notepad software Generate an 1 In the main window toolbar select Tools Generate Reports Assay Comparison Help Data Explorer Repo rt Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Passwo
105. ly or manually assigned to an assay as defined by the analysis criterion For a list of Auto Codes and the corresponding analysis criteria see page 22 Status The analysis status of the assay For more information see Status menu on page 70 DNA Plate The name or barcode of the source DNA plate that is the DNA plate that was used to seed the reaction plate DNA plate name The software displays the source DNA plate name if the user included the name in the file page 7 or in the sample set file page 105 MULTI The software assigns the name MULTI whenever there is more than one plate in the study with the same assay For more information see Select a multiplate on page 71 No DNA Plate The software displays No DNA Plate for any reaction plates that do not have a name or multiplate assigned Priority Code The priority code assigned by a user to the assay in the Assay Management window used to perform searches used to facilitate searches for example a gene name can be used as a priority code Chromosome The chromosome assigned by a user to the assay in the Assay Management window Comments Comments entered by a user from the Assay Management window or from the Comments tab o f the Analyze window Notes Applied Biosystems AutoCaller Software User Guide 57 Search for assays 1 Notes Chapter 4 View and Edit Data Search a study for assays in a study
106. might indicate an under performing assay a poor quality sample or a null allele sigma_separation The measure of cluster separation and cluster tightness MAF lt population gt The total number of times as a percentage that a minor allele occurs in the specified population Note MAF Minor allele frequency the minor allele is the least frequent of the two alleles Minor Allele lt population gt The minor allele genotyped for the specified population 1 or 2 Minor allele information is available only if a minor allele was assigned for this assay Note If a user selected a base in the Assay Management window the genotype for each sample is AA TT and so on codes The Auto Code s automatically or manually assigned to an assay as defined by the analysis criterion For a list of Auto Codes and the corresponding analysis criteria see page 22 comments Comments entered by a user from the Assay Management window or from the Comments tab o f the Analyze window Assay amp Well For the selected study the Assay amp Well Report contains summary information for each Report well of each assay as described below The Assay amp Well Report is useful for exporting genotypes for downstream analysis A B c D E E G H 1 j Autocaller Version 3 2 0 2 assay name plate barcode dna plate sample name well number genotype confidence allele 1 allele 2 3 C 26334975 20 A302GL4M D
107. mplete review the information for each assay Each line in the Assay Info Load Progress dialog box includes the following information Text file name Line number Assay status Assay data for assay name gt successfully parsed or an error message If the software displays an error message for an assay the assay was not imported Note Line 1 always displays the error message Invalid chromosome because Line 1 in the text file lists the column headings and not any assay information After reviewing assay information click Close The new or updated assay information is displayed in the Assay Management window m Assay Info Load Progress DME Autocaller Assay Info File txt Lime 2513 DME Autocaller Assay Info File txt Line 2514 DME Autocaller Assay Info File txt Line 2515 DME Autocaller Assay Info File txt Line 2516 DME Autocaller Assay Info File txt Line 2517 DME Autocaller Assay Info File txt Line 2518 DME Autocaller Assay Info File txt Line 2519 DME Autocaller Assay Info File txt Line 2520 DME Autocaller Assay Info File txt Line 2521 DME Autocaller Assay Info File txt Line 2522 DME Autocaller Assay Info File txt Line 2523 DME Autocaller Assay Info File txt Line 2524 DME Autocaller Assay Info File txt Line 2525 DME Autocaller Assay Info File txt Line 2526 DME Autocaller Assay Info File txt Line 2527 DME Autocaller Assay Info File txt Line 2528 DME Autocaller Assay Info File txt Line 2529 DME Autocalle
108. ng system This guide uses the following conventions Bold text indicates user action For example Type 0 then press Enter for each of the remaining fields e talic text indicates new or important words and is also used for emphasis For example Before analyzing always prepare fresh matrix A right arrow symbol gt separates successive commands you select from a drop down or shortcut menu For example Select File K Open gt Spot Set Right click the sample row then select View Filter K View All Runs Two user attention words appear in Applied Biosystems user documentation Each word implies a particular level of observation or action as described below Note Provides information that may be of interest or help but is not critical to the use of the product IMPORTANT Provides information that is necessary for proper instrument operation accurate chemistry kit use or safe use of a chemical Applied Biosystems AutoCaller Software User Guide V Preface How to obtain more information Safety alert words Examples of the user attention words appear below Note Users at the Administrator and Scientist User Levels are allowed to edit data Users at the Production User Level are not allowed to edit data IMPORTANT The AutoCaller software is intended for SNP genotyping experiments only Be sure to open an Allelic Discrimination AD plate document Safety alert words also appear in user
109. notype to 12 Change Genotype to 22 kas Change Genotype to UDT 9 2 j b Omit selected Wells 9 1 1 i Include selected Wells 20 Genotype 11 2 Genotype 12 12 Genotype 22 80 Genotype 00 0 Low ROX 0 NTC 2 Edit genotypes in the Data Table pane 1 Inthe Assay Selection pane select the desired assay You can select Asingle assay to edit the assay for an individual reaction plate or Amultiplate to edit the assay across reaction plates Look for MULTI in the Plate Barcode column There may be several multiplates the software creates a multiplate for any assay that was run on more than one reaction plate 2 In the Data Table pane click the Genotype field for the sample you want to edit Note You can edit only one sample at a time in the Data Table pane When you select the sample in the Data Table pane the corresponding sample point in the Plot View pane is highlighted 3 From the Genotype drop down menu select the appropriate option 1 Homozygous VIC dye e 12 Heterozygous 22 Homozygous FAM dye 00 Undetermined genotype Sample Name Row Column Allele 1 Allele 2 Predicted Genotype Genotype ROX Confidence Population Gender TT ec 72 a a NN rann a A17 0 711 1 794 68 1 Default No Gender Fal N16 T 0 77 11 1 614 45 1 Default No Gender L17 1 46 0 7811 1 821 48 1 Default No Gender ns 1 47 0 7211 1 738 27 1 Default No Gender C17 1 47 0 711 1 540 32 1 Def
110. nt window click _ From the main window toolbar select Tools Manage Studies Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences Add a new study to the database to access the Study Creation dialog box us Study Management Name Date Created Sample Set Platform Assays Comments P A 08 June Genotyping 06 16 2008 Generic Sample Set Plate 7 First test of the new instrument ad j All 2007 Samples 06 16 2008 Generic Sample Set Plate 8 Lymphoma Study 106 17 2008 Generic Sample Set Plate 0 IWork done by Smith Lab 3 In the Study Creation dialog box enter basic study information Notes a In the Enter Study Name field enter a name for your study that is descriptive and easy to remember b From the Choose Platform drop down menu select Plate to indicate that you are using a 96 or 384 well reaction plate or OpenArray to indicate you are using data collected from the OpenArray NT Imager Genotyping System Note You cannot mix data with different platforms in a single study Applied Biosystems AutoCaller Software User Guide 19 Chapter 3 Manage Studies and Assay Information Create studies c From the Choose Sample Set drop down menu select Generic Sample Set if you have not imported any sample set files into the AutoCaller software or you do not want to use sam
111. ntrol Sample Study Choose Control Sample NA17227 3 INA17227 INA17263 INA17207 8 Names Du mE 4 INA17208 Assay Name 23 L NA17201 3 5 NA17262 Choose Study All 2007 Samples Assay Collection INA17225 Plate Barcode 5 6 Criteria Date Loaded TC Code Any TC Code Status Any Status DNA Plate Any DNA Plate Priority Code Chromosome Comments 9 Click Next 10 Click Browse then navigate to and select a destination folder 11 Click Report The AutoCaller software Displays the results in the Report window Exports the data as a text txt file and saves the file to the selected destination folder 12 Click Close to close the Report window 13 Open the destination folder to confirm that the export was successful The txt file name includes the report type wild type comparison the date and time the report was exported and the study name 14 Open the txt file in a spreadsheet or simple text application Notes 102 Applied Biosystems AutoCaller Software User Guide Appendix A Manage Sample Set Files This appendix covers E Appendix OVeEVIeW asi h02csc0 cee iisi ioeie bad bau Ra dido ob sans weak 104 NH Createa sample set file is ccc K eR torona EERE RECO EE RATRE 105 B Import a sample set file as a aa x 0 r eee een nee 106 B Manage sample sets rossu rg R a R a RR cette een RA 109 E Create a study using a sample set 0 0 0 ee te terenne Eren
112. o edit the assay for an individual reaction plate or Amultiplate to edit the assay across reaction plates Look for MULTI in the Plate Barcode column There may be several multiplates the software creates a multiplate for any assay that was run on more than one reaction plate 2 In the Plot View pane draw a box around the samples points to omit The corresponding samples in the Data Table pane are highlighted 3 Right click anywhere in the Plot View pane then select Omit Selected Wells from the pop up menu Notes Applied Biosystems AutoCaller Software User Guide 76 Chapter 4 View and Edit Data w Edit data m Assay ABCxy1 DHA Plate DHA set C View Genotype Type Cartesian n Zoom Print Plot Change Genotype to 11 Change Genotype to 12 Change Genotype to 22 Change Genotype to UDT EEN BARA EAS E a S 1 ot i Omit selected Wells 3h T 4 Include selected Wells 7 NE ee et 02040608 10 12 1 4 16 18 2022 24 26 28 30 32 3 4 36 38 40 42 44 vic Genotype 11 2 Genotype 12 12 Genotype 22 79 Genotype 00 1 Low ROX 0 NTC 2 The selected well s become less intensely shaded and the Omitted check box in the Data Table pane is checked The statistics in the Statistics tab except for the MaxL Metrics are immediately recalculated without the values from the omitted wells The wells remain omitted from any further analysis After omitting wells you can e Click
113. oes not have run data associated with it To delete assays which area associated with run data see page 52 1 From the main window toolbar select Tools gt Manage Assays Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences 2 In the Assay Management window a Select the assay s you want to delete Note Press Ctrl click or Shift click to select multiple assays b Click m Delete the selected assays Assay Management Any edits done below will immediately be saved to the database Chromosome Priority Code Actual Allele 1 Actual Allele 2 Display Allele 1 Display Allele 2 Comment C 31366214 30 3 Atthe prompt click OK to delete the assay s from the AutoCaller software database Note Ifa study has run data associated with the assay the software displays an error message and does not delete the assay You can delete assays and associated run data in the Data Explorer window see page 51 4 Click Close to close the Assay Management window Notes Applied Biosystems AutoCaller Software User Guide 47 Chapter 3 Manage Studies and Assay Information Manage assay collections Manage assay collections Create an assay Notes collection Create an assay collection when you want to search for more than one assay at a time in the Search dialog box
114. of Applied Biosystems Inc or its subsidiaries in the U S and or certain other countries OpenArray is a trademark of BioTrove Inc TaqMan is a registered trademark of Roche Molecular Systems Inc Microsoft and Windows are registered trademarks of Microsoft Corporation All other trademarks are the sole property of their respective owners Part Number 4385543 Rev C 09 2008 Contents Preface T tees V How to use this guide K a XR K 8 ER A X RE A R RE eens V How to obtain more information ees vi How to obtain SUPOT ss lt 699 6 0 9 9 Re Re R RR ees vii Safety Information s ua x a9 e xaO 9C Rc 9n am es ix Safety conventions used in this document cee eee eee eee ix Workstation safety is c 644 eevee ee xad eeu Shi ede sed sk X4 A e ER x Chapter 1 Ts le Tre e wm 1 About the Applied Biosystems AutoCaller Software eee eee cease 2 About user levelS ses a a a aan eee 3 Urs ae 4 Chapter 2 Preparation Tasks aia 4a wwe kek See ee oS ee wee heen wns 5 Chapter overview 000 cee eee eee 6 Set upan SDS file sesia maii aaya a ai aaa a ii eee 7 Set up an OpenArray file n a nnan nauan aanne aanraai 13 Set up anm EDS file x eoe oe SO a dodoa hia ghee aiia aika Aa eR cR Ra 13 Log In to the AutoCaller software 2 0 00 0 0 ccc ccc ne 15 Chapter 3 Manage Studies and Assay Information 17 Chapter overview lellleeelll eee 18 Create Studies ssas
115. om the omitted wells The wells remain omitted from any further analysis After omitting wells you can e Click E Assign Genotypes to reassign genotypes and codes based on the included wells e Click Repeat Auto Analysis to reassign only codes based on the included wells To include an omitted sample 1 2 3 4 5 Click the sample to be included Right click and select Include wells associated with sample name At the prompt click Yes to include all wells for the sample Click OK in the message box The wells for this sample are included for any analysis In the Analyze window the selected well s are reshaded the Omitted check box in the Data Table pane is unchecked and the statistics in the Statistics tab are calculated with the values from these wells When you are finished click E3 Close to close the Data Explorer window Delete comments 1 2 Notes In the Assay Selection pane select the desired assay Click the Comments tab 80 Applied Biosystems AutoCaller Software User Guide Chapter 4 View and Edit Data 4 Edit data e 3 Click Clear all existing comments All comments for the selected assay are cleared 4 Click Save to database Note When you delete the comments the software displays your user name and the date and time you deleted the comments Additionally the software still displays 9 in the Comments tab to indicate that comments had
116. omosome Comments 7 E Search l Clear Cancel Notes Applied Biosystems AutoCaller Software User Guide 59 View data View data Required user level Analyze Window elements Chapter 4 View and Edit Data 8 Go to View data on page 60 for information on viewing the data within the Analyze window When you import an assay into the AutoCaller software database the software automatically analyzes the data on import This section explains how to view the analyzed data in the Analyze window If you want to edit the data and reanalyze it see Edit data on page 73 To perform the procedures in this section log in to the AutoCaller software at any User Level The assays returned by the search are displayed in the Analyze window For information on using the Analyze window see the sections cross referenced below E Analyzing Study 08 June Genotyping anbe Genotype Plot View pane page 62 Genotype 11 2 Cartesian Genotype 12 12 Low ROX 0 x Dms Change Settings Assay ABCxy1 DNA Plate DNA_set_C View Genotype Type Cartesian Genotype 22 79 NTC 2 Assay Selection Plate Barcode plate_C MULTI ABCxy1 MULTI NEW 16x24 Assay Name DNA Plate Status Instrument Format plate B DNA set B RUTO FAIL 9 EZ jplate D DNA set D RUTO FAIL 16x24 Suo jmurrsTUji0 MULTI NEW Te 5 assay s were found that meet your search criteria
117. oose Study drop down menu select the study you want the xml file imported into Note You can import the same xml file into more than one study Note If you select Use study indicated in the file the AutoCaller software displays an error message and does not import the xml file 4 Click Browse to navigate to and select the file or folder you want to import The file or folder name is displayed in the Choose File field Note If you select a folder all xml files in the folder are imported Notes Applied Biosystems AutoCaller Software User Guide 121 Fog Appendix B Manage xml Files me Import xml files into a study 5 Click Load to import the selected file or folder into the AutoCaller software The Loading XML File dialog box appears while the file is being imported 9 Load Setup 2 _ C Conduct Auto analysis Choose Study Example Study s NEN 0 3 j If F Choose File rt RESTEST DME data test 2007 04 23 12 07 xml Browse 4 Load Cancel 6 When the status bar in the Loading XML File dialog box displays 70096 a Review the information for each assay Column Description Assay Name The assay name or ID number Plate The name or barcode of the reaction plate in which the assay was run The name or barcode is entered by the user in the SDS file page 7 DNA Plate The name or barcode of the source DNA plate that is the DNA plate that was used to se
118. or assays Comparison in two different studies The Assay Comparison Report is useful when you want to Report Compare the same assay run with the same samples but with different run conditions for example different master mix different amounts of DNA and so on Runcontrol samples on every reaction plate then compare the results to a validation study The Assay Comparison Report is exported as two text txt files A comparison txt file that contains the results of the comparison A mismatches txt file that contains a summary of discrepancies Note The reports provide information only for the assays in the studies that meet the report criteria you specify see Generate an Assay Comparison Report on page 96 Notes Applied Biosystems AutoCaller Software User Guide 93 Notes Chapter 5 Publish Data Creating a comparison report Comparisons txt file A B d D E F G H I I 1 Oligo Name S1 DNA Plate S2 DNA Plate Wells 96 Matched Mismatched 96 UDTs S2 00 S1 00 S2 00 S1 11 S2 0051 12 S2 00 S1 22 S 2 C 29712728 10 MULTI MULTI 94 100 0 0 0 0 0 0 3 C 31366037 10 MULTI MULTI 94 100 0 0 0 0 0 0 4 C 31366086 10 MULTI MULTI 94 100 0 0 0 0 0 0 5 C 31366087 10 MULTI MULTI 94 100 0 0 0 0 0 0 6 C 31366214 30 MULTI MULTI 94 100 0 1 063829787 1 0 0 0 7 C 33171049 10 MULTI MULTI 94 0 100 0 0 0 0 0 8 C 33291755 10 MULTI MULTI 94 100 0 0 0 0 0 0 9 C
119. ose File field Note If you select a folder all files in the folder are imported Applied Biosystems AutoCaller Software User Guide 27 wa Chapter 3 Manage Studies and Assay Information Import files 5 Click Load to import the selected file or folder into the AutoCaller software The Loading dialog box appears while the file is being imported us Load Setup 2 L 7 Conduct Auto analysis Choose Study 08 June Genotyping v N 3 Choose File 31xml from open rrayVBEH 73 BEH74 BEH75 xml 6 When the File Progress field in the Loading dialog box displays Done a Review the information for each assay Column Description Assay Name The assay name or ID number Plate The name or barcode of the reaction plate in which the assay was run The name or barcode is entered by the user in the file page 7 DNA Plate The name or barcode of the source DNA plate that was used to seed the reaction plate e DNA plate name The software displays the source DNA plate name if the user included the name in the file page 7 or in the sample set file page 105 No DNA Plate The software displays No DNA Plate for any reaction plates that do not have a name or multiplate assigned Wells The number of wells in the reaction plate containing sample assay Status SUCCESS or ERROR Assay Codes The Auto Code s automatically or manually assigned to an assay as defined by
120. osystems has any authority to modify the terms of this Limited Warranty Statement or to bind Applied Biosystems to any affirmation representation or warranty concerning the product that is not contained in this Limited Warranty Statement and any such modification affirmation representation or warranty made by any agent employee or representative of Applied Biosystems will not be binding on Applied Biosystems unless in a writing signed by an executive officer of Applied Biosystems This warranty is limited to the buyer of the product from Applied Biosystems and is not transferable Some countries or jurisdictions limit the scope of or preclude limitations or exclusion of warranties of liability such as liability for gross negligence or willful misconduct or of remedies or damages as or to the extent set forth above In such countries and jurisdictions the limitation or exclusion of warranties liability remedies or damages set forth above shall apply to the fullest extent permitted by law and shall not apply to the extent prohibited by law Notes Applied Biosystems AutoCaller Software User Guide 127 van Appendix C Software Warranty Information Limited product warranty Notes 128 Applied Biosystems AutoCaller Software User Guide Administrator call Cartesian coordinates confidence value EDS file experiment MAF normalized reporter Glossary User Level in the Applied Biosystems AutoCall
121. periment on any of these instruments you 1 Create an EDS file with information about each well in the reaction plate including the sample names and assay IDs 2 Run the reaction plate on the instrument The data from the run is collected and stored in the EDS file After the run you can import the EDS file into the AutoCaller software database The AutoCaller software analyzes the EDS file data upon import use the AutoCaller software to view and edit the data Note Only 7500 and 7500 Fast instruments running 7500 Software v2 0 or greater create EDS files To ensure that the EDS file is imported correctly into the AutoCaller software database set up the file so that it includes the following information Sample name Assay ID Either imported from the Assay Information file AIF or entered manually Correct information for the negative control wells IMPORTANT You must label all negative control wells If you label the negative control wells as water blank and so on the AutoCaller software does not recognize them as negative control wells Reaction plate name or barcode Applied Biosystems AutoCaller Software User Guide 13 0 Chapter 2 Preparation Tasks Set up an EDS file Set up an EDS file Notes Optional AutoCaller software study information Applied Biosystems recommends that you include the above information when you first create an EDS file If needed however you can add this
122. plate assigned Wells The number of wells in the reaction plate containing sample assay Status SUCCESS or ERROR Assay Codes The Auto Code s automatically or manually assigned to an assay as defined by the analysis criteria For a list of Auto Codes and the corresponding analysis criteria see page 22 Notes Applied Biosystems AutoCaller Software User Guide 31 mila Chapter 3 Manage Studies and Assay Information Import files b Review the statistics information Stats Ifthe Assays Errored field displays 0 the EDS file s were imported successfully Ifthe Assays Errored field displays gt 0 some or all of the EDS file s were not imported See Importing errors on page 32 c Optional Click Export to export and archive the information in the Loading dialog box d Click Close ll Loading EDS File eds SHP1 12345 1 Ho DHA Plate 96 SUCCESS TC8 SHP Assay 1 this is my barcode 1 mySourceDNABC 96 SUCCESS TC21 6a C 11711420 30 Example 1 Ho DNA Plate 24 SUCCESS TC1 Finished reading 6b a EE te Total Assays Read 3 Assays Imported 3 Assays Errored 0 Plates Read 0 l 6d Done Close J Export EXE 6c On import the AutoCaller software automatically analyzes the data in the EDS files To search for assays and view edit the data see Chapter 4 on page 55 Importing errors Ifthe AutoCaller software did not successfully import a f
123. ple set files for this study The appropriate sample set if you have already imported sample set files into your study Note To use sample sets you must first create sample set files then import the files into the AutoCaller software database Sample set files contain information about each sample in a reaction plate For more information on sample set files see Appendix A on page 103 d In the Choose Target Populations pane f you selected Generic Sample Set in step c select Default This is the only option available for the Generic Sample Set Ifyou selected a sample set in step c the populations identified for that sample set are displayed Select one or more populations Note Press Ctrl click or Shift click to select multiple populations The software calculates statistics for the selected populations The calculated statistics appear in the Statistics tab of the Analysis window For more information see Statistics tab on page 67 e Optional In the Comments field enter comments for this study f Click Next us Study Creation Basic Study Info Basic Study Setup Enter Study Name 3a Choose Platform Plate v 3b Choose Sample Set Generic Sample Set v 3c Choose Target Populations 3d Comments 3e 3f Notes 20 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information NEN Create studies 4 Complete the Automation Se
124. pplied Biosystems AutoCaller Software User Guide 23 ww Chapter 3 Manage Studies and Assay Information Import files Import files Import SDS files When you import SDS files created for allelic discrimination plates in the 7900HT System SDS software into the AutoCaller software database the software Imports all run data associated with the assays directly into a study You can use the software to search studies for assays then view and edit the assay run data For more information see Chapter 4 on page 55 Imports the assay names ID numbers into the Assay Management window For more information see Edit assay information on page 41 IMPORTANT Before you import your SDS files set up the SDS files to include information that can be successfully accessed by the AutoCaller software see Set up an SDS file on page 7 Import an 1 From the main window toolbar select File Load SDS File to Database to open SDS file the Load Setup dialog box for importing SDS files Tools Help New Analysis Window Load SDS File to Database Load XML File to Database Load TaqMan Open rray to Database Load EDS File to Database Exit 2 Choose an Auto analysis option When an SDS file is successfully imported the AutoCaller software automatically calls the genotypes for each assay in the file In the Load Setup dialog box Deselect the Conduct Auto analysis check box to track which assays are new All a
125. prompt click Yes 3 If you have omitted wells for any of the assays in this study the Omitted Wells dialog box opens Omitted Wells 3 This task contains omitted wells How would you like to handle them Leave omitted wells out of the analysis Deselect omit on all wells before analyzing Cancel To continue to omit the wells in the analysis click Leave omitted wells out of the analysis The omitted wells retain their omitted status and are not re genotyped or Toinclude all wells in the analysis click Deselect omit on all wells before analyzing The status of the omitted wells changes to included and they are re genotyped Notes Applied Biosystems AutoCaller Software User Guide 39 Wu Chapter 3 Manage Studies and Assay Information Manage studies The Reanalyzing Study Name window opens and displays the progress of the re genotyping Hy Reanalyzing 7900test x etrieving data for assay PORgh9 Genotyping amp analyzing assay PORgh9 pdating database for assay PORgh9 ultiplate Assay PORgh9 genotyped and analyzed etrieving data for assay STUij10 Genotyping amp analyzing assay STUiji0 pdating database for assay STUij10 ultiplate Assay STUij10 genotyped and analyzed trieving data for assay VWXkl11 Genotyping amp analyzing assay VWXk111 Week Multiplate Analysis is complete eee 4 When the analysis is complete click Close Note If you have changed the
126. r Assay Info File txt Line 2530 Assay data for C 2228477 30 successfully parsed Assay data for C 8878812 30 successfully parsed Assay data for C 8878813 20 successfully parsed Assay data for C 8878814 10 successfully parsed Assay data for C 8878820 20 successfully parsed Assay data for C 11617931 20 successfully parsed Assay data for C 26251036 20 successfully parsed Assay data for C 25642994 20 successfully parsed Assay data for C 433116 20 successfully parsed Assay data for C 21540127 30 successfully parsed Assay data for C 32876912 10 successfully parsed Assay data for C 32876931 10 successfully parsed Assay data for C 30966814 10 successfully parsed Assay data for C 222172188 10 successfully parsed Assay data for C 11617922 10 successfully parsed Assay data for C 25642968 20 successfully parsed Assay data for C 8878782 10 successfully parsed Assay data for C 2469257 40 successfully parsed DME Autocaller Assay Info File txt Loading assay information into the database DME Autocaller Assay Info File txt Assay information for 1375 assays loaded into the database Process complete 5 Click Close to close the Assay Management window 44 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information Edit assay information Edit assay information in the Assay Management window View or edit assay informat
127. r in Applied Biosystems user documentation at points in the document where you need to be aware of relevant hazards Each alert word IMPORTANT CAUTION WARNING DANGER implies a particular level of observation or action as defined below Definitions IMPORTANT Indicates information that is necessary for proper instrument operation accurate chemistry kit use or safe use of a chemical N i Ye Indicates a potentially hazardous situation that if not avoided may result in minor or moderate injury It may also be used to alert against unsafe practices N WEN ey Indicates a potentially hazardous situation that if not avoided could result in death or serious injury N Diei Indicates an imminently hazardous situation that if not avoided will result in death or serious injury This signal word is to be limited to the most extreme situations Applied Biosystems AutoCaller Software User Guide ix Safety Information Workstation safety Examples The following examples show the use of safety alert words IMPORTANT The sample name run folder name and path name combined can contain no more than 250 characters Neen MUSCULOSKELETAL AND REPETITIVE MOTION HAZARD These hazards are caused by potential risk factors that include but are not limited to repetitive motion awkward posture forceful exertion holding static unhealthy positions contact pressure and other workstation environmental fac
128. r mix used in TaqMan genotyping assays A low ROX dye value may indicate mixing or pipetting errors Samples flagged as Low ROX are not genotyped and cannot be edited Notes 22 Applied Biosystems AutoCaller Software User Guide Notes Chapter 3 Manage Studies and Assay Information ww Create studies Criterion Auto Code Description Min 96 Genotyped TC20 Minimum percentage of samples that must be genotyped for each assay Assays with values less than the specified minimum are flagged Max 96 ROX Wells TC17 Maximum percentage of samples that can have a low ROX dye value see Min ROX above Assays with values greater than the specified maximum are flagged A high percentage of samples with low ROX dye values may indicate mixing or pipetting errors NTC Avg Max TC18 Maximum amount as an average of signal FAM or VIC dye allowed for no template controls NTCs Assays with high NTC signal values are flagged High NTC signal values may indicate contamination of the NTC well s Non specific VIC TC9 Maximum amount of non specific VIC dye signal allowed in the homozygous FAM dye cluster Assays where the average signal value is greater than the specified maximum are flagged In a perfect assay samples points in the FAM dye cluster have an average VIC dye Rn value of 0 Values greater than the specified maximum may indicate non specific p
129. rator or Scientist User Level For information on User Levels see About user levels on page 3 104 Applied Biosystems AutoCaller Software User Guide Appendix A Manage Sample Set Files wu Create a sample set file Create a sample set file You can create sample set files for a multiplate study IMPORTANT To use a sample set in an AutoCaller software study create and import the sample set file into the AutoCaller software before you create the study page 112 Create a sample 1 Open spreadsheet program such as Microsoft Excel software set file for a multiplate study 2 Online one enter a name for the text file 3 Online two enter names for each source DNA plate in the study for example DME 03 DME 04 and so on IMPORTANT If you are performing duplicate runs of the same data be sure to give the duplicates different plate names If you use the same plate name for each duplicate the AutoCaller software does not import the duplicates the software assumes the data has already been imported 4 On the following lines enter information for each sample You can list the samples in any order but you must follow these parameters Include all samples and all NTCs from all the reaction plates in the study Enter one sample per line Enter the sample name Optional Enter the population gender and source information for each sample Note You do not need to include population
130. rd Generate Reports Preferences Notes 96 Applied Biosystems AutoCaller Software User Guide Chapter 5 Publish Data a Creating a comparison report 2 In the Report window select Assay Comparison then click Next E Report zum Choose Report Type Assay Comparison nt studies 3 Select the report criteria for Study 1 a From the Choose Study drop down menu select Study 1 Study 1 1s the first of the two studies you want to compare Note For Study 1 Applied Biosystems recommends that you select the study with fewer assays and compare it to the bigger study with the greater number of assays The AutoCaller software lists all assays in Study 1 and compares them to any identical assays in Study 2 For example if Study 1 contains 10 assays that meet the report criteria and Study 2 contains 100 the software performs a comparison for those 10 assays in Study 1 If Study 1 contains 100 assays that meet the report criteria and Study 2 contains 10 the software performs a comparison for all 100 assays in Study 1 b Optional In the Assay Name field enter the name or ID number of the assay for which you want to export data You can use an asterisk as a wild card For example if you enter 245 the software exports data for all assays with names that include a 245 sequence C 232456789 20 C 332456789 20 and so on If you do not specify the assay name or ID number the software exports data for
131. re User Guide Preface How to obtain support Send us your Applied Biosystems welcomes your comments and suggestions for improving its user comments documents You can e mail your comments to techpubs appliedbiosystems com IMPORTANT The e mail address above is only for submitting comments and suggestions relating to documentation To order documents download PDF files or for help with a technical question go to www appliedbiosystems com then click the link for Support See How to obtain support below How to obtain support For the latest services and support information for all locations go to www appliedbiosystems com then click the link for Support At the Support page you can Search through frequently asked questions FAQs Submit a question directly to Technical Support Order Applied Biosystems user documents MSDSs certificates of analysis and other related documents Download PDF documents Obtain information about customer training Download software updates and patches In addition the Support page provides access to worldwide telephone and fax numbers to contact Applied Biosystems Technical Support and Sales facilities Applied Biosystems AutoCaller Software User Guide vii Preface How to obtain support viii Applied Biosystems AutoCaller Software User Guide Safety Information Safety conventions used in this document Safety alert words Four safety alert words appea
132. robe binding and cleavage Non specific FAM TC10 Maximum amount of non specific FAM dye signal allowed in the homozygous VIC dye cluster Assays where the average signal value is greater than the specified maximum are flagged In a perfect assay samples points in the VIC dye cluster have an average FAM dye Rn value of 0 Values greater than the specified maximum may indicate non specific probe binding and cleavage Weak VIC TC7 TC6 Minimum as an average Rn value of the VIC dye homozygote Assays with average values less than the specified minimum are flagged with TC7 If both VIC and FAM Rn values are less than the specified minimum assays are flagged with TC6 Weak FAM TC8 TC6 Minimum as an average Rn value of the FAM dye homozygote Assays with average values less than the specified minimum are flagged with TC8 If both VIC and FAM Rn values are less than the specified minimum assays are flagged with TC6 Min Sigma Separation TC15 Minimum measure of cluster separation and cluster tightness Assays with values less than the specified minimum are flagged Min P value Per Population TC21 Minimum p value for each population Assays for which the samples have a p value lt 0 05 are 95 likely to have genotype frequencies that do not conform to Hardy Weinberg Equilibrium HWE expectations That is there are too few homozygotes or too few heterozygotes A
133. s you can e Click Assign Genotypes to reassign genotypes and codes based on the included wells e Click Repeat Auto Analysis to reassign only codes based on the included wells To include omitted wells in the Data Table pane right click then select Include Selected Wells from the pop up menu The selected well s are reshaded the Omitted check box in the Data Table pane is unchecked and the statistics in the Statistics tab are immediately recalculated Notes 78 Applied Biosystems AutoCaller Software User Guide Chapter 4 View and Edit Data A Edit data Omit all wells for a sample 1 Select Tools gt Data Explorer AS Help Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences 2 In the Data Explorer window click to open a study then click Samples to view the samples in the study B AutoCaller Data Explorer Use the Data Explorer to browse the contents of the database and remove Plates and Assays AS from studies Removable items can be removed with a Right click Delete or using the trash can icon E Studies H E 08 June Genotyping H 3 All 2007 Samples H 3 Lymphoma Study J PlateAStudy H G Plates S O Samples NA10859 NA14474 Sample NA17102 NA17103 NA17104 NA17105 N A17106 N A17107 N A17108 NA17109 N A17110
134. s here MULTIC 26334975 20 MULTI 0 NEW N A N A N A 99 47 0 245989305 2 N A null Column Description assay_name The assay name or ID number plate_barcode The name or barcode of the reaction plate in which the assay was run dna_plate The name or barcode of the source DNA plate that is the DNA plate that was used to seed the reaction plate e DNA plate name The software displays the source DNA plate name if the user included the name in the file or in the sample set file s MULTI The software assigns the name MULTI whenever there is more than one plate in the study with the same assay e No DNA Plate The software displays No DNA Plate for any reaction plates that do not have a name or a multiplate assignment status The analysis status of the assay chromosome The chromosome assigned to the assay if a chromosome was selected for this assay allele1 The allele being coded with the VIC dye probe Allele 1 information is only available if Allele 1 was assigned for this assay allele2 The allele being coded with the FAM dye probe Allele 2 information is only available if Allele 2 was assigned for this assay Applied Biosystems AutoCaller Software User Guide 85 Notes Chapter 5 Publish Data Creating a report from a study Column Description percent_genotyped The percentage of samples on the reaction plate genotyped for each assay This is useful for DNA QC statistics a low percentage
135. say at a time 2 To sort data click a column heading For example to sort the assays by the source DNA plate name click DNA Plate The assays are sorted by plate name in alpha numerical order 2 Assay Selection Assay Name Plate Barcode DNA Plate Status 1 C 26334975 20 A302GL4M DME 03 AUTO PASS ME 04 C 26334975 20 4302GL4H DME AUTO PASS C 26334975 20 MULTI C 26334975 20 MULTI NEW 3 assay s were Found that meet your search criteria To change the analysis status of the assay see Edit data on page 73 IMPORTANT You must belong to the Administrator or Scientist User Level to change the assay status Notes Applied Biosystems AutoCaller Software User Guide 61 Chapter 4 View and Edit Data View data Plot View pane Notes The Plot View pane displays a plot of the selected assay Each sample point in the plot is color coded by the assigned genotype as shown in the legend located beneath the plot You can print the Plot View pane To view data in the Plot View pane To change the data displayed in the plot select a data type from the drop down menu Genotype Displays data by genotype If a user has not edited the genotypes the software displays the predicted genotypes If the genotypes have been edited the software displays the edited genotypes You can edit the genotypes in three ways manually page 73 by clicking Assign Genotypes to reassi
136. ssay that was run on more than one reaction plate 2 To view the data for the multiplate select the assay In the Plot View the software displays the data for all the plates overlaid in one view Notes Applied Biosystems AutoCaller Software User Guide 71 Chapter 4 View and Edit Data View data 3 To return to individual views of each plate select an individual plate 2 EA g dy A p S anre Assay Selection Genotype Cartesian Hints Change Settings z Assay Name Assay ABCxy1 DNA Plate MULTI View Genotype Type Cartesian al AUTO FAIL STUIjLO MULTI STUIj10 MULTI NEW 7900 16x24 NWXHI1 plate B DNA set B AUTO FAIL 7900 16x24 NWXHI1 plate D DNA set D AUTO FAIL 7900 16x24 WWXKI1 IMULTI VWAXKI 1 MULTI NEW 7900 16x24 8 assay s were found that meet your search criteria Statistics Codes Comments Assay Info Allele Frequencies i Population Allele i Allele 2 Global 0 09 0 91 Default 0 09 0 91 084 088 082 09 100 104 108 112 MI a m i vic Genotyped 100 00 Genotype 11 2 Genotype 12 12 Genotype 22 80 Genotype 00 0 Low ROX 0 NTC 2 Status NEW Sample Name Well Address Allele 1 Allele 2 Pr
137. ssays from the SDS file are given the status NEW for more information see Assay Selection pane on page 60 Select the Conduct Auto analysis check box to automatically apply Auto Codes page 22 to each assay in the SDS file 3 Select the study to import From the Choose Study drop down menu in the Load Setup dialog box select one of the following Notes 24 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information ww Import files Select Use study indicated in the file to import the SDS file into the study name gt indicated in the SDS file see Set up an SDS file on page 7 This option allows you to import multiple SDS files into multiple studies at the same time For example if you select a folder in step 4 below the AutoCaller software automatically imports each SDS file into the study name gt indicated in that SDS file even if all of the SDS files indicate different studies Note If you select Use study indicated in the file and the SDS file does not include a study name the AutoCaller software displays an error message and does not import the SDS file Select the study you want the SDS file imported into Note You can import the same SDS file into more than one study 4 Click Browse to navigate to and select the file or folder you want to import The file or folder name is displayed in the Choose File field Note If you select a folder all SDS files
138. ssays to the collection from a text file txt a In the Assay Collection Management dialog box click Import b In the dialog box that opens locate the file containing the assay collection and click Open The file should contain each assay name on a separate line c Verify that the assays in the Assays in the Collection list are correct To remove an assay from the collection click the name of the assay in the Assays in the Collection list and then click Click Save to save the assay collection then Close to close the dialog box At the prompt click Yes Select Tools Manage Assay Collections Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences Select the collection to delete In the Choose a Collection list a Click the name of the assay collection to be deleted b Click Delete At the prompt click Yes to delete the assay collection then Close to close the dialog box At the prompt click Yes 50 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information mila Delete assays and plates Delete assays and plates Delete an assay You can delete an assay from a study even if there is data associated with the assay from a study 1 Select Tools K Data Explorer Stree Help Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manag
139. the analysis criteria For a list of Auto Codes and the corresponding analysis criteria see page 22 b Review the statistics information Stats Ifthe Assays Errored field displays 0 the OpenArray file s were imported successfully Ifthe Assays Errored field displays 70 some or all of the OpenArray file s were not imported See Importing errors on page 32 c Optional Click Export to export and archive the information in the Loading dialog box d Click Close Notes 28 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information wae Import files E Loading XML File xml_from_autocaller E m 13530 1U AjUZAUXC 1 HS D ba DULLESS TUZ 6a E mti4783 10 A300RH4Q 1 H6S C 384 SUCCESS TC20 E mt14783 10 A302X8YD 1 Nes_D 64 SUCCESS TC20 Finished reading 6b 4 reeeo Stats Total Plates Read 83 Plates Imported 83 Plates Errored 0 Timing for Read and Analyze XML Data elapsed 2 min 15 595 sec 6d 6e ui 100 0 l Close Export On import the AutoCaller software automatically analyzes the data in the OpenArray files To search for assays and view edit the data see Chapter 4 on page 55 Import EDS files 1 From the main window toolbar select File Load EDS File to Database to open the Load Setup dialog box for importing EDS files Tools Help New Analysis Window Load SDS File to Databas
140. the assay was imported into the AutoCaller software database Export Date The date the assay was exported in xml format Applied Biosystems AutoCaller Software User Guide 69 A Chapter 4 View and Edit Data View data To view information for the selected assay click the Assay Info tab Name Statistics Codes 3 Comments Assay Info Assay Name Plate Barcode DNA Plate Barcode Platform lis this a redo lat DNA Plates Chromosome Allele 1 Value C 26334975 20 mM A302GL4M DME 03 Plate No NIA N A x Status menu The Status menu displays the analysis status assigned to the selected assay Status Assigned By Reason AUTO PASS AUTO FAIL Software The AutoCaller software assigns AUTO PASS if the assay passes all of the analysis criteria selected for the study The AutoCaller software assigns AUTO FAIL if the assay fails one or more of the analysis criteria selected for the study HOLD NEW REPLICATE REDO MANUAL PASS MANUAL FAIL User Assign HOLD to an assay when you want to review or have another user review the assay before reporting data Assign NEW to an assay newly imported into the AutoCaller software database Assigning the NEW status is useful when you want to find and review new assays before reporting data Assign REPLICATE to indicate that the
141. these functions see Chapter 4 on page 55 Import assay information from a text file Overview There are two types of assay information files that you can import into the AutoCaller software database a data file in SDS EDS or OpenArray formats or a text txt file When you import a data file the AutoCaller software imports assay names or ID numbers that is shown in the Assay Management window and all run data associated with the assays see Import files on page 24 When you import a text file txt the AutoCaller software imports basic information about assays that is shown in the Assay Management window but it does not import any run data Import a text file to Add new information to be shown in the Assay Management window for an assay Update existing information to be shown in the Assay Management window for an assay Instructions for creating and importing a text file start on page 42 Notes Applied Biosystems AutoCaller Software User Guide 41 Chapter 3 Manage Studies and Assay Information Edit assay information Create the Create a text file txt to add basic information for many assays to the AutoCaller text file software database at the same time 1 Open a spreadsheet program such as Microsoft Excel software 2 On line one enter the following column headings Column Heading Description of Column Contents Assay ID The assay name or ID number as it appears
142. tion Graph Panel Predicted LeS Ae Polar v Hints Change Settings Assay ABCxy1 DNA Plate MULTI View Predicted Genotype Type Polar log Radius Genotype 11 2 Genotype 12 12 Genotype 22 80 Genotype 00 0 Low ROX 0 NTC 2 Data Table pane The Data Table pane displays the following information for each sample in the selected assay Column Description Omitted When checked indicates the well is omitted from the calculations for this assay Sample Name The name of the sample Well Address The location of the sample in the reaction plate For example P18 indicates that the sample is located in row P column 18 Allele 1 Rn normalized reporter value of the VIC dye signal Allele 2 Rn normalized reporter value of the FAM dye signal Predicted Genotype The genotype automatically assigned by the AutoCaller software Genotype The genotype edited by a user Note If the genotype is not edited by a user the predicted genotype is displayed in this column ROX The ROX dye level in the well Note ROX dye is in the TaqMan master mix used in TaqMan genotyping assays Confidence The confidence value for the sample point The confidence value indicates the likelihood that the point belongs to the cluster the cluster is defined by the software Notes Applied Biosystems AutoCaller Software User Guide 65 4 Chapter 4 View and Edit Dat
143. tors N Eie Do not attempt to lift or move the computer or the monitor without the assistance of others Depending on the weight of the computer and or the monitor moving them may require two or more people Workstation safety Correct ergonomic configuration of your workstation can reduce or prevent effects such as fatigue pain and strain Minimize or eliminate these effects by configuring your workstation to promote neutral or relaxed working positions rmi MUSCULOSKELETAL AND REPETITIVE MOTION HAZARD These hazards are caused by potential risk factors that include but are not limited to repetitive motion awkward posture forceful exertion holding static unhealthy positions contact pressure and other workstation environmental factors To minimize musculoskeletal and repetitive motion risks Use equipment that comfortably supports you in neutral working positions and allows adequate accessibility to the keyboard monitor and mouse Position the keyboard mouse and monitor to promote relaxed body and head postures Applied Biosystems AutoCaller Software User Guide Chapter 1 Introduction This chapter covers B About the Applied Biosystems AutoCaller Software n nnan uaunua naa 2 B Aboutuser levels ios oes sk erem er ERR URSCEYG STRE OE eds deer sens 3 a Work ss der tbe pire perqeience iere dere Eel QU am tee a ge doe eee deat 4 Applied Biosystems AutoCaller Software User Guide 1 Chapter
144. ttings dialog box a To edit a value for a criterion double click the Value cell then enter the desired value Note Applied Biosystems recommends accepting the default values for the analysis criteria b If you want the software to Apply a criterion to the study select the Enabled check box Ignore a criterion deselect the Enabled check box Note The types of analysis criteria Name column and the Auto Codes are predefined in the AutoCaller software and cannot be edited For more information see About the automation settings on page 22 c Click Finish 4a 4b UH Study Creation Automation Settini k Please choose settings appropriate for the platform and instru nents to be used in this study The default entries in the value column of tHe table below are l or the 7900 instrument These parameters may be innapropriate whin using instruments other than the 7900 Default values For flourescent intensity autc mation settings Min Rox Max ROX Wells NTC Avg Max Non specific VIC Non specific FAM Wak VIC Weak FAM have not been defined For the OpenArray platfor n hence these automation settings are disabled by default when creating a Study fhr use on the OperiArrayPlatForm Mame Value Enabled Auto Code Min Genotype Confidence 0 95 v Min ROX 200 v Min Genotyped 0 TZ TC20 Max ROX Wells 10 v TC1
145. tual Allele 2 Display Allele 1 Import the 1 From the main window toolbar select Tools Manage Assays text file Help Data Explorer Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences 2 Inthe Assay Management window click Load or update assay information Il Assay Management Any edits done below will immediately be saved to the database Name Chromosome Priority Code Actual Allele 1 Actual Allele 2 Display Allele 1 Display Allele 2 Comment C 29712728 10 6 C 33171049 10 como C 34275587 10 3 Select the text file In the Choose a file with assay information dialog box a Browse to and select a file PPARD SLC22A4 TAPL SLC22A4 TAP2 TPMT aana a anaa b Click Open The Assay Info Load Progress dialog box appears while the assay information is being imported Notes Applied Biosystems AutoCaller Software User Guide 43 Notes Chapter 3 Manage Studies and Assay Information Edit assay information E Choose a file with assay information 3a LO OME Autocaller Assay Info File txt pi sx a3 G8 8 File Name DME Autocaller Assay Info File txt Files of Type TXT files txt X Con 3b 4 When the Assay Info Load Progress dialog box displays Process co
146. tudy drop down menu select a study Optional In the Assay Name field enter the name or ID number of the assay for which you want to export data You can use an asterisk as a wild card For example if you enter 245 the software exports data for all assays with names that include a 245 sequence C 232456789 20 C 332456789 20 and so on If you do not specify the assay name or ID number the software exports data for all assays in the study Optional In the Assay Collection drop down menu select The assay collection in which you want to export data Define a new collection to define a new assay collection for use as a search criterion See page 48 for instructions Optional In the Plate Barcode field enter the barcode for the reaction plate Note Entering a barcode is useful when you want to export data for all assays run on a single reaction plate 100 Applied Biosystems AutoCaller Software User Guide Chapter 5 Publish Data Creating a comparison report 7 Optional In the Criteria pane specify any of the following criteria to narrow the set of assays exported Field To specify this criterion Date Loaded Click I Choose Date Assays Were Loaded then select the date the assay was imported into the AutoCaller software database TC Code Select the Auto Code from the drop down menu Status Select the analysis status from the drop down menu DNA Plate
147. udy Date Created The date the study was created Sample Set The name of the sample set selected when the study was created If a sample set was not selected Generic Sample Set is displayed Platform The consumable used in the experiment Plate indicates a 96 or 384 well reaction plate e Open Array indicates a TagMan OpenArray Genotyping Plate Assays The number of assays present in the study Comment Comments entered when the study was created Notes 34 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information ww Manage studies Edit a study Change basic study information 1 From the main window toolbar select Tools Manage Studies Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences 2 In the Study Management window a Select the study you want to edit b Click f Edit an existing study us Study Management Name Date Created Sample Set Platform Assays Comments 08 June Genotyping 06 16 2008 Generic Sample Set Plate First test of the new instrument All 2007 Samples 06 16 2008 Generic Sample Set Plate js Lymphoma Study 06 17 2008 Genetic Sample Set Work done by Smith Lab Im Mid 3 In the Edit Study dialog box select the Basic Study Information tab default 4 Edit the information
148. uide 15 wu Chapter 2 Preparation Tasks Log In to the AutoCaller software Optional You can change your password at any time Change your M password 1 From the main window toolbar select Tools r Change Password Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences 2 Complete the Change Password dialog box a Enter your original password b Enter a new password c Enter the new password again to confirm it Change Password Original Password New Password Retype New Password OK Close 3 Click OK 4 At the prompt click OK to change your password Notes 16 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information This chapter covers Nu Chapter Vet VIeW a qud sad nee MEA Du AUUS d bbe Tees orare decease 18 B Create StUdleS cos sess torente t EE Z EEE a Eae kad ewes 19 E Iuiportf1es cose beide Eon tpa dee ox pde de dne ux 24 B Manase stldles viu escsosooevegdpngeudus sex coal PURA shane 34 M Edit assay information s 235326 oo Te Che made repe Cae Peor E P oo 41 B Manage assay collections eg gn r ge cece cette n enine Ea 48 lA Delic assays and plates 2 0 dces cute pRes ue QEON HEIC URDU ed 54 Applied Biosystems AutoCaller Software User Guide 17 9 Chapter 3 Manage Studies and Assay Information Chapter
149. ver there is more than one plate in the study with the same assay e null The software displays null for any reaction plates that do not have a name or multiplate assigned S1 Well Num For Study 1 81 Well Num and Study 2 Prod Well Num the reaction plate well numbers for the samples with mismatched genotypes Prod Well Num 1 Genotype For Study 1 81 Genotype and Study 2 Prod Genotype the genotypes of the mismatched samples Prod Genotype Wild Type The Wild Type Sample Comparison Report is useful for backcrossing experiments For Sample the selected study the Wild Type Sample Comparison Report Comparison Compares the selected control sample the wild type to the remaining samples in all Report assays The remaining samples are identified as being like the wild type or different from the wild type Sums the number of times each sample is like the wild type then calculates the percentage across all assays in the study For example if you select SampleX as the control sample the software compares SampleX to the remaining samples in each assay If SampleY is run in three assays and is like SampleX in all three assays the total number of times SampleY is like SampleX is 3 and the percentage 1s 100 Note The report provides information only for the assays in the study that meet the report criteria you specify see Generate a Wild Type Sample Comparison Report on page 99 Notes App
150. w will immediately be saved to the database Sample Name T Population Gender Source B 5 NA10B59 NA10859 F Coriell a NA14474 African American F Coriell INA14476 African American F Coriell INA17102 African American M Coriell INA17103 African American M Coriell NA17104 African American M Coriell INA17105 African American M Coriell INA17106 African American M Coriell INA17107 African American M Coriell INa17108 African American M Coriell INA17109 African American M Coriell INA17110 African American F Coriell INA17111 African American M Coriell INA171 12 African American F Coriell INA17113 African American F Coriell INA17114 African American M Coriell INA17115 African American M Coriell INA17116 African American F Coriell INA17117 African American M Coriell INA17118 African American F Coriell INA171 19 African American F Coriell INA17120 African American F Coriell INA17121 African American F Coriell INA17122 African American F Coriell INa17123 African American F Coriell 92 samples in list Add Update Samples 6a Close 6 Toadda sample set file or to update the AutoCaller software database after you have made changes to the original sample set file txt a Click Add Update Samples to open the Read a tab delimited sample information file dialog box b Browse to and select a sample set file txt c Click Read to add or update the sample set file information Notes 110 Applied Biosystems AutoCaller Softwar
151. x ROX Wells 10 v TC17 NTC Avg Max 2 G TTC1S Non specific VIC 2 ica GS Non specific FAM 2 v TC10 Weak VIC 1 v TC7 TC6 Weak FAM 1 v TC8 TC6 Min Sigma Separation 10 G ITC15 Min P value per Po 0 05 v rcz1 5 dear save cae 6 Atthe prompts click OK to save your changes to the study 7 Click Close to close the Study Management window 38 Applied Biosystems AutoCaller Software User Guide Chapter 3 Manage Studies and Assay Information ww Manage studies Reassign genotypes for multiplate assays with NEW status You can assign genotypes for all multiplate assays in a study that have the status NEW Regenotyping also reassigns the genotypes in the individual assays 1 From the main window toolbar select Tools Manage Studies Data Explorer Manage Assays Manage Studies Manage Sample Sets Manage Users Manage Assay Collections Change Password Generate Reports Preferences 2 In the Study Management window a Select the study for which you want to reassign genotypes b Click gt Re genotype multiplates in selected study uu Study Management Name Date Created Sample Set Platform Assays Comments a 08 June Genotyping 06 16 2008 Generic Sample Set Plate Iu First test of the new instrument All 2007 Samples 06 16 2008 Generic Sample Set Plate Lymphoma Study 06 17 2008 Generic Sample Set Work done by Smith Lab C c Atthe
152. y Creation dialog box enter basic study information a In the Enter Study Name field enter a name for your study that is descriptive and easy to remember b From the Choose Platform drop down menu select Plate to indicate that you are using a 96 or 384 well reaction plate Note Choosing a platform is only for tracking purposes The platform selection does not affect data analysis c From the Choose Sample Set drop down menu select the appropriate sample set d In the Choose Target Populations pane select one or more populations Note Press Ctrl click or Shift click to select multiple populations Note The software calculates statistics for the selected populations The calculated statistics appear in the Statistics tab of the Analyze window For more information see Statistics tab on page 67 e Optional Enter any comments in the Comments field f Click Next Notes Applied Biosystems AutoCaller Software User Guide 113 w Appendix A Manage Sample Set Files Create a study using a sample set Study Creation Basic Study Info Basic Study Setup Enter Study Name lt 3a Choose Platform Plate iv 3b Choose Sample Set Feline Lymphoma Study v 3c Choose Target Populations Tabby Siamese Calico 3d Comments 3e 3f 4 Complete the Automation Settings dialog box a To edit a value for a criterion double click the Value cell then enter the desired valu
153. ystems AutoCaller Software database Also called a plate document The measure of cluster separation and cluster tightness A subset of data in the Applied Biosystems AutoCaller Software database that consists of a set of DNA samples run against a number of different TaqMan genotyping assays You can create multiple studies in the AutoCaller software database to organize your data based on projects and experiments An experiment in which you run new assays on known DNA samples in order to establish assay performance Applied Biosystems AutoCaller Software User Guide A adding an assay to an assay collection 50 comments to a study 20 comments to an assay 68 administrator user level definition 129 analysis status editing 76 Analyze window Assay Info tab 69 Assay Selection pane 60 Codes tab 68 Comments tab 68 Data Table pane 65 opening additional 71 Plot View pane 62 Statistics tab 67 Applied Biosystems contacting vii Technical Support vii assay and sample report contents 87 assay and well report contents 86 assay collection creating 48 deleting 50 editing 49 importing from text file 49 using as search criterion 58 assay comparison report contents 93 Assay Info tab contents 69 assay information editing 45 assay report contents 85 Assay Selection pane contents 60 assays deleting 47 deleting from a study 51 assumptions for using this guide v Auto Codes editing 75 table of 22 automation

Applied Biosystems AutoCaller™ Software User Guide (PN 4385543)

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Applied Biosystems AutoCaller&trade; Software User Guide (PN 4385543)

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Applied Biosystems AutoCaller™ Software User Guide (PN 4385543)