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GenomeStudio Genotyping Module User Guide

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1. B Allele Freq is set to NAN for loci included NOTE in the IntensityOnly category These are markers such as non polymorphic probes which do not provide genotypes or SNP markers showing unusual clustering patterns during the standard clustering process GenomeStudio Genotyping Module v1 0 User Guide 104 CHAPTER 7 Performing LOH and Copy Number Analysis Log R Ratio 5978266_A 6 F c D U 2 2 X a O 15 20 30 40 50 60 70 80 90 100110120130740150160170180190 Base Position Mb heterozygotes homozygotes Figure 84 Theta vs B Allele Frequency The Log R Ratio subcolumn is based on normalized intensity data In single sample analysis mode the Log R Ratio for a sample is the log base 2 ratio of the normalized R value for the SNP divided by the expected normalized R value For loci included in GenomeStudio statistics such as Call Rate the expected R value is computed by linear interpolation of the R value at the SNP s theta value for a sample relative to the R values of the surrounding clusters Part 11319113 Rev A Log R Ratio 105 Because no clusters are generated for loci in the Intensity Only category the Log R Ratio for these loci is adjusted so that the expected R value is based on the weighted mean of the cluster itself The Log R Ratio is displayed the same way for these loci as it is for loci included in GenomeStudio statistics in tools such as the IGV In paired sample analys
2. Today 1 25 2007 End Date Use End Date Sur Mon Tue Wed Thu Fri 3 od 3 4 E 7 8 9 10 11 12 14 15 16 17 18 13 21 22 23 24 EA 2 eg 29 30 31 1 2 Today 1 25 2007 Cancel Figure 16 Select Target Dates 11 Optional Select Use Start Date and choose a start date in the calendar on the left Figure 17 12 Optional Select Use End Date and choose an end date in the calendar on the right Figure 17 Part 11319113 Rev A la Select Target Dates Start Date W Use Start Date Sun Man Tue Wed Thu Fr Sat SB Bf gee FO o2 33 A 5 Bb 7 3 O 10 Ti 12 13 14 15 16 19 20 21 22 23 24 25 Jb 27 20 29 30 3 Choosing a Project Name and Location r End Date W Use End Date Sun Mor Tue Wed Thu Fr Sat 26 2 28 1 2 4 5 Ek 7 8 d 10 T 12 13 14 15 16 J3 zJ vel Ww 23 24 25 26 27 28 29 30 3 17 Today 3717 2006 Today 3 17 2006 s XCancel Figure 17 Selecting Target Dates 13 Click OK The manifests load the clusters are imported and the SNP statistics are calculated A heritability and reproducibility errors dialog appears Figure 18 2 Do you wish to update all heritability and reproducibility errors This operation may take some time Figure 18 Update Heritability amp Reproducibility Errors If you click Yes the Evaluating Heritability status bar appears Figure 19 and heritability and reproducibility are calculated Beadstud
3. G3 Mame Tests E3 Manifests a Data 4 Miscellaneous Figure 107 Project Window GenomeStudio Genotyping Module v1 0 User Guide 144 CHAPTER 8 User Interface Reference Log Window The Log window Figure 108 is a simple console providing wo Select Al la Copy Nd Save Ov MI Gd Q tmn Warnings J Info Log 11 2 2008 8 45 30 PM 11 2 2008 8 45 38 FM 11 2 2000 8 45 00 PM 11 2 2008 8 45 38 PM 11 2 2008 8 45 39 PM 11 2 2000 8 45 39 PM 11 2 2008 9 01 26 Figure 108 Table 18 Option Select All Copy Save Clear Grid Time Severity Message Source feedback on GenomeStudio processes The Log window displays errors in red Loading CpG kiwi Fen Loading MREASE Sorting gene aot anons fles Pring the Ace hangad Evert Firing he Genome loot inched ever Human Buld 35 1 Genome amp loaded Indo 38 Log Window Log Window Options Toolbar Button if used Function Selects all log entries Copies log entries to the clipboard eo e El Saves all log entries f Clears all log entries Toggles the grid on and off Displays the time the log entry was generated Displays the severity of the log entry Displays the text description of the log entry Displays the source of the log entry Part 11319113 Rev A Main Window Menus Main Window Menus 145 The following tables list the selection available from the GenomeStudio Genotyping Module s main window menu
4. 15759 0 7220 0 252 5 7686 0 01 MitoA1592 9020 15925 0 7038 0 259 4 4550 0 02 MitoA1616 9010 16163 0 6955 i 0 204 i 3 1160 0 04 MitoA1616 9038 16164 0 7220 0 204 2 3603 0 01 MitoA1738G 9066 1738 0 7161 0 204 6 0207 i 0 021 MitoA3349G 9031 3349 0 7038 0 254 6 6822 a 0 03 MitoA3481G 9034 3481 0 7038 0 198 4 6341 A 0 02 MitoA3548G 9054 3548 0 6423 i 0 223 5 4554 0 07 MitoA3721G 9025 3721 0 6955 B 0 238 5 9389 B 0 03 MitoA4025G 9057 4025 0 7038 0 262 7 3069 0 031 MitoA4105G 9011 4105 0 6379 i i 0 243 i 2 8216 0 90 MitoA4825G 9014 4825 0 7038 0 243 0 0375 4 1938 0 027 b Rows 561466 Disp 561466 Sel 1 Filter Filter is not active Figure 103 Full Data Table on C XQ BBN 2 3 3333 SS Sj S S 3 33333 23223233 3 3 5 The annotation columns of the Full Data Table are listed and described in Table 11 Table 11 Full Data Table Columns Visible by Column Description Type Default Index Row index of the SNP integer Y Name Name of the SNP string Y Address Bead type identifier integer Y Chr Chromosome of the SNP string Y GenomeStudio Genotyping Module v1 0 User Guide 128 CHAPTER 8 User Interface Reference Table 11 Full Data Table Columns continued Visible by Column Description Type Default Name of the manifest to Manifest which the SNP belongs S N Position C
5. 11319113 Rev A Detachable Docking Windows 141 The samples table also includes per manifest subcolumns The manifest name for example HumanHap300 appears above the subcolumn list in the Samples Table The subcolumns are described in Table 17 Table 17 Samples Table Per Manifest Subcolumns Visible by Column Description Type Default Barcode number of the Universal Array Sentrix ID Product to which this sample was string d hybridized Sentrix Position Section bundle on the product string Y Imaging Date Date on which the product was scanned string N Scanner ID ID of the scanner on which the product string N was scanned PMT Green Green PMT setting of the scanner on which SEE N the product was scanned 9 Red PMT setting of the scanner on which PMT ines the product was scanned E N Software Version of the BeadScan software used to en N Version scan the product I User name of the person logged into the Look PC on which the product was scanned un D p05 Grn 5th percentile of A allele intensity integer N p50 Grn 50th percentile of A allele intensity integer N p95 Grn 95th percentile of A allele intensity integer N p05 Red 5th percentile of B allele intensity integer N p50 Red 50th percentile of B allele intensity integer N p95 Red 95th percentile of B allele intensity integer N GenomeStudio Genotyping Module v1 0 User Guide 142 CHAPTER 8 User Interface Reference lable 17 Samples Table Per Manifest Subcolumns continued e Vis
6. Figure 3 License Agreement Click Yes to accept the software license agreement The GenomeStudio Framework and Genotyping Module are installed on your computer along with any additional GenomeStudio modules you selected Figure 4 Incense Agreement Praducts Available for Installation senomestudio Product Framework Genotyping Module Gene Expression Module Methylation Module Protein Analysis Module ANA Sequencing Module ChIP Sequencing Module DNA Sequencing Module 10229106 10829151 10 529166 1 0 4 29247 1 01 2818 User Guide 1 0 10 29203 1021 29193 101329222 Figure 4 Install Uninstalling GenomeStudio DNA Seq Module BSSBESEBE Software Copyright Notice Documentation Serial Number Software Illumina GenomeStudio 2008 jeer Guide c Illumina Inc 2003 2008 All rights reserved ser Guide Notice This software is protected by United States and intemational copyright laws and other intellectual and industrial property laws This software or any portion thereof may not be copied re distributed disclosed modified displayed dissembled reverse assembled re compiled reverse complied or otherwise reverse engineered sold or re sold in whole or in part without the prior written consent of Illumina Inc Unauthorized reproduction or distribution of this software or any portion of it may result in severe civil and criminal penalties User Guide User Guide User Guide User Guide T This
7. GenomeStudio Genotyping Module v1 0 User Guide An Integrated Platform for Data Visualization and Analysis FOR RESEARCH ONLY ooo e 000 ILLUMINA PROPRIETARY u m n a Part 11318815 o QO OQO Notice This publication and its contents are proprietary to Illumina Inc and are intended solely for the contractual use of its customers and for no other purpose than to operate the system described herein This publication and its contents shall not be used or distributed for any other purpose and or otherwise communicated disclosed or reproduced in any way whatsoever without the prior written consent of Illumina Inc For the proper operation of this system and or all parts thereof the instructions in this guide must be strictly and explicitly followed by experienced personnel All of the contents of this guide must be fully read and understood prior to operating the system or any parts thereof FAILURE TO COMPLETELY READ AND FULLY UNDERSTAND AND FOLLOW ALL OF THE CONTENTS OF THIS GUIDE PRIOR TO OPERATING THIS SYSTEM OR PARTS THEREOF MAY RESULT IN DAMAGE TO THE EQUIPMENT OR PARTS THEREOF AND INJURY TO ANY PERSONS OPERATING THE SAME Illumina Inc does not assume any liability arising out of the application or use of any products component parts or software described herein Illumina Inc further does not convey any license under its patent trademark copyright or common law rights nor the similar rights of others
8. Mismatch 229 U2 match expected O GE Mismatch ll42 U3 match expected Bl ct Mismatch 279 US match expected Bl cc Bismatch 1611 US match expected l Theta i PCR Uniformity High AT 21 GC control 1742 U2 match expected PB High GC 625 GC control 484 US match expected 0 40 0 60 0 80 1 Theta Gender Figure 43 Example GoldenGate Controls Dashboard Excluded samples are not displayed in the W NOTE Controls dashboard For further information about these controls please refer to the assay manual for your specific application Part 11319113 Rev A Exporting Controls Data 47 Exporting Controls Data You may want to view a controls data file if you are interested in the numerical details of the data shown in the controls dashboard To export controls data perform the following steps 1 In the controls dashboard select File Export Data Figure 44 BE Controls Export data Allele Specific Extension Page Setup Print Previews Print Close Figure 44 Exporting Controls Data The Save As dialog appears Figure 45 GenomeStudio Genotyping Module v1 0 User Guide 48 CHAPTER 3 Viewing Your Data Save As Save in 7 My Computer Qo F pe m My Recent 5 DVD CD RW Drive D Documents Desktop My Documents sr My Computer a My Network File name ControiD ashboard csv Places Save as type csv files csv z Figure 45 Saving the Controls Da
9. cond SAMI ROOL Unknown 5AMI Roo coos SAMI ROOL Unknown SAMI ROD1 cons SAMI RDDI Unknown SAMI ROD1 coor SAMI RDODI Unknown SAMI Roo CODE SAMI RDDI Unknown Roo cong wooo cJ Oo E oo Poe SAMI RDDZ Unknown Roo cond SAMI RDDZ Unknown Roo coos SAMI RDDZ Unknown Roo CODE SAMI RDDZ Unknown Roo COD m na Tan Ta BA a Rows 60 Disp 60 Sel 1 Filker Filker is not active m mm Figure 37 Displaying Marked Samples Part 11319113 Rev A Marking Samples 41 Displaying the Perform the following steps to display the legend in the Legend SNP Graph or Sample Graph 1 Right click in the graph The context menu appears Figure 38 Mark Selected Points k Clear Marks Fr Shaw Legend Figure 38 Displaying the Legend 2 Select Show Legend The legend appears and includes the name of your mark Figure 39 Figure 39 Legend Displaying Mark Name GenomeStudio Genotyping Module v1 0 User Guide 42 CHAPTER 3 Viewing Your Data Excluding Samples Some samples may be of poor quality in some regard e g they may not have hybridized well In this case you would not want to include them in your clustering GenomeStudio allows you to manually include or exclude samples To manually exclude samples perform the following steps 1 Inthe Samples Table or SNP Graph select the sample s you want to exclude Right click to bring up the context menu
10. recordType Identities each row of data in the file as calls or Score Call Each row of data in the file is for each DNA sample there will be two rows of data for each DNA sample one with A B or H call and another with the corresponding Gencall score for that call data Actual data calls or scores for each DNA sample and locus Part 11319113 Rev A Reproducibility and Heritability Report 95 Reproducibility and Heritability Report The Reproducibility and Heritability Report is the error output of the GenomeStudio Genotyping Module To generate a Reproducibility and Heritability Report 1 Select Analysis Reports Create Reproducibility and Heritability Report The Reproducibility and Heritability dialog appears Figure 81 Reproducibility and Heritability Report Save in G Sample5heets SE Lr E Ni My Recent Documents Deskto p My Documents Fr Mo Computer a a aj z aly al a ES al m Ai bly Aletwork File name estt Reproducibility and Heritability Report csv Save Save as type csv Files csv Cancel E Figure 81 Reproducibility and Heritability 2 n the File Name text box a default name appears for the report You can leave the name as it is or make changes 3 In the Save In dropdown menu at the top of the screen or to the left of the main window browse to the location where you would like to save the report 4 Click Save to
11. 98 Example Parent Child Heritability 99 Reproducilbility and Heritability Report P P C Heritability 99 Example Parent Parent Child Heritability 100 Errors Table COM No TP 125 Full Data Table Columns rn 127 Full Data Table Per Sample Subcolumns 128 SNP Table Commins oe pissssresad aitat edet dieit ay m E du 130 Paired Sample Table Columns 0 135 Paired Sample Table Per Pair Subcolumns 135 Samples Table Columns au ca dra cie bd Aare 137 Samples Table Per Manifest Subcolumns 141 Log Window ODTONS eee sps e Ear suria siti ape dees ae 144 File Menu Functions e s ua Seu ae essen 145 Edit Menu F netions ei ig Geena gre are sue mr RR ETE 147 View Men FUNCTIONS s saa sa anna arena YNG 147 Analysis Menu Functions x 4424020004 4449 IS ems 148 Tools Menu PINO naasa ama AG risponde de eee esos 150 Windows Menu Functions leen 150 Help Menu Functions s xoa miembro En Suh ended 150 Graph Window Toolbar Buttons amp Functions 151 Table Windows Toolbar Buttons amp Functions 153 Graph Window Context Menu 2 222222 000 ee eee 155 Full Data Table Context Menu 0 0a 156 SNP Table Context Mens s acci 0s Eraser 156 Samples Table Context Menu 0000 eee 157 GenomeStudio Genotyping Module v1 0 User Guide xvi List of Tables Table 32 Error Table Context Menu 0 cee
12. MitoA1310 1513271006 E 0 0763 18 MitoA1326 15135271004 A 0 2985 18 MitoA1378 15139271004 A 0 3199 20 MitoA1423 1513271004 A 3273 24 Mita amp lad58 15135271004 A 0 3156 22 MitoA1521 15139271004 A 0 2571 23 MitoA1524 1513271004 A 0 2741 24 Mita amp 1530 15139271004 5 0 2446 25 MitaA1575 1513271004 A 0 307 26 MitoA1592 1513271004 A 0 2904 27 MitaA1616 1513271004 A 0 2931 28 MitoA1616 1513271004 A 0 307 29 Mita amp 1738 15139271004 A 0 3015 30 Mita A3349 15135271004 A 0 2904 31 MitoAS481 1513271004 A 2804 32 Mita amp 3548 1513271004 A 24 33 Mita amp 3721 1513271004 A 2831 34 Mita A4025 1513271004 A 0 2904 35 MitoA4105 15135271006 5 0 2367 36 MitaA4825 15135271004 A 0 2904 37 MitoA4918 1513271004 A 0 3015 38 MitaA5391 1513271004 A 0 2931 38 MitaA5657 15139271004 A 0 2931 AH lit AS Figure 71 i LL ALL Sample Final Report GenomeStudio Genotyping Module v1 0 User Guide 82 CHAPTER 6 Generating Reports DNA Report The DNA Report is a comma delimited text file csv file that includes the columns described in Table 1 To generate a DNA Report 1 Run the Report Wizard by selecting Analysis Reports Report Wizard The Report Type dialog appears 2 Select DNA Report Figure 72 Genotyping Report a 2 P i What type of report would you like to generate U m n a Final Report Locus Summary o
13. Options Projects 2 Click Restore Defaults 3 Click OK The default cluster and plot colors are restored SNP Graph Error Display In the SNP Graph if there are any P C parent child or P P C parent parent child errors in your data the child appears as an X and the parent appears as an O Samples with reproducibility errors appear in the SNP Graph as squares Figure 29 rss006008 rs 1397354 040 0 60 040 06 Norm Theta Norm Theta Figure 29 P C Error Left Reproducibility Error Right If you click an error entry in the Errors table the associated samples are highlighted in yellow in the SNP Graph Figure 30 GenomeStudio Genotyping Module v1 0 User Guide CHAPTER 3 Viewing Your Data 0 40 0 60 Norm Theta Norm Theta Figure 30 P C Error and Reproducibility Error Highlighted in SNP Graph re3006008 rs1397354 0 40 0 60 Cartesian and Polar Coordinates You can view the SNP Graph in either polar or Cartesian coordinates Figure 31 Cartesian coordinates use the X axis to represent the intensity of the A allele and the Y axis to represent the intensity of the B allele Polar coordinates use the X axis to represent normalized theta the angle deviation from pure A signal where 0 represents pure A signal and 1 0 represents pure B signal and the Y axis to represent the distance of the point to the origin The Manhattan distance A B is used rather than the Euclidian distance sqrt
14. default selections when creating subsequent Final Reports 7 Click Next The Destination dialog appears Figure 69 Genotyping Report sao Where would you like to save your report U m n a Output Path c TestData Repository Projects GT Tests Browse Report Name Tests Finalkeport Cancel lt Back Hest gt Finish Figure 69 Destination 8 Click Finish GenomeStudio Genotyping Module v1 0 User Guide 80 CHAPTER 6 Generating Reports The progress bar alerts you to the status of your report Figure 70 8 GenomeStudio Progress Status Processing sample 1 Cancel Figure 70 Report Progress Your report is saved in the location you specified Part 11319113 Rev A Final Report 81 EJ Microsoft Excel Test5 FinalReport txt File Edit View Insert Format Tools Data Window H IGHASGB TR NN BA S amp Snagit Ej Window B T yd share As Application ge WebEx Settings S Al r Header A a Se a ae 1 Header 2 BSGT Ver 1 0 8 Frocessin AA 4 Content HumanHapS55lN3 A bpm 5 Num SNP 561466 B Total SNP 561466 7 Num Sam b 8 Total Sarny 5 9 Data SNP Name Sample ID Allele1 Tc amp llele Ti GC Score 11 MitoA1004 1513271004 A 0 3107 12 MitaA1055 1513271004 A 0 2904 13 MitoA1125 1513271004 A 0 2904 14 MitoA1146 1513271004 A 0 307 15 MitaA1181 1513271004 A 0 2931 16 MitoA1230 15139271004 A 0 3015 17
15. or if your data tables have been filtered you may be presented with additional dialogs which allow you to filter the resulting report data A Final Report is a report that contains the allele calls of your samples To generate a Final Report 1 Run the Report Wizard by selecting Analysis Reports Report Wizard The Report Type dialog appears Figure 63 Part 11319113 Rev A Final Report 73 2232 oa 9 Genotyping Report E What type of report would you like bo generate lu m na 2 38 aad Figure 63 Report Type Final Report is selected by default 2 Click Next The Included Samples dialog appears Figure 64 GenomeStudio Genotyping Module v1 0 User Guide 74 CHAPTER 6 Generating Reports aoa aoa eo Genotyping Report Which samples would you like to include in your report lu m na Samples Visible in Khe samples Cable remove Fi bere samples Figure 64 Included Samples 3 Select the samples you would like to include in this Final Report 4 Click Next The Final Report Format dialog appears Figure 65 Part 11319113 Rev A Final Report 75 Report Wizard Final Report Format Genotyping Report mug u How would you like bo Format your Final report U m n a Standard Matrix 3rd Party Standard Format Options Displayed Fields Available Fields SNP Name Sample Name P Sample ID Sample Group 4llele1 Top Hide gt Sample Index Alleles
16. 3 Select Exclude Selected Samples Figure 40 Samples Table 2 amp Ba di d Hara BQ v Sample ID POS arn p50 Grn p35 Grn p05 10365 4lia 13970 43 13 82 43 14474 4 BEC ET 305 317 311 alz Exclude Selected Samples Include Selected Samples 2955 4205 4210 4410 Recalculate Statistics for Selected Samples Recalculate Statistics for All Samples Estimate Gender for Selected Samples Display Image Set Aux Value Figure 40 Excluding Selected Sample The sample s you selected are excluded from your sample group You can use the SNP Graph to evaluate sample quality If you click on a sample in the samples table all of the SNPs for that sample are plotted in the SNP Graph Part 11319113 Rev A Plotting Excluded Samples 43 Plotting Excluded Samples If you have excluded one or more samples from your sample group you may still want to plot them in the genoplot To plot excluded samples in the genoplot 1 Select Tools Options Project The Project Properties dialog appears Figure 41 Project Properties No call Threshold Options 0 1500 E Plot excluded samples Colors AA r3 Red AB um Purple Plot Background III white BE mm Blue Plot Foreground am Black Selected C elow Female Y 5NP3 participating in SNP Statistics Exclude Female Y 5NP3 from SNP Statistics This option will use the sample s gender and the SMF Chr columns t
17. 49 Analysis Cluster all SNPs 2 0 ee 52 Clustering POE rs ccs en ed or EO et eee amps ares 53 Reviewing Clusters aurcs ade tue RR PEG RAE NA rk 54 ECG e NCC a samea Heute ie Ba a ean seas eae ane genome 56 Export Cluster Positions Selected 57 Save Cluster Positions llle 58 Importing Phenotype Information l l 61 Phenotype Information File 0 0 ee eee eee 61 Selected Samples 2 eee ee eee 62 Samples Table Context Menu 00 000 63 Populating the Gender Column 000 022s e ee 63 Selected Samples 0a 64 Samples Table Context Menu 000 lalala 65 Sample Properties ode necu os ceases diese One ow eee ese 66 SNP Graph Showing Paired Samples 67 Select Column Plug In Form uns ae iaceat cioe m po weist 70 REPON TYPO saco dde rer erari dd SA IS Odio pad det dre ie d 73 Included Samples 0 0 0 eee eee eee 74 Final Report Format i206 roe des deed rer POE Io Benes 75 Final Report Standard Format Options 76 Final Report Matrix Format Options 77 Final Report 3rd Party Options 0 00 78 BEA si e raea a een e oe ae pe ae a i a e 79 IR DON T ROCIIGS a Re GA een A AEE aan a 80 Sample Final Report eee eee ee eee 81 Part 11319113 Rev A Figure 72 Figure 73 Figure 4 Figure 5 Figure 6 Figure Figure 78 Figure 79 Figure 80
18. Chromosomes for Analysis 118 Autobookmark Analysis liliis 118 Analysis is Complete 0 00 eee eee 119 Select Column Plug In FOE s ui aeg bbb eine eee ae 120 GenomeStudio Genotyping Module Default View 122 SNP OPR AY 123 Sample Graph es escacs ami sewa apia a aa ne a og 124 EITOIS Table ne a BADA ae ave heed Inda aire s Rae 124 SNP Graph Alt sausai a ag Geers peed eo a S m 126 Fal Data Waele ere en san ae hae een es 127 NPETE a a are ee AA 130 Paired Sample T3Dbl6x a 435 oui trd e y hi su Yu Rae d ird 134 Samples T3lbl8asssscea un ore aod dba ee dolia ds oe de dea 137 Project NON Pr 143 Log ee AA AA 144 Sample Sheet Example a 165 GenomeStudio Genotyping Module v1 0 User Guide xiii Table 1 Table 2 Table 3 Table 4 Table 5 Table 6 Table 7 Table 8 Table 9 Table 10 Table 11 Table 12 Table 13 Table 14 Table 15 Table 16 Table 17 Table 18 Table 19 Table 20 Table 21 Table 22 Table 23 Table 24 Table 25 Table 26 Table 27 Table 28 Table 29 Table 30 Table 31 List of Tables DNA Report Column Descriptions 84 Locus Summary Report Column Descriptions 88 Locus x DNA Report Column Descriptions 94 Reproducibility and Heritability Report Duplicate Mense o P Meee on oe Vee ens 97 Example Duplicate Reproducibility 98 Reproducilbility and Heritability Report P C Heritability
19. Database Show Only Selected Rows Configure Marks Mark Selected Rows Select Marked Rows I H_H_iiHH___ Figure 59 Samples Table Context Menu 4 Select Sample Properties The Sample Properties window appears Figure 60 GenomeStudio Genotyping Module v1 0 User Guide 66 CHAPTER 5 Analyzing Your Data Sample Properties ImageRepository SampleGroup SampleN ame SamplePlate Samplewell EJ Phenotypic Data Age BloodPressure_Diastolic BloodPressure_Systolic BloodT ype Unknown Ethnicity Gender Unknown Height PhenotypeNegl PhenotypeNeg2 Misc Figure 60 Sample Properties 5 Click in the right hand column of any properties you want to edit and type new values 6 Click OK The updated column properties are displayed in the Samples table Image Viewer edit the Image Repository x To change the path to images displayed in the NOTE property Analyzing Paired Samples Paired sample data can be useful for analyzing chromosomal aberrations GenomeStudio includes a Paired Sample Table with columns that show the differences in various statistical measures between a pair of samples a subject sample and a reference sample Paired samples can be created in two ways Part 11319113 Rev A Analyzing Paired Samples 67 by designating subject and reference pairs in the sample sheet used to create a project by designating subject and reference samples using the paired samples editor Once
20. Figure 81 Figure 82 Figure 83 Figure 84 Figure 85 Figure 86 Figure 87 Figure 88 Figure 89 Figure 90 Figure 91 Figure 92 Figure 93 Figure 94 Figure 95 Figure 96 Figure 97 Figure 98 Figure 99 Figure 100 Figure 101 Figure 102 Figure 103 Figure 104 Figure 105 Figure 106 Figure 107 Figure 108 Figure 109 List of Figures DNA Report Selected occas eda p eed eee ie eode a o bn do 82 LEGION ote near ten ooh eo ee Ja S 1T 83 Sample DNA Report 84 Locus Summary Report Selected 86 Destination Locus SUmmary nennen 87 Sample Locus Summary Report 000005 88 Locus x DNA Selected nennen dma Mad a KAKANAN NA 91 Destination Locus x DNA 0 0 00 eee eee 92 Sample Locus x DNA Report 0 0022 eee 93 Reproducibility and Heritability llle 95 View Reproducibility and Heritability 96 Sample Reproducibility and Heritability Report 96 Theta vs B Allele Frequency 104 LOG KR dc PP P PUTEM 106 SAN SiS rae cae pees qned aen ete a ee gef eap Go 107 CNV Region Display a 110 Display CNV Analysis 65444200 debes tani ba eec enema 111 Illumina Genome Viewer llle 113 Favorite Data Plots Selected 020 020s 114 lo ago ne Go a en eee eee ee eae ees 115 Autobookmark Analysis llli 116 Selecting Samples for Analysis 117 Selecting
21. If you want to select a project from LIMS continue to Selecting a Project From LIMS Ifyou want to load sample intensities outside of LIMS perform the following steps a Type a name for your project in the Project Name text box b Click Next to advance to the Loading Sample Intensities dialog c Continue to Loading Sample Intensities Outside of LIMS on page 19 Part 11319113 Rev A Choosing a Project Name and Location 13 Selecting a To select a project from LIMS Project From 1 Inthe GenomeStudio Project Wizard Project Location LIMS dialog Figure 10 choose Select from LIMS 2 The GenomeStudio Project Wizard Select LIMS Project dialog appears Figure 11 GenomeStudio Project Wizard Select LIMS Project Genotyping Project a a a 3 Please Select a LIMS Project U m n a Institute G Login Investigator Project x Optional Script File Browse Gen Call Threshold 0 15 Cancel lt Back Het gt Finish Figure 11 Select LIMS Project 3 Click Login to access the Login Infinium LIMS dialog 4 Select the Setup tab Figure 12 GenomeStudio Genotyping Module v1 0 User Guide 14 CHAPTER 2 Creating a New Project GM Login Infinium IMS Login Setup id worstation 000 gogo Enter URL and Por Figure 12 Login Infinium LIMS Setup 5 Inthe Setup tab enter the following e URL e Port Number 6 Select the Login tab Figure 13
22. Line Plot Displays a line plot of the table data Scatter Plot Displays a scatter plot of the table data Histogram Displays a histogram of the table data GenomeStudio Genotyping Module v1 0 User Guide 154 CHAPTER 8 User Interface Reference Table 27 Table Windows Toolbar Buttons amp Functions continued Toolbar Button Function s Box Plot Displays a box plot of the table data Frequency Plot Displays a frequency plot of the table data Pie Chart Displays a pie chart of the table data Heat Map Full Data Table only Allows you to generate a new heat map or open an existing heat map New subcolumn Allows you to create a new subcolumn Column Chooser Displays the Column Chooser dialog box Filter Rows Displays the Filter Table Rows dialog box Clear Filter Removes the filter e 4 fj le m le E 5 Part 11319113 Rev A Context Menus Context Menus 155 The tables in this section describe context menu selections for the GenomeStudio Genotyping Module Table 28 describes graph window context menu selections Table 28 Selection Define AA cluster using selected SNP Define AB cluster using selected SNP Define BB cluster using selected SNP Cluster this SNP Cluster this SNP Excluding Selected Samples Configure Mark Mark Selected Points lt Add New gt Clear Marks lt All gt Exclude Selected Samples Include Selected Samples Show Legend Show Exclud
23. Name Coraci 5 P P Bertabiliby F req 22 Sample 5 Saeripls_ b Sample 7 4273 23 Sampla B Sample 8 Sample 10 4260 0 9035 24 Sampa 11 Sampa 12 Zampla 13 4254 1 ora 25 Sample 14 Sample 15 Sample 16 4256 f 0 3339 25 Figure 83 Sample Reproducibility and Heritability Report Click No if you do not want to view the Reproducibility and Heritability Report The Reproducibility and Heritability Report is saved at the location you specified but it does not display You can return to it later Part 11319113 Rev A Column Descriptions and Examples Reproducibility and Heritability Report 2 The following sections include Reproducibility Report column descriptions and examples of the three main report sections Duplicate Reproducibility Parent Child Heritability gt Parent Parent Child Heritability Duplicate Reproducibility Columns Table 4 describes the columns of the Duplicate Reproducibility section of the Reproducibility and Heritability Report Table 4 Reproducibility and Heritability Report Duplicate Reproducibility Column Rep1 DNA Name Rep2 DNA Name Correct Errors Total Repro Freq Description Name of the sample designated as replicate 1 Name of the sample designated as replicate 2 Number of loci with consistent replicate genotype comparisons Number of loci with inconsistent replicate genotype comparisons Number of total genotype comparisons one genotype comparison pe
24. O O oo0o0o000000000000o0o000o0o000 Ofm 100 0 000 0000 000 0 0 000 0 00 07 om T a zd 0 2904 0 2904 The SNP Table columns are listed and described in Table 13 Table 13 SNP Table Columns Visible by Column Description Type Default Index Row index of the SNP integer bi Name Name of the SNP string Y Manifest Manifest from which this SNP was loaded string N Chr Chromosome of the SNP string b Position Chromosomal position of the SNP integer N Address Bead type identifier for this SNP integer Y GenTrain Score Measure of the cluster quality for the SNP float Y Part 11319113 Rev A Table 13 Column Orig Score Edited Cluster Sep ChiTest 100 Het Excess AA Freq AB Freq BB Freq Call Freq Minor Freq Aux Rep Errors P C Errors SNP Table Columns continued Description Original unedited GenTrain Score for SNP Flag indicating whether the SNP was edited after initial clustering positions were identified 1 gt edited 02 unedited Measure of the cluster separation for the SNP that ranges between O and 1 Normalized a p value calculated using genotype frequency The value is calculated with 1 degree of freedom and normalized to 100 individuals Measure of the excess of heterozygotes for the SNP based on Hardy Weinberg Equilibrium O indicates no excess of heterozygotes Negative values indicate a deficiency of heterozygotes Frequency of AA calls Frequency of AB c
25. Re BRIT B Paren Repository EWestDatalRopasitary SamploData1GoldenGatolLinkageDataUngensityData E TestDstaRepository SampleData GoldenGale LinksgeDstslntensityData E TestData Repository SampleData GoldenGate LinkageDatamensityData E TestData Ropasitory SampleData GoldenGate inkageDatauntensityData EM estData Repository SampleDotaVGoldenGateVinkageDatauntensi yData E TestData Repository SampleData GoldenGate LinkageData ntensityData E TestDataiRepository SampleDataiGoldanGatell inkageDatalntensityData E N estData Repository SampleDataVGoldenGateW mkageDatauntensi yData E TestData Repository SampleData GoldenGatellinkageDatalintensityData E WestData Repository SampleDataiGoldanGate inkageDatalintonsityData E TestOata Repository SampleData GoldenGateLinkageDalalintonsityData EATestData Repository SampleDatavGoldenGateV inkageDatauntensityData E ATestDataRepositoryGampleDatalGoldenGatelLinkageDatauntensityData E NTestDataRepositoryXSampleDatavGoldenGateV inkageDatauntensityData E TestDats Repository SampleData GoldenGate LinkageDatauntensityData E TestData Repository SampleData GoldenGate LinkageDatalniensityData E TestOata Repository SampleData GoldenGate LinkageDatalintonsityData E MT estDstaRepositoryVGampleDatavGoldenGateVinkageDatauntensit y Data E WestData Repository SampleData GoldenGate LinkageDataimensityData E TestDatalRopository SampleData GoldonGato LinkageDatauingensityData E NestDats R
26. Repository is the directory that contains your SNP manifests This directory is necessary because the name s of the SNP manifest is contained in the sample sheet and the GenomeStudio Genotyping Module needs to know where to find it Part 11319113 Rev A Loading Sample Intensities Outside of LIMS 21 To select a sample sheet data repository and manifest repository 1 Browse to the locations of your sample sheet data repository and manifest repository 2 Click Next The Cluster Positions dialog appears Figure 23 GenomeStudio Project Wizard Cluster Positions Genotyping Project 229 a IF vou have an existing cluster File that you want En import U m n cluster positions From enter it here Otherwise you can cluster the samples you ve selected to determine cluster positions Import cluster positions From a cluster File Gluster File c TestData Repository GT S50K Manifest BDCHP 1X10 HUMANHAPS Browze Project Settings Options A a Project Creation 4ctians Pre Calculate Cluster SMPs Pre Calculate should only be 17 calculate Sample and SNP Statistics used For memory based projects y pa calculate Heritability This option will improve speed but requires 4 5 more memory Gen Call Threshold 0 15 Optional Script File Browse Cancel lt Back Het gt Finish Figure 23 Cluster Positions The number of samples that can be loaded into physical
27. Sample Properties dialog from which you can change values for sample data such as sample group sample name gender and phenotype properties or change the path to associated image files Allows you to upload selected samples to the Illumina Controls Database 158 CHAPTER 8 User Interface Reference Table 31 Samples Table Context Menu continued Selection Description Update Project from LIMS Updates the current project with the most recent information available in the LIMS database Send Requeue to LIMS Sends LIMS Actions Contains a subset of information about a requeued sample to actions related to LIMS The LIMS Actions the IMS database q P menu option and its related suboptions are only available if you are logged into LIMS Set to Needs Requeue Adds a note in the Requeue Status column for a sample that this sample needs to be requeued Clear Requeue Clears the requeue note in the Requeue Status column for a sample Show Only Selected Rows Shows only selected rows in the Samples Table Configure Marks Configures marks Creates a new mark and marks Mark Selected Rows Add New rn Select Marked Rows Selects marked rows Clear Marks lt All gt Clears all marks Part 11319113 Rev A Context Menus 159 Table 32 describes Error Table context menu selections Table 32 Error Table Context Menu Selection Show Only Selected Rows Edit Replicates Edit Parental Relationships Configure Mar
28. The GenomeStudio application suite unzips Figure 1 GenomeStudio 2008 1 HEENNEENEEE Figure 1 GenomeStudio Application Suite Unzipping Part 11319113 Rev A Installing the Genotyping Module 3 The Illumina GenomeStudio Installation dialog box appears Figure 2 amp Illumina GenomeStudio Installation s 3 Exit Install Selected Products Modules Products Available for Installation Software Copyright Notice Software Illumina GenomeStudio 2008 c Illumina Inc 2003 2008 All rights reserved Framework 1 0 2 23106 User Guide are Notice This software is protected by United States and 10825151 User Guide international copyright laws and other intellectual and industrial property laws This software or any portion thereof 1 05 29166 User Guide may not be copied re distributed disclosed modified displayed dissembled reverse assembled re compiled Genotyping Module Gene Expression Module F F F Meteo Mode T 1042327 amd ee oe E Illumina Inc Unauthorized reproduction or distribution of this v 1 01 23173 User Guide a 5 Sy paan of it may result in severe civil and IV Iz I Protein Analysis Module RNA Sequencing Module DIU prec Gne This Software is licensed for use under an End User err AMA Software License amp greement CHIP Sequencing Module 0 21 29193 User Guide ILLUMINA END USER SOFTWARE LICENSE 1 0 13 29222 User Guide AGREEMENT DNA Sequencing Module IMPO
29. Top SMP Index GC Score z Show SNP Aux Allele1 Forward Allelez Forward Allele1 Design Eis U Group by f sample SNP General Options Favorite Formats Total Rows 3368796 Tab Comma Default zl Estimated 50 3 MB Create map Files Save Current A Samples File Estimated File 80 3 MB 6 Size Cancel lt Back Next gt Finish Figure 65 Final Report Format 5 Select a format for your Final Report Standard In Standard format all data are presented in rows in the Final Report You can choose the fields that will be included in a standard Final Report See Final Report Standard Format on page 76 Matrix In Matrix format rows represent SNPs and columns represent samples You can choose to include the GenCall score or just output the genotypes See Final Report Matrix Format on page 77 3rd Party In 3rd Party format you can specify the desired output style of the Final Report based on the target application for downstream analyses See Final Report 3rd Party Options on page 78 GenomeStudio Genotyping Module v1 0 User Guide 76 CHAPTER 6 Generating Reports Final Report Standard Format Genotyping Report How would you like to Format your Final report Standard C Matrix Standard Format Options Displayed Fields SMP Mame Sample ID Allele 1 Top Allele Top GC Score Hide Show Group by sample Favorite Formats
30. a lasso to select samples in the graph window Zoom mode Toggle this button on to zoom in or out in the graph window When toggled on the cursor changes to a allowing you to zoom in to the graph Pressing the Ctrl key on voli keyboard while in this mode allows you to zoom out Automatically scale X axis Automatically scales the X axis for the currently displayed graph only Automatically scale Y axis Automatically scales the Y axis for the currently displayed graph only s 8 Part 11319113 Rev A Table Windows Toolbar 153 Table Windows Toolbar Table 27 lists and describes GenomeStudio s Genotyping Module Table Windows toolbar buttons and their functions Table 27 Table Windows Toolbar Buttons amp Functions Toolbar Button B je El Function s Calculate Samples Table only Calculates all samples This button only appears if there are samples that need to be calculated Select all Rows Highlights all the rows in the table Copy to Clipboard Copies the selected columns or rows to the clipboard Export to File Exports the selected item s to a file Import Columns Imports sample data from a file you specify Sort Column Ascending Sorts columns in the sample table in ascending order Sort Column Descending Sorts columns in the sample table in descending order Sort by Column s Allows you to sort the sample table data by a column or columns you select
31. area is defined by the GenCall Score cutoff Select T Shade Call Regions in the graph window toolbar to apply color to the genoplot calling regions in the graph window These shaded regions correspond to the no call threshold GenomeStudio Genotyping Module v1 0 User Guide 32 CHAPTER 3 Viewing Your Data To set a lower threshold for valid calls within GenomeStudio pertorm the following steps 1 Select Tools Options Project 2 Inthe No Call Threshold area select a lower limit for valid calls within GenomeStudio Illumina recommends that you use a GenCall w NOTE Score cutoff of 0 15 for Infinium products and l 0 25 for GoldenGate products By default samples lying within the dark red region are called AA samples lying within the dark purple region are called AB and samples lying within the dark blue region are called BB Figure 28 Figure 28 Shaded Call Regions E Shading of clusters is toggled off by default Ww NOTE and is available for the polar graph only To change the colors for cluster calls Part 11319113 Rev A SNP Graph Error Display 33 1 Goto Tools Options Projects 2 In the Colors area use the dropdown menus to change the default colors for the AA AB and BB genotypes as well as for selected samples plot foreground and plot background 3 Click OK The clusters display with the assigned colors To restore default colors to clusters and plot properties 1 Goto Tools
32. information about the CNV Region Display see Viewing the CNV Analysis Region Display on page 109 7 Inthe CNV Analysis dialog click OK The CNV Analysis dialog closes Part 11319113 Rev A Selecting the Active CNV Analysis Deleting a CNV Analysis Viewing the CNV Analysis Region Display CNV Analysis 109 To select the active CNV Analysis 1 In the Current CNV Analyses area of the CNV Analysis dialog select the CNV analysis you want to make active 2 Click OK The analysis you selected is now active The active CNV analysis is the analysis used in the CNV Region Display and in the Full Data Table To delete a CNV analysis Inthe CNV Analysis dialog right click on the analysis you want to delete and select Remove Analysis The analysis you selected is deleted from the list of available CNV analyses The CNV Analysis Region Display is a heat map that shows copy number values for all samples across the genome Samples are displayed on the X axis and chromosomal position is displayed on the Y axis To view the CNV Analysis Region Display 1 In the GenomeStudio main window select Analysis Show CNV Region Display The CNV Analysis Region Display appears Figure 87 GenomeStudio Genotyping Module v1 0 User Guide 110 CHAPTER 7 Performing LOH and Copy Number Analysis CN Region Display Lu m in 4 a 3 m A chro chr chr8 chr9 chr10 1674M chr11 1510M Samp
33. save the report GenomeStudio Genotyping Module v1 0 User Guide 96 CHAPTER 6 Generating Reports The View Reproducibility and Heritability Report dialog box appears Figure 82 Would you like ko view this Reproducibility and Heritability Report Yes Figure 82 View Reproducibility and Heritability 5 Doone of the following Click Yes to view the Reproducibility and Heritability Report The Reproducibility and Heritability Report appears Figure 83 E3 r crosnft Excel Demo _Repeoducibility_Merdtability Feportide GH Be Cdt bew Insert Format Took Data Window Hep AdobePDF Jug diutT454nunA 752 c r N ugws o ae dip Sri psy window or on Bu A x dg 1 Reproducibility and Hentability Report 2 Feenarne WReproducibility and Herilabilay Fori cav 3 Run date Tuesday klarch 20 2006 BE AM oO FLO 3T A ONAS 100 ProjectName Report GenCall Version 7 amp 3 0 Low GenCall Score Cutoff 0 2500 MiA B Duplicate Raproducibhillny 7 Repi DMA Marne Rep DMA Marne Correct amp Errars Hepra Fre B Sample 1 Sample 1 R ama n 1 Sampla Sampba LEE F 314 gr EO pla 4 5 pa s HB 4104 SEM O 9755 10 Sample 3 Sample 3 R 2283 1 Sample 4 FH 4311 ri n sean 14 P C Haritability I5 Parent DMA Name Chad OMA Mare H Carnet Errors Pot HesiLabilily Freq ri pee 16 Sample 1 Sample 2 4232 O SEA 17 Sample 3 Supe 4 4311 1 18 TH 20 P P Heritability 20 Pami DHA Name Parent OMA Mame Child DIA
34. you designate paired samples the pairs appear in the Paired Sample Table When paired sample data are loaded in the Paired Sample Table certain features are enabled These include the following Analysis Calculate Paired Sample LOH CN Scores In the SNP Graph graphical elements indicate which samples are paired Figure 61 shows an aqua line designating a paired sample subject and reference SNP Graph CN EESE AIR s t re 100064178 0 40 0 60 Marm Theta Figure 61 SNP Graph Showing Paired Samples In the IGV paired sample data becomes available for plotting and autobookmarking GenomeStudio Genotyping Module v1 0 User Guide 68 CHAPTER 5 Analyzing Your Data Using Concordance Features Exporting Allele Calls Importing Allele Calls Use the concordance features described in the following sections to compare data from different projects If you want to compare the allele calls in your current project to allele calls in another project you can export the allele calls from your current project and import them into other projects Y To export allele calls and import them into NOTE another project the sample names in each project must be the same Allele calls for sample names that do not match will not be compared To export allele calls from your current project 1 Select Analysis Export Allele Calls The Export Allele Calls dialog appears Browse to the directory wher
35. 00000000 DTOITDTITDTITDTIODTODTODTTWTTTTTDTTDTTT O TI Ern ues Ron rS SS RS S PONG ET ES LO DENN E PIS RS EP US RS x ses xd x e e eel Ln ioa don n aon a 2c cocococcoooccociucoccooccococococococoocococ POOO dd DD odd Slslalsl lslalwisl lslalslamlolsiolols igure 77 Sample Locus Summary Report Column The Locus Summary Report includes the columns described in Descriptions Table 2 Table 2 Locus Summary Report Column Descriptions Column Description Row Row number Locus_Name Locus name from the Manifest IllumiCode Name No Calls it Calls Locus ID from the Manifest Number of samples with GenCall score below the call region threshold Tools Options Flags Number of samples with GenCall score above the call region threshold Part 11319113 Rev A Locus Summary Report 89 Table 2 Locus Summary Report Column Descriptions Column Call_Freq A A_Freq A B_Freq B B Freq Minor Freq GenTrain Score 5096 GC Score 1096 GC Score Het Excess Freq ChiTest P100 Cluster Sep AA T Mean Description Call frequency or call rate calculated as follows Calls HNo_Calls Calls Frequency of homozygote allele A calls Frequency of heterozygote calls Frequency of homozygote allele B calls Frequency of the minor allele If the number of AA lt number of BB for a sample the frequency for the minor allele A for that sample is 2 AAs ABs for the sample divided by 2 AAs ABs BBs fo
36. 010 Apr 07 20C HumanHar 151327100 D calls 15132710C WGO00010 Apr 07 20C HumanHar 151327100 0 Score Call 0 2804 0 2904 15132710C WGO00010 Nov 27 200 HumanHar 151327100 D calls 151327 10C WGO00010 Nov 27 200 HumanHar 151327100 0 Score Call 0 2904 0 2904 15132710C WGO00010 Nov 27 200 HumanHar 151327100 0 calls 15132710C WGO00010 Nov 27 200 HumanHar 15132710C 0 Score Call 0 2804 0 2904 151327 10C WGO0010 Nov 27 200 HumanHar 151327100 0 calls 15132710C WGO00010 Nov 27 200 HumanHar 151327100 0 Score Call 0 2804 0 2904 15132710C WGO00010 Nov 27 200 HumanHar 151327100 D calls 15132710C WG00010 Nov 27 200 HumanHar 151327100 0 Score Call 0 2804 0 2904 35 Figure 80 Sample Locus x DNA Report GenomeStudio Genotyping Module v1 0 User Guide 94 CHAPTER 6 Generating Reports Column The Locus x DNA Report is a comma delimited text file csv file Descriptions that includes the columns described in Table 3 Table 3 Locus x DNA Report Column Descriptions Column Name Description instituteLabel Customer s unique sample ID for the DNA sample plateWell Concatenation of the Sample Plate and Sample Well imageDate Imaging date for that sample oligoPoolld Name of the OPA e g GS0001111 OPA bundleld Identifier of the bundle which includes the array barcode row column customer provided non unique sample name status Flag for whether or not these data came from the last run through Autogenopipe O last run 50 older runs
37. 26 lists GenomeStudio s Genotyping Module graph window toolbar buttons and their functions Table 26 Graph Window Toolbar Buttons amp Functions Toolbar Button Function s Polar coordinates Displays locus using polar coordinates Cartesian coordinates Displays locus using Cartesian coordinates Plot normalized values Allows you to toggle normalization on or off in the SNP Graph Make dots larger Makes each dot representing an individual locus appear larger on the screen Make dots smaller Makes each representing an individual locus appear smaller on the screen i le le ET UE Copy plot to clipboard Copies the current plot to the clipboard i Shade call regions Applies colored shading to each cluster Loci falling within the dark shaded region of each color are considered to be within the call range above the GenCall Score threshold Loci displayed within the light shaded region of each color are considered to be outside of the call range Default mode Toggle this button on to activate an arrow cursor that allows you to select samples in the graph window with a rectangle Pan mode Toggle this button on then drag the graph in the direction you want dll GenomeStudio Genotyping Module v1 0 User Guide 152 CHAPTER 8 User Interface Reference Table 26 Graph Window Toolbar Buttons amp Functions continued Toolbar Button Function s Lasso mode Toggle this button on to draw
38. 3 In the column plug ins table select a row from the list of available column plug ins Optional Type a new name for the subcolumn in the New Subcolumn Name text field Optional To edit any pre defined properties click in the right hand column of the Column Plug In Properties table and enter new values Click OK The new subcolumn is created and appears in the Full Data Table Part 11319113 Rev A 72 72 82 86 91 95 Chapter 6 Generating Reports Topics Introduction Final Report DNA Report Locus Summary Report Locus x DNA Report Reproducibility and Heritability Report GenomeStudio Genotyping Module v1 0 User Guide 72 CHAPTER 6 Generating Reports Introduction Final Report This chapter describes GenomeStudio Genotyping Module report types and how to generate each of these reports GenomeStudio includes a Report Wizard which streamlines the report creation process for the following report types Final Report DNA Report Locus Summary Report Locus x DNA Report In addition if report plug ins are available the name of the plug in report automatically appears at the bottom of the report type list in the Custom Report dropdown menu Figure 63 GenomeStudio also allows you to manually create a Reproducibility and Heritability Report The following sections describe the NG NOTE general process for creating reports If your data includes zeroed SNPs or excluded samples
39. 51327100 38487 522979 0 9315 0 3234 02877 0 3889 0 4672 0 4541 0 2477 2151327100 38497 522969 0 9314 0 3237 0 28656 0 3897 0 467 04541 0 2476 3151327100 38496 522970 0 9314 0 3234 0 2877 0 3889 04672 0 4541 0 2477 4151327100 38514 522952 10 9314 0 3237 0 2066 0 3897 0 467 04541 0 2476 5151327100 38496 522970 0 9314 0 3234 O2677 0 3889 O4672 0 4541 0 2477 6 151327100 36514 522952 08314 0 3237 0 2666 0 3897 0 467 04541 0 2476 Figure 4 Sample DNA Report Column The DNA Report includes the columns described in Table 1 Descriptions Table 1 DNA Report Column Descriptions Column Name Description Row Row number DNA_Name DNA name No Calls Number of loci with GenCall scores below the call region threshold Tools Options Flags Number of loci with GenCall score above the call region Calls threshold Call frequency or call rate calculated as follows Call_Freq Calls HNo_Calls Calls Part 11319113 Rev A DNA Report 85 Table 1 DNA Report Column Descriptions continued Column Name A A_Freq A B_Freq B B Freq Minor Freq 5096 GC Score 1096 GC Score 0 1 Description Frequency of homozygote allele A calls Frequency of heterozygote calls Frequency of homozygote allele B calls Frequency of the minor allele If the number of AA number of BB for a sample the frequency for the minor allele A for that sample is 2 AAs ABs for the sample divided by 2 AAs ABs BBs for the Sr acro
40. A A B B Select to display the plot in polar coordinates Select to display the plot in Cartesian coordinates Part 11319113 Rev A Normalization 35 mele Crach Ere SNP Graph alt x SAP Graph temple Cranh Errors Tabla SAE Graph Alt SIPI 550209 xh lal e p bo ixi 31000840 r1 Uus Hen nter zz Et 4b 666 Norm Theta Hara Inte mito A Figure 31 Polar Coordinates Left amp Cartesian Coordinates Right Normalization You can view the SNP Graph in either normalized or raw format Click 1 Normalization to turn normalization on or off Figure 32 shows a sample graph in polar coordinates with normalization turned off left and with normalization turned on right SNP Graph Sample Graph Errors Table SNP Graph Alt L x SNP Graph Sample Graph Errors Table SNP Graph Alt p M kike 83 B 809 2 9 m t B9b 1 o Ba BO O 1485978268 A 1485978269 A 8 7 6 5 4 3 2 1 0 4 Figure 32 Normalization Turned Off Left amp Normalization Turned On Right Adjusting Axes To zoom in and out on the graphs Click Zoom Mode In zoom mode you can GenomeStudio Genotyping Module v1 0 User Guide 36 CHAPTER 3 Viewing Your Data e Click the left mouse button to zoom in e Click the right mouse button to zoom out Alternatively using your mouse wheel you can e Roll up to zoom in e Roll down to zoom out To change an axis Position your cursor over an
41. C Rep a MitoA1004 MitoA1055 MitoA1125 MitoA1146 MitoA1181 MitoA1230 MitoA1310 Mito41326 MitoA1378 MitoA1423 MitoA1458 MitoA1521 MitoA1524 MitoA1530 MitoA1575 MitoA1592 Mito41616 Mito41616 MitoA1738G MitoA3349G MitoA3481G MitoA3548G MitoA3721G MitoA4025G MitoA4105G MitoA4825G Jz z S S13 3223323 223a aa aa aa aa aaa en E Dono 0 Er i 0000 0 0000 0 En s Dono 0 0000 0000 0 0000 000 0 0000 Im C 0 0000 0 0000 0 0000 1 0000 0 0000 0 0000 0 0000 1 0000 0 0000 0 0000 0 0000 1 0000 1 0000 0 0000 0 5000 1 0000 0 0000 0 0000 0 0000 1 0000 0 0000 0 0000 0 0000 1 0000 0 0000 0 0000 0 0000 1 0000 0 0000 B 0 0000 0 0000 0 5000 0 0000 1 0000 0 0000 0 0000 1 0000 0 0000 1 0000 0 0000 0 0000 1 0000 0 3333 0 5000 0 5000 0 0000 1 0000 0 0000 1 0000 0 0000 0 0000 1 0000 0 0000 1 0000 0 0000 0 0000 1 0000 0 0000 1 0000 0 0000 0 0000 1 0000 0 0000 1 0000 0 0000 0 0000 1 0000 0 0000 1 0000 0 0000 0 0000 1 0000 0 0000 1 0000 0 0000 0 0000 1 0000 0 0000 1 0000 0 0000 0 0000 1 0000 0 0000 1 0000 0 0000 0 0000 1 0000 0 0000 1 0000 0 0000 0 0000 1 0000 0 0000 1 0000 0 0000 0 0000 1 0000 0 0000 0 0000 0 0000 1 0000 1 0000 p 0000 1 0000 D 0000 D 0000 1 0000 o0000000000000000000000 Rows 561466 Disp 561466 Sel 1 Filter Filter is not active Figure 104 SNP Table o Cs PE AE me JE m JE mm ccc ccc ccc 02020200202000 i O
42. DNA Report Locus x DINA Cancel lt Back Next gt Finish Figure 7 2 DNA Report Selected 3 Click Next The Destination dialog appears Figure 73 Part 11319113 Rev A DNA Report 83 Genotyping Report soo Where would you like to save your report U m n a Output Path c TestDatalRepository Projects GT Test5 Browse Report Name Test5_DNAReport Cancel lt Back Hert gt Finish Figure 73 Destination 4 Browse to select an output path for your DNA Report A report name is generated by default You can give your DNA Report a different name by typing the name in the Report Name text field 6 Click Finish Your DNA Report Figure 74 is saved with the name and parameters you assigned to it in the location you specified GenomeStudio Genotyping Module v1 0 User Guide 84 CHAPTER 6 Generating Reports EJ Microsoft Excel Test5 DNAReport csv File Edit View Insert Format Tools Data Window Help Adobe PDF 0EUB3 5A FA aa FI A 4 ilios oJ ara amp Snagit Ej Window mug E Share As Application gt WebEx Settings E e E w fe DNA Report on C TestData Repository Projects GT Test5 Test5_DNAReport csy a 1 DNA Rep at on C TestData Repository Projects GT Testo TestS_DNAReport csv LOCI DNAs ProjectNar GenCall Y Low GenCall Score Cutoff 0 1500 DNA Nam No Calls Calls Call Rate WA Freq AB Freq B B Freq Minor Frec5096 GC 1096 GC 0 1 11
43. Default General Options Tab Comma Create map files Samples File 6 Save Current 292 illumina C 3rd Party Available Fields Sample Name P Sample Group Sample Index SNP Index SMP Aux Allele1 Forward Allele2 Forward Allelei Design HEN LI C SNP Total Rows 3368796 wr Estimated Size 80 3 MB Estimated File Size 30 3 MB Cancel Back Next gt Finish Figure 66 Final Report Standard Format Options a To select the fields included in your Final Report select one or more fields from the Available Fields list and click Show to add them to the Displayed Fields List b Choose whether you want to group by sample or by SNP c Continue to Step 6 Part 11319113 Rev A Final Report 77 Final Report Matrix Format Genotyping Report iw T How would vau like to Format your Final report U m n a C Standard Matrix C 3rd Party Matrix Format Options Use Top Strand v v include GencCall score General Options Favorite Formats Total Rows 561466 Tab Comma Defaut El Estimated 25 7 MB Create map Files Save Current a E Samples File Estimated File 25 7 MB 6 Size Cancel lt Back Next gt Finish Figure 67 Final Report Matrix Format Options a Inthe Use dropdown menu select one of the following options Top strand Forward strand Design strand AB b Ifyou want to inc
44. GenomeStudio Before you can create a new subcolumn you must first make column plug ins available to GenomeStudio To make column plug ins available to GenomeStudio do one of the following Ifthe column plug in has an install program Run the install program The column plug in is installed in the correct directory and is now available to GenomeStudio If the column plug in does not have an install program Copy the dll file for the column plug in to the following directory C Program Files lllumina GenomeStudioGenomeStudio Plugins The column plug in is now available to GenomeStudio To create a subcolumn based on a column plug in GenomeStudio Genotyping Module v1 0 User Guide 70 CHAPTER 5 Analyzing Your Data 1 Select Analysis Create Plug In Column The Select Column Plug In Form dialog appears Figure 62 Select Column Plugin x A new column can be created by selecting a CalumnPlugin and a new Column name Genome5 tudio will create the new column by passing the project data to the user designed algorithm and populating the column with the results A ColummPlugin is an algorithm written in CH using the ICalumnPlugin interface It allows the user ta customize calculated columns according to project specific data Details of generating a ColummPlugin can be found in the documentation New Subcolumn Name g Default Column Name Column Plugin Properties Figure 62 Select Column Plug In Form 2
45. Genotype of the reference sample string Y Genotype of the subject sample string Y Probability that there is loss of fias Y heterozygosity in a region of interest Estimate of the actual copy number at an individual locus ngat i Statistical confidence level between O and indicating whether or not a copy number change has occurred Values of fo Y N 1 indicate no copy number change Values of approximately O indicate copy number change The Samples Table Figure 106 contains information for each DNA sample loaded into GenomeStudio The Samples Table has the same column re ordering properties as the SNP Table Part 11319113 Rev A Detachable Docking Windows 137 Samples Table 8 amp 8 ith GA S la B BEIGE Sample ID pos arn p50 arn p85 arn p05 Red p50 Red p35 1513271004 Unknown Er DIL a 1513271005 Unknown 2471 7606 954 SERE 1513271004 Unknown 2016 O 56 gaz aL 1513271005_ Unknown 471 F606 334 675 1513271004_ Unknown 2016 156 gez SUL 1513271005 Unknown 2471 F606 934 SERE 4 Rows Disp 6 Sel Filter Filter is not active Figure 106 Samples Table Table 16 Samples Table Columns Column Description Type irr v Index Row index of the sample integer Y Sample ID Sample identifier string Y Gender User specified gender for the sample string Y p05 Grn 5th percentile of A allele intensity integer Y p50 Grn 50th percentile of A allele intensity integer Y p95 Grn 95th percentile of A allele intensit
46. Illumina Inc further reserves the right to make any changes in any processes products or parts thereof described herein without notice While every effort has been made to make this guide as complete and accurate as possible as of the publication date no warranty of fitness is implied nor does Illumina accept any liability for damages resulting from the information contained in this guide 2005 2008 Illumina Inc All rights reserved Illumina Solexa Making Sense Out of Life Oligator Sentrix GoldenGate DASL BeadArray Array of Arrays Infinium BeadXpress VeraCode IntelliHyb iSelect CSPro iScan and GenomeStudio are registered trademarks or trademarks of Illumina Inc All other brands and names contained herein are the property of their respective owners GenomeStudio Genotyping Module v1 0 User Guide Revision History Title Part Number Revision GenomeStudio Genotyping Module 11317113 Rev A v1 0 User Guide BeadStudio Genotyping Module 11284301 Rev A v3 2 User Guide BeadStudio Genotyping Module 11207066 Rev C User Guide BeadStudio Genotyping Module 11207066 Rev B User Guide BeadStudio Genotyping Module 11207066 Rev A User Guide GenomeStudio Genotyping Module v1 0 User Guide Date November 2008 December 2007 February 2007 March 2006 December 2005 Table of Contents NO ee aa r ee ee ae we beans os li REVISION FISTO ne Eure ana siaiu Eee Erna ne ae V PIDO C Oneness cotes
47. Login Infinitum LIMS Login User username Password ane wv OF amp Cancel Enter username and password Figure 13 Login Infinium LIMS Login Part 11319113 Rev A Choosing a Project Name and Location 15 7 Enter your username and password 8 Click OK The Login Infinium LIMS dialog closes You are returned to the Select LIMS Project dialog Figure 14 9 On the Select LIMS Project dialog make the following selections from the dropdown menus e Institute e Investigator Project GenomeStudio Project Wizard Select LIMS Project Genotyping Project af a M Please Select a LIMS Project U m n a Institute Login Investigator Project cj Optional Script File Browse Gen Call Threshald 0 15 Cancel lt Back Hegt gt Finish Figure 14 Select LIMS Project If you have loaded information for a pre existing project the warning shown in Figure 15 appears GenomeStudio Genotyping Module v1 0 User Guide 16 CHAPTER 2 Creating a New Project Project Figure 15 Select LIMS Project Warning If you do not want to overwrite existing projects files select different options in the Select LIMS Project dialog 10 Click Finish The Select Target Dates dialog appears Figure 16 Select Target Dates Start Date Use Start Date Sun Mon Tue Wed Thu Fri 29 20 31 3 9g b B 3 Te 12 13 14 15 16 17 13 20 21 22 23 24 Jb 27 20 29 30
48. RTANT READ CAREFULLY THIS IS A LICENSE AGREEMENT THAT YOU ARE REQUIRED TO ACCEPT BEFORE INSTALLING AND USING ILLUMINA INC SOFTWARE CAREFULLY READ ALL THE TERMS AND CONDITIONS OF THIS LICENSE AGREEMENT BEFORE PROCEEDING WITH THE DOWNLOADING AND OR gt INSTALL ATION MF THIS SNFTWARE YAN ARE NAT Install j u m n a Startup Complete _ SS Figure 2 Selecting GenomeStudio Software Modules 2 Read the software license agreement in the right hand side of the Illumina GenomeStudio Installation dialog box 3 In the GenomeStudio Product area select Genotyping Module The GenomeStudio Framework works in conjunction with GenomeStudio software NG NOTE modules Select the Framework and one or more GenomeStudio modules to install and have your serial number s available 4 Inthe Serial Number area enter your serial number for the Genotyping Module and can be found on an insert Serial numbers are in the format NOTE 1 l l included with your GenomeStudio CD GenomeStudio Genotyping Module v1 0 User Guide 4 CHAPTER 1 Overview Illumina GenomeStudio Installation Cf Exit Ca Install Selected Products Modules Optional Enter the serial numbers for additional GenomeStudio modules if you have licenses for additional GenomeStudio modules and want to install them now Click Install The Software License Agreement dialog box appears Figure 3 Accept License Agreement
49. Report a different name by typing the name in the Report Name text field 6 Click Finish Your Locus Summary Report Figure 77 is saved with the name and parameters you assigned to it in the location you specified GenomeStudio Genotyping Module v1 0 User Guide 88 CHAPTER 6 Generating Reports Ej Microsoft Excel Test5 Locussummary csv Bd Eile Edit View Insert Format Tools Data Window Help Adobe PDF EUER FALL nA 4 9 m B 4 ile egi amp Snagit Ef Window 9 E B ie Share As Application m Locus S LOCI 5 DNAs amp gt WebEx Settings B e E ummary on C TestData Repository Projects GT Test5 Test5 LocusSummary csv ProjectNar GenCall i Low GenCall Score Cutoff 0 1500 Locus Narlllumicode No Calls Calls Call Freq AYA Freq AB Freq B B Freq Minor FrecGentrain 25096 1 MitoA1004 9 05E 06 2 MitoA1055 9 06E 06 3 MitoA1125 9 04E 08 4 MitoA1146 9 02E 06 5 MitoA1181 9 05E 06 6 MitoA1230 9 07E 08 7 MitoA1310 9 02E 05 8 MitoA1325 9 01E 06 9 MitoA1376 9 05E408 10 MitoA1423 9 07 E408 11 MitoA1458 9 07 E408 12 MitoA1521 9 03E 03 13 MitoA1524 9 06E 06 14 MitoA1530 9 04E 06 15 MitoA1575 9 05E 06 16 MitoA1592 9 02E 06 17 MitoA1616 9 01E 06 18 MitoA1616 9 04E 06 19 MitoA1738 9 07E 03 20 lta act 9 DE hulit ad 0 O 0 726 0 7036 0 7036 0 722 0 6955 0 7161 0 6679 0 7128 0 7357 0 7433 0 7312 0 6644 0 6649 0 4777 0 722 0 7036 0 6955 0 722 0 7161 oo 000000000 U 0
50. Reprodueibility Error Highlighted in SNP Graph 34 GenomeStudio Genotyping Module v1 0 User Guide xil List of Figures Figure 31 Figure 32 Figure 33 Figure 34 Figure 35 Figure 36 Figure 37 Figure 38 Figure 39 Figure 40 Figure 41 Figure 42 Figure 43 Figure 44 Figure 45 Figure 46 Figure 47 Figure 48 Figure 49 Figure 50 Figure 51 Figure 52 Figure 53 Figure 54 Figure 55 Figure 56 Figure 5 Figure 58 Figure 59 Figure 60 Figure 61 Figure 62 Figure 63 Figure 64 Figure 65 Figure 66 Figure 67 Figure 68 Figure 69 Figure 70 Figure 71 Polar Coordinates Left amp Cartesian Coordinates Right 35 Normalization Turned Off Left amp Normalization Turned On MOM 35 SNP Graph Selected Samples Shown in Yellow 37 Congue Marke ereus eead KANAN eh ea RR ro e vai 38 Neminga Mark a sae na de Ed nn RESET ERA SIR UP E ES 38 Selecting a Color fora Mark 00 a 39 Displaying Marked Samples 40 Displaying the Legend 0a 41 Legend Displaying Mark Name esee 41 Excluding Selected Sample 0 0 0 0 ee eee 42 Project PrOperTIGS ee oun gcd Hon one en Ge PEAK Para 43 Column CHOOSE cC 45 Example GoldenGate Controls Dashboard 46 Exporting Controls Data su aaa Bawa ome are qo 47 Saving the Controls Dashboard 0 0000 ce eee eee 48 Contamination Dashboard 0 eee eee ee
51. Software is licensed for use under an End User Software License Agreement User Guide ILLUMINA END USER SOFTWARE LICENSE AGREEMENT User Guide IMPORTANT READ CAREFULLY THIS IS A LICENSE AGREEMENT THAT YOU ARE REQUIRED TO ACCEPT BEFORE INSTALLING AND USING ILLUMINA INC SOFTWARE CAREFULLY READ ALL THE TERMS AND CONDITIONS OF THIS LICENSE AGREEMENT BEFORE PROCEEDING WITH THE DOWNLOADING AND OR INSTALLATION FIF THIS SAFTWARE YALL ARE NOT xl illumina Installing GenomeStudio The Installation Progress dialog box notifies you that installa tion is complete Figure 5 Part 11319113 Rev A Installing the Genotyping Module 5 Installation Progress X 1 Installation complete Figure 5 Installation Complete Click OK 9 In the Illumina GenomeStudio Installation dialog box Figure 4 click Exit You can now start anew GenomeStudio project using any GenomeStudio module you have installed See Chapter 2 Creating a New Project for information about starting a new Genotyping project GenomeStudio Genotyping Module v1 0 User Guide 6 CHAPTER 1 Overview Genotyping Module Workflow The basic workflow for genotyping analysis using Illumina s GenomeStudio Genotyping Module is shown in Figure 6 E t Optional Optional Figure 6 Genotyping Analysis Workflow Part 11319113 Rev A Chapter 2 Creating a New Project Topics 8 Introduction Starting the New Project Wizard 11 Choosing a Pro
52. able 30 SNP Table Context Menu Selection Description Cluster Selected SNP Clusters a selected SNP Zero Selected SNP Zeroes a selected SNP Set Aux Value Sets the aux value of a SNP Show Only Selected Rows Shows only selected rows in the SNP Table Configure Marks Configures marks Mark Selected Rows Add New Creates a new mark and marks selected rows Select Marked Rows Selects marked rows Part 11319113 Rev A Table 30 Selection Clear Marks lt All gt Context Menus 157 SNP Table Context Menu continued Description Clears all marks Table 31 describes Samples Table context menu selections Table 31 Selection Exclude Selected Sample Include Selected Sample Recalculate Statistics for Selected Sample Recalculate Statistics for All Samples Estimate Gender for Selected Samples Display Image Set Aux Value Sample Properties Upload Selected Samples to Illumina Controls Database GenomeStudio Genotyping Module v1 0 User Guide Samples Table Context Menu Description Excludes the selected sample Includes the selected sample Recalculates statistics for selected samples Recalculates statistics for all samples Estimates gender for the selected samples Image will be displayed only if you have access to the idat Tile the locs locus file the xml file and either the jpg or tif image file for the sample or sample section Sets the aux value of a sample Opens the
53. all threshold low GenCall Score Cutoff Equals Correct Errors Heritability frequency calculated as Correct Total Part 11319113 Rev A Reproducibility and Heritability Report 99 Table 7 is an example of the Parent Child Heritability section of a Reproducibility and Heritability Report Table 7 Example Parent Child Heritability Parent Genotype nl AA AA P C Heritability d Genotype Correct Errors Freq BB O 1 0 AB 1 0 1 No call 0 0 NAN Parent Parent Child Heritability Columns Table 8 describes the columns of the Parent Parent Child Heritability section of the Reproducibility and Heritability Report Table 8 Reproducilbility and Heritability Report P P C Heritability Column Parent DNA Name Parent2 DNA Name Child DNA Name Correct Errors Total P P C Heritability Freq Description Name of the sample designated as parent 1 ina P P C relationship Name of the sample designated as parent 2 in a P P C relationship Name of the sample designated as child in a P P C relationship Number of loci with consistent Parent1 Child and Parent2 Child genotype comparisons Number of loci with inconsistent Parent1 Child or Parent2 Child genotype comparisons Number total of loci that contribute to the trio heritability analysis Does not include loci where Parent1 Parent2 or Child have genotypes with intensities that fall below the no call threshold low GenCall Scor
54. alls Frequency of BB calls Overall call frequency Minor allele frequency If the number of AA number of BB for a sample the frequency for the minor allele A for that sample is 2 AAs ABs for the sample divided by 2 AAs ABs BBs for the sample across all loci User set auxiliary value for the SNP Number of reproducibility errors for this SNP as allele comparisons between replicates Number of parent child heritability errors for the SNP compared among parent child genotypes GenomeStudio Genotyping Module v1 0 User Guide Detachable Docking Windows Type float integer float float float float float float float float integer integer integer Visible by Default Y lt lt n lt 132 CHAPTER 8 User Interface Reference Table 13 Column P P C Errors AA T Mean AA T Dev AB T Mean AB T Dev BB T Mean BB T Dev AA R Mean AA R Dev AB R Mean AB R Dev BB R Mean BB R Dev SNP ILMN Strand SNP Table Columns continued Description Number of parent parent child heritability errors for the SNP compared among parent parent child genotypes Theta value of the center of the AA cluster in normalized polar coordinates Standard deviation in theta of the AA cluster in normalized polar coordinates Theta value of the center of the AB cluster in normalized polar coordinates Standard deviation in theta of the AB cluster in normalized
55. and our partners A CNV Analysis computes CNV Value and CNV Confidence for chromosomal regions in each sample CNV Value usually represents an estimated copy number while CNV Confidence is a relative score indicating confidence in the accuracy of the copy number estimate Creating a To create a CNV analysis CNV Analysis 4 Goto Analysis CNV Analysis The CNV Analysis dialog appears Figure 86 CNY Analysis Fa Create New CNY Analysis Calculate New CNY Analysis CNY Analysis Name TO Calculate Only Selected Samples Copy 0 MMDakRed v Copy 1 E DarkOrange Copy 2 E DarkGreen v Copy 3 EE DakBue l Copy 4 B Buevoe gt Current CNY Analyses Name Version Samples Created Bins Minimum Maximum Figure 86 CNV Analysis 2 Select a CNV algorithm from the dropdown list GenomeStudio Genotyping Module v1 0 User Guide 108 CHAPTER 7 Performing LOH and Copy Number Analysis ki You must have previously installed one or NOTE more CNV analysis St in order for them to appear in the dropdown list 3 Optional Select the Calculate Only Selected Samples checkbox 4 Optional Change the CNV Analysis name Optional Adjust the CNV Analysis input parameters 6 Click Calculate New CNV Analysis The CNV analysis begins and a progress message appears When the analysis is complete the CNV Region Display appears Figure 87 For more
56. asa hack ca KAG eee DA Cha Base 69 Part 11319113 Rev A Table of Contents x Chapter 6 Generating Reports 71 POU o Pr 72 Fine REOON soe ae e ne EEE E 72 DNA REPOM o u acto daii AA AA AA 82 Column Descriptions ern ee ee AMA E ERR RR 84 HOCUS Summary Repon sn S a apa tere 86 Column Descriptions os dd eral ictu d es Ges sa aora 88 FOCUS X DNA REPON szene teen 91 Column Descriptions dos i aps Ves Rd WE EEE EEE 94 Reproducibility and Heritability Report 95 Column Descriptions and Examples 27 Chapter 7_ Performing LOH and Copy Number Analysis 101 langolo tren o PT TI r 102 B Allele Frequency 4 ac 04 na 102 Kod dici RE a oat ae eee ee oe ee ee Ree dere 104 CNV Anal ySlona524 Banner re 107 Creating a CNV Analysis sas v taies e ed ec RS 107 Selecting the Active CNV Analysis 109 Deleting a CNV Analysis 2 2 2222 22222 109 Viewing the CNV Analysis Region Display 109 Viewing CNV Analysis Data in the Full Data Table 111 Converting CNV Analysis Data into Bookmarks 111 gi ase 66645560 ce coe ees eee eer sou bored woe ee 112 Using Auto bookmarking Plug ins 112 Using Column Plug Ins eu s daran san a G48 ee ede eee ae 119 Chapter 8 User Interface Reference 121 IDOL Eleni i c r 122 Detachable Docking Windows 0000 eee 123 Graph Wi
57. ata Table Figure 103 contains all data for every sample To sort the Full Data Table by any column 1 Click the header of the column you want to use as a basis for sorting the table 2 Do one of the following Part 11319113 Rev A Detachable Docking Windows 127 Click E to sort by the column in ascending order P Click zt to sort by the column in descending order Click api to sort by multiple columns Full Data Table SNP Table Paired Sample Table Be FB AF a 68 an B 0 E Y 1513 005 A MitoA1004 10045 0 3107 0 00 MitoA1055 ao M 10551 j Le 207 D 009 j 35 n 3 2689 0 2904 0 02 MitoA1125 9039 M 11252 1 0 7038 0 302 0 356 0 115 0 223 AP 0 2904 0 03 m 0 2904 0 02 MitoA1146 9019 11468 0 7220 0 257 5 8391 0 01 MitoA1181 9047 11813 0 6955 i i 0 257 5 1321 0 04 Mito41230 9065 12309 0 7161 0 249 3 9980 0 01 MitoA1310 9017 13106 0 8879 0 223 0 9687 0 04 MitoA1326 9014 13264 0 7128 0 257 6 0810 0 02 MitoA1378 9059 13781 0 7357 i F 0 218 1 2190 i 0 04 MitoA1423 9069 14234 0 7433 0 233 2 1243 0 01 MitoA1458 9069 14583 0 7312 0 178 1 4806 0 051 MitoA1521 9031 15219 0 6644 0 267 5 3567 0 07 MitoA1524 9060 15245 0 6849 F 0 272 3 8263 0 041 MitoA1530 9044 15302 0 4777 0 248 i 3 2703 0 027 MitoA1575 9075
58. axis and use the mouse wheel To scroll along an axis Click hold and drag over an axis To view different SNPs on the same scale Turn off Auto Scale X axis or Auto Scale Y axis Selecting Samples You can select samples in the SNP Graph in a variety of ways P In Default Mode click and drag on the graph to draw a rectangle When you release the button all points in the rectangle are selected In draw a region When you release the button all points in the shape you have drawn are selected Lasso Mode click and drag on the graph to For the SNP Graph selecting rows in the Samples Table selects the corresponding samples in the SNP Graph To select additional samples without losing your original selection press and hold the Ctrl button and click additional samples in the Samples Table The selected samples are shown in yellow by default Figure 33 Part 11319113 Rev A Marking Samples 37 rs 551515 0 40 0 60 0 80 Marm Theta Figure 33 SNP Graph Selected Samples Shown in Yellow To temporarily transfer to 4 h Pan Mode Position the cursor over an ub region of the genoplot not over a cluster then press and hold the Shift key To temporarily transfer to 7 Lasso Mode Press and hold the Z key Marking Samples After you have selected samples you may choose to mark them in a particular color Mark colors are persistent which means that the mark colors remain w
59. ay not apply to a different sample set of interest Paired Sample Table integer Y The Paired Sample Table Figure 105 shows statistics for paired samples Full Data Table Paired Sample Table Oe aa 1118 c y als a IB 6 E v s 9 amp MitoA1004 MitoA1055 MitoA1125 MitoA1146 MitoA1181 Mito A1230 MitoA1310 MitoA1326 MitoA1378 MitoA1423 MitoA1458 MitoA1521 MitoA1524 MitoA1530 MitoA1575 MitoA1592 MitoA1616 Mito41616 MitoA1738G MitoA3349G MitoA3481G MitoA3548G MitoA3721G MitoA4025G MitoA4105G MitoA4525G 1 9048 M 2 zi T C T C T C A G A G 10045 9058 10551 z2 11468 11813 12309 13106 13264 13781 14234 14583 15219 15245 15302 15759 15925 16163 16164 1738 3349 3481 3548 3721 4025 4105 4825 2 3 33 EE x5 55 553 S 3233 32323 II UE Rows 561466 _Dip 561466 Saki Fiter Fiter is not active Figure 105 Paired Sample Table Part 11319113 Rev A Table 14 Column Index Name SNP Address Chr Position Table 15 Column Theta Ref Theta Sub Detachable Docking Windows 135 The Paired Sample Table columns are listed and described in Table 14 Paired Sample Table Columns Description Row index of the SNP Name of the SNP SNP Bead type identifier for the SNP Chromosome of the SNP Chromosomal position of the SNP Type in
60. cted for cluster position Cluster positions are generated from a large set of normal individuals The B Allele Frequency can also be referred to as copy angle or allelic composition It is easier to visualize genotyping data for all SNPs within a chromosomal region using B Allele Freq rather than theta values This is true because B Allele Freq exhibits less locus to locus variation than the theta values for a given sample The transformation of theta values to allele frequencies allows for improved measurements and better visualization of both LOH and copy number changes B allele freq is described by the following equation B allele freq O if theta lt tAA 0 5 theta tAA tAB tAA if theta tAB 0 5 0 5 theta tAB tBB tAB if theta lt tBB 1 if theta gt tBB Part 11319113 Rev A B Allele Frequency 103 where tAA mean theta value of all genotypes in the AA cluster 9 yp plotted in polar normalized coordinates tAB mean theta value of all genotypes in the AB cluster GENO NP plotted in polar normalized coordinates tBB mean theta value of all genotypes in the BB cluster 9 yp plotted in polar normalized coordinates Figure 84 shows a comparison of plotting theta and B Allele Freq for the same sample on chromosome 5 The B Allele Freq plot exhibits less variation than the theta value plot Notice the three clusters representing two homozygote clusters and one heterozygote cluster
61. d at project creation Updates SNP statistics Allows you to edit include or exclude replicates for a sample Allows you to edit include or exclude P C and P P C relationships for a sample Updates replicate P C and P P C heritability information in various columns and reports Toolbar Button if used Part 11319113 Rev A Main Window Menus 149 Table 22 Analysis Menu Functions continued Selection Reports View Controls Dashboard View Contamination Dashboard Paired Sample Editor Calculate Paired Sample LOH CN Show Genome Viewer Import Allele Calls Export Allele Calls Remove Imported Allele Calls Create Plug in Column Function Toolbar Button if used Allows you to create any of the following Reproducibility and Heritability Report Final Report DNA Report Locus Summary Report Locus x DNA Report Custom Reports if installed v ow vv v Displays the controls dashboard Displays the contamination controls dashboard for GoldenGate data Displays the Paired Sample Editor dialog from which you can edit the list of paired samples Calculates LOH and copy number related scores for paired samples Displays the Illumina Genome Viewer Displays the Import Allele Calls dialog which allows you to select a directory from which to import allele calls Displays the Export Allele Calls dialog which allows you to select a directory to which you want to export allele calls Re
62. d sample involved in the error For a parental relationship error the genotype of the child Sample index of the Parent1 sample involved in the error Sample ID of the Parent1 sample involved in the error For a parental relationship error the genotype of Parent1 For a replicate error the genotype of replicate 1 Sample index of the Parent2 sample involved in the error Sample ID of the Parent2 sample involved in the error For a parental relationship error the genotype of Parent2 For a replicate error the genotype of replicate 2 Index number of the SNP where the error occurred Name of the SNP where the error occurred GenomeStudio Genotyping Module v1 0 User Guide Type integer string integer string string integer string string integer string string integer string Visible by Default Y 125 126 CHAPTER 8 User Interface Reference Data Table SNP Graph Alt The SNP Graph Alt Figure 102 is an alternate SNP graph that you can display along with the SNP Graph to compare different views within GenomeStudio SMP Graph Sample Graph Errors Table SNP Graph Alt kejk 1 Balm e gt a re151 7243 0 40 0 60 Marm Theta Figure 102 SNP Graph Alt The Data Table contains the Full Data Table by default In the Data Table you can toggle between the Full Data Table the SNP Table and the Paired Sample Table Full Data Table The Full D
63. e Cutoff Heritability frequency calculated as Correct Total GenomeStudio Genotyping Module v1 0 User Guide 100 CHAPTER 6 Generating Reports Table 9 is an example of the Parent Parent Child Heritability section of a Reproducibility and Heritability Report Table 9 Example Parent Parent Child Heritability Sone ne Bano a Correct Errors vertat AA BB AB 0 AA AA BB 0 1 o AA AB BB 0 1 o AA No call AB 0 0 NAN Part 11319113 Rev A 102 102 104 107 112 Chapter 7 Performing LOH and Copy Number Analysis Topics Introduction B Allele Frequency Log R Ratio CNV Analysis Plug ins GenomeStudio Genotyping Module v1 0 User Guide 102 CHAPTER 7 Performing LOH and Copy Number Analysis Introduction GenomeStudio provides visualization tools and detection algorithms to analyze both single and paired samples for loss of heterozygosity LOH and copy number CN changes In the GenomeStudio Genotyping Module the primary tool for displaying the results of LOH or CN analysis is the Illumina Genome Viewer IGV For more information about the IGV see the GenomeStudio Framework User Guide This chapter describes the tools you can use for LOH and copy number analysis B allele frequency Log R ratio Algorithm plug ins e Autobookmarking plug ins e CNV Analysis plug ins e Column plug ins Report plug ins B Allele Frequency The B Allele Freq for a sample shows the theta value for a SNP corre
64. e Data Plots Form Table Source GT Samples Sample Mame Favorite Data Plots 1512271004 A4 qt 1512271004 amp qe 1512271004 A id 1512271005 A qe 1512271005 A qt 1513271005 A id SubColumn Names SubCalumns INE m X Allele Freg Cancel Figure 90 Favorite Data Plots Selected 3 Click OK The IGV becomes prominent Figure 91 Part 11319113 Rev A Plug ins 115 Illumina Genome Viewer IGV Microarray File Edit view Data Analysis Help F Active Genome Human Build 36 1 Edit 2 Update Immediate Mode FF a 1 4 Data Plots ax Mo Table Name Sample subColumns Data Series Positive mas Megative m ESs Line Style So Line width y screen pixels Smooth Series Positive Mn i i s Yd Negative Biss 7 Line Style Line Width Data Properties Display Properties Figure 91 IGV 4 Select Analysis Run Autobookmark The Autobookmark Analysis dialog appears Figure 92 GenomeStudio Genotyping Module v1 0 User Guide 116 CHAPTER 7 Performing LOH and Copy Number Analysis Auto Bookmark Analysis Active Module Genotyping Select Auto Bookmark Analysis Algorithm Algorithm Name Descripti ChromoZone NET Illurnina inc 0 8 0 Detects chromosomal aberrations in single sample mode Homozygosity Detector Ilumina inc 1 0 3 Detects stretches of homozygosity copy neutral LOH and LOH i
65. e you want to save the allele calls from your current project Click OK The allele calls are saved to the directory you designated If you have previously exported and saved allele calls from a project you can import these saved allele calls into a different project to calculate concordance To import allele calls into a project 1 3 Select Analysis Import Allele Calls The Import Allele Calls dialog appears Browse to the location where you previously saved allele calls that you exported from a different project The files available to import are listed in the Files Found section of the Import Directory area Click OK Part 11319113 Rev A Using Column Plug Ins 69 The allele calls are imported They populate the Import Calls column in the Full Data Table and concordance is calculated Concordance Concordance calculations appear in two locations Calculations Inthe Full Data Table in the Concordance subcolumn Inthe Samples Table in the Concordance column Columns showing concordance are not NG NOTE visible by default To display these columns use the Column Chooser Using Column Plug Ins You have the option to install column plug ins as part of the GenomeStudio install process or to create custom column plug in algorithms These plug ins are used to create custom subcolumns in the Full Data Table This open plug in architecture allows you to add to the standard features available in
66. ed Samples Auto Scale Axes GenomeStudio Genotyping Module v1 0 User Guide Graph Window Context Menu Description Uses the selected sample s to determine the size and position of the AA genotype cluster Uses the selected sample s to determine the size and position of the AB genotype cluster Uses the selected sample s to determine the size and position of the BB genotype cluster Determines cluster locations and score for each locus Determines the cluster locations for each locus except those you have excluded Marks selected samples in a color you choose Allows you to create a new mark Clears all marks Excludes selected samples from the genoplot Includes selected samples in the genoplot Displays the genoplot marks legend Shows excluded samples Automatically scales the axes 156 CHAPTER 8 User Interface Reference Table 28 Graph Window Context Menu continued Selection Description Launches the Graph Control Properties Settings dialog Table 29 describes Full Data Table context menu selections Table 29 Full Data Table Context Menu Selection Description Show Only Selected Rows Shows only selected rows in the Full Data Table Configure Marks Configures marks Mark Selected Rows Add New Creates a new mark and marks selected rows Select Marked Rows Selects marked rows Clear Marks lt All gt Clears all marks Table 30 describes SNP Table context menu selections T
67. eee ee 159 Table 33 Data Section Required and Optional Columns 163 Table 34 Frequently Asked Questions 00000005 168 Part 11319113 Rev A Chapter 1 Overview Topics Introduction Audience and Purpose Installing the Genotyping Module O N N nm Genotyping Module Workflow GenomeStudio Genotyping Module v1 0 User Guide 2 CHAPTER 1 Overview Introduction This user guide describes Illumina s GenomeStudio M v1 0 Genotyping Module The GenomeStudio Genotyping Module is used to analyze data collected using Illumina s GoldenGate and Infinium genotyping assays Audience and Purpose This guide is written for researchers who want to use the GenomeStudio Genotyping Module to analyze data generated by performing Illumina s GoldenGate or Infinium assays This guide includes procedures and user interface information specific to the GenomeStudio Genotyping Module For information about the GenomeStudio Framework the common user interface and functionality available in all GenomeStudio Modules refer to the GenomeStudio Framework User Guide Installing the Genotyping Module To install the GenomeStudio Genotyping Module 1 Put the GenomeStudio CD into your CD drive If the Illumina GenomeStudio Installation screen appears Figure 2 continue to Step 3 If the CD does not load automatically double click the GenomeStudio lt version gt exe icon in the GenomeStudio folder on the CD
68. elected No only the Gender Est column of the samples table is populated with the estimated gender for the samples you selected GenomeStudio Genotyping Module v1 0 User Guide 64 CHAPTER 5 Analyzing Your Data Editing the Properties of Selected Samples To edit the properties of selected samples 1 Inthe Samples table select one or more samples to edit The selected samples are highlighted in dark blue Figure 58 Samples Table 5 e g d 21 t 23 a Mw 88 BI 9 va Sample ID p05 arn p50 arn p35 Grn p05 Red p50 Rec Ye 511 eni Male Male Male Male Male Male Male Male Male Male Male Male Rows 96 Disp 96 5el 3 Filter Filter is not active Figure 58 Selected Samples 312 Jet 329 308 297 ere 24 25 298 315 296 297 4418 4268 4428 4444 4078 3986 3701 3678 3976 4118 4348 4157 2 Right click anywhere on the selected samples 3 The context menu appears Figure 59 Part 11319113 Rev A Editing the Properties of Selected Samples 65 Samples Table ih E amp Gi 21 1 23 E e la e BI 69 Y f Sample ID p 5 Grn p50 Grn p35 Grn p05 Red p50 Rec Exclude Selected Samples Include Selected Samples Recalculate Statistics For Selected Samples Recalculate Statistics For All Samples Estimate Gender for Selected Samples Display Image Set Aux Value Sample Properties Upload Selected Samples to Illumina Controls
69. epository VGampleDataVGoldenGaleVnkageDatantensityData E TestData Repository SampleData GoldenGate LinkageDataintensityData EATestOata E TestData Repository SampleData GoldenGate LinkageDataintensityData PPC Par PPC ParE TestDatalRepository SamplaData GoldenGatellinkageDatallntensityData E TestOatelR E TestDsta Repository SampleData GoldenGate LinkageDsta ntensityData PPC3 ParPPC3 ParE TestDatalRepository SampleData GoldenGate inkageDatalintansityData E TestData Repository SampleData GoldenGate inkageDatalntensityData E TestDataiepositorySsmpleDatavGoldenGateV inkageDataluntensityData E TestData Repository SampleData GoldenGate LinkageDataiimensityData E TestOata Repository SampleData GoldenGate inkageDatalingensityData _ E TestData Repository SampleData GoldenGateLinkageDataumensityDats E TestData Repository SampleData GoldenGate LinkageDataimensityData E WestData Repository SampleData GoldenGate inkageDataVntensityData F Teatfhetal Rennatory SamnlelataWinidentsale inkane Lat alinterred Mata SampleData GoldenGateLinkageDatalintensityData 165 166 APPENDIX A Part 11319113 Rev A Appendix B Troubleshooting Guide Topics 168 Introduction 168 Frequently Asked Questions GenomeStudio Genotyping Module v1 0 User Guide 168 APPENDIX B Introduction Use this troubleshooting guide to assist you with any questions you may have about the GenomeStudio Genotyping Module Frequently A
70. er Filter is not active 1513271004_ Unknown 1513271005_ Unknown Errors Table 1513271004 Unkn an hon LE m Ba joel RIAL Zt 23 19 E M 9 ld EI 6 ile 5 Unknown Parent1 Parent Unknown Error Child Re Child Rep Re Parenti Rep Rep Type p Index pe GType i 3 pf Source 11 2 2008 10 29 24 Loading snp data General 11 2 2008 10 29 58 Copying temp file General 11 2 2008 10 29 58 Reading CNY Data General 11 2 2008 10 29 58 Setting Heredity and Replicates General 11 2 2008 10 29 58 New project has been created General 11 2 2008 10 30 01 Opened Test5 Project Framework LOG Last 10 30 PM Errors 0 Warn 0 Info 17 Samples Table Data Table Log Window Figure 98 GenomeStudio Genotyping Module Default View Part 11319113 Rev A Detachable Docking Windows 123 Detachable Docking Windows Graph Window Detachable docking windows provide a flexible way to customize GenomeStudio s user interface to suit your analysis needs The following sections describe each of the Genotyping Module s detachable docking windows and their component tabs The graph window contains the SNP Graph by default In the graph window you can toggle among the SNP Graph the Sample Graph the Errors Table and the SNP Graph Alt SNP Graph The SNP Graph plots all samples for the currently selected SNP in the Full Data Table or SNP Table Figure 99 SMP Graph n n 0 60 N
71. ere in the Samples Table Type integer integer integer float float float float float integer integer Visible by Default Y Part 11319113 Rev A Detachable Docking Windows 139 Table 16 Samples Table Columns continued Visible by Column Description Type Default Genotype for this sample for the SNP l Genotype currently selected in the SNP Table eser GenCall score for this sample for the SNP Core currently selected in the SNP Table I Sample Name Sample name string N Sample Group Sample group string N Sample Plate Sample plate string N Sample Well Well within the sample plate string N Gender Est Estimated gender of the individual from string N which the sample was acquired Displays a note Needs Requeue if the Requeue Status sample is marked to be requeued string N otherwise this column is blank Concordance across all SNPs for Concordance 7 r sample float N Ethnicity Ethnicity of the individual from which this string N sample was acquired Age Age of the individual from which this integer N sample was acquired Weight Weight in kg of the individual from which string N this sample was acquired Height in meters of the individual from Height which this sample was acquired REMIS x Blood Pressure Systolic blood pressure of the individual l Systolic from which this sample was acquired oe ni Blood Pressure Diastolic blood pressure of the individual nee N Diastol
72. g Samples creeks cheb oe e Rt 9 edidi KNA BANGA 37 Displaying the Legend 0 eee eee 41 Excluding Samples paawa na DFA NAKA Ed eed eek Pede d 42 Plotting Excluded Samples 0 0 aa 43 Customizing the SNP Table xa a ama ka ERE RE Gases E 44 Viewing the Controls Dashboard 46 Exporting Controls Data so dra 3 rasanten 47 Viewing the Contamination Dashboard 49 Generating Clusters 51 WMO SUCH One ee 4 44 ne a ee ie dae sae ees 52 Running the Clustering Algorithm 52 Reviewing Clusters m 53 Editing CUSE e ausu cerere eet Rage v2 2 9 05 55 19 drca nae 55 Redefining the Cluster x aano eb eo dr hie dcr uds 55 Excluding Samples EN TEC 59 Shifting the Cluster Location 2 2222222222 55 Changing the Cluster Height Width 55 Exporting the Cluster File su 2 000 ens tre dor scene ec hera 56 Analyzing Your Data ees 59 lige L 60 Importing Phenotype Information lees 60 Estimating the Gender of Selected Samples 62 Editing the Properties of Selected Samples 64 Analyzing Paired Samples 22222222 66 Using Concordance Features 0 eee eens 68 Exporting Allele Calls AA n 68 Importing Allele Calls vea qs di drin aan Lea cay 68 Concordance Calculations 7 aaa ka Kae Bann 69 Using Column Plug Ins z7 a
73. hen you select a different SNP Marks overwrite the default genotyping colors To mark selected samples 1 Right click on the graph and select Configure Marks from the context menu The Configure Marks dialog appears Figure 34 GenomeStudio Genotyping Module v1 0 User Guide 38 CHAPTER 3 Viewing Your Data Configure Marks Marking Names gt Cancel Figure 34 Configure Marks 2 Click Add to create a new mark The Select Mark Name dialog appears Figure 35 Select Mark Name Sample Group 1 E DimGray v Figure 35 Naming a Mark 3 Give your mark a color by selecting a color from the pulldown menu Figure 36 Part 11319113 Rev A Marking Samples 97 IE DimGray DarkSeaGreen BE ForestGreen BE LimeGreen PaleGreen EN DakGreen BE Green C Honeydew IE SeaGreen P MediumSeaGreen LL FF SpringGreen Figure 36 Selecting a Color for a Mark 4 Enter a name for your mark in the text field Click OK The selected samples appear in the SNP Graph and in the Samples Table in the color you chose Figure 37 GenomeStudio Genotyping Module v1 0 User Guide 40 CHAPTER 3 Viewing Your Data SMP Graph bil 1 ENT M rs 857748 0 40 0 60 Morn Theta Samples Table B Bs 4 CA s A Hr Sentrix Sample SAMI ROOL Unknown SAMI ROD cool 308 A SAMI ROOL Unknown 5SAMI ROD1 coo 3 SAMI ROOL Unknown SAMI RO01 coos SAMI ROOL Unknown 5AMI Roo
74. hromosomal position of the integer N Score for that SNP from the GenTrain Score GentTrain clustering algorithm float Y FRAC A Fraction of the A nucleotide float Y in the top genomic sequence FRAC C Fraction of the C nucleotide float y in the top genomic sequence FRAC G Fraction of the G nucleotide fdat y in the top genomic sequence FRAC T Fraction of the T nucleotide in igat y the top genomic sequence The per sample subcolumns of the Full Data Table are listed and described in Table 12 Table 12 Full Data Table Per Sample Subcolumns Aa Visible by Column Description Type Default GType Genotype of this SNP for the sample string Y Score Call score of this SNP for the sample float Y Theta Normalized Theta value of this SNP for the Hoat y sample R The normalized R value of this SNP for float Y the sample X Raw Raw intensity of the A allele integer N Y Raw Raw intensity of the B allele integer N Part 11319113 Rev A Detachable Docking Windows Table 12 Full Data Table Per Sample Subcolumns continued Column B Allele Freq Log R Ratio Top Alleles Import Calls Concordance Orig Call CNV Value CNV Confidence Description Normalized intensity of the A allele Normalized intensity of the B allele B allele theta value of this SNP for the sample relative to the cluster positions This value is normalized so that it is zero if theta is less than or equal to the AA cluster s theta mean 0 5 if it i
75. ible by Column Description Type Default 10th percentile GenCall score over all SNPs p10 GC for this sample If displayed as 0 000 this float N column needs to be manually recalculated 50th percentile GenCall score over all SNPs p50 GC for this sample If displayed as 0 000 this float N column needs to be manually recalculated Percentage of SNPs expressed as a Call Rate decimal whose GenCall score is greater float N than the specified threshold Context Menu LIMS Options The following LIMS options are available in the Samples Table context menu if you are logged into LIMS gt LIMS Actions e Update Project From LIMS Send Requeue to LIMS Set to Needs Requeue Clear Needs Requeue Export Cluster Positions to LIMS Update Project from LIMS For more information about the LIMS options available from the Samples Table context menu see Context Menus on page 155 of this manual Part 11319113 Rev A Detachable Docking Windows 143 Project The Project window Figure 107 identifies the manifest s loaded Window for your project and has a data section that identifies all of the Universal Array product barcodes used in your project You can expand a barcode and view the samples loaded on that Universal Array product by clicking the to its left Double clicking a sample brings up the Image Viewer which displays the corresponding array image if the image is available in the same directory as the intensity files Project
76. ic from which this sample was acquired 9 Blood Type Blood type of the individual from which this string N sample was acquired GenomeStudio Genotyping Module v1 0 User Guide 140 CHAPTER 8 User Interface Reference Table 16 Samples Table Columns continued Column Phenotype Pos 1 Phenotype Pos 2 Phenotype Pos 3 Phenotype Neg 1 Phenotype Neg 2 Phenotype Neg 3 Comment Tissue Source Calls No Calls Excluded Description Type Positive phenotype 1 of the individual from which this sample was acquired Hing Positive phenotype 2 of the individual from Ta which this sample was acquired SES Positive phenotype 3 of the individual from js which this sample was acquired iL Negative phenotype 1 of the individual from NER this sample was acquired zum Negative Por 2 of the individual E from which this sample was acquired Sring Negative Pup 3 of the individual kaa from which this sample was acquired Sring User defined field in which you can record custom comments This field maintains a list of all previously string entered comments You can access comments from the context menu by right clicking from within the column Tissue source of the individual from which n this sample was acquired 9 Number of loci on which this sample is being called Image Number of loci on which this sample is not ses being called I 1 Sample is excluded meda 0 Sample is included 9 Visible by Default N Part
77. ing GenomeStudio nananana 4 Installation Complete CER 5 Genotyping Analysis Workflow 2 0 llle 6 Starting a New Project New Project Area 9 Starting a New Project File Menu 10 GenomeStudio Project Wizard Welcome 11 GenomeStudio Project Wizard Project Location 12 select UMS Projeti nassen aus Gee STREP SALES EE 13 Login Infinium LIMS Setup a aco ict 26050 54098 oem dia aes 14 Login Infinium LIMS Login llle 14 Select LIMS PEO CC E2 au urat no bor out ai iiini i iai NAK 15 Select LIMS Project Warning 2 222222 000 c eee eee 16 Select Target Oates cs ade Sco inre PURIS PEN Pd det 16 Selecting Target Dales acens ssi ae nive EPUM METRI TM RE 17 Update Heritability amp Reproducibility Errors 17 Evaluating Heritabllity ucc os Baa v p P Esau 846 840088 17 Sample Requeue Status auan 18 Loading Sample Intensities llle 19 Loading Sample Intensities Using a Sample Sheet 20 Custer POSMONS ss puteo RETIA Saar ISI DUA EE 21 Loading Sample Intensities by Selecting Directories with Intensity Pres csa Y dene pe Rer TEE P POOR USE 23 Loading Sample Intensities by Selecting Directories CU id2s PTT 24 Cluster d OS EIOTIS CE 26 SMP escena ust nen nee SESS I IPIE 30 Shaded Call REGIONS s un ABA mO ADAN ARAWAN AGA ence 32 P C Error Left Reproducibility Error Right 33 P C Error and
78. ing Sample Intensities Genotyping Project Please specify the samples you want to load by identifying the U n a sample sheet and associated data and manifest repositories TT Use sample sheet to load sample intensities C Load sample intensities by selecting directories with intensity Files Cancel lt Back Hert gt Finish Figure 21 Loading Sample Intensities 2 Click Next The Loading Sample Intensities dialog appears Figure 22 GenomeStudio Genotyping Module v1 0 User Guide 20 CHAPTER 2 Creating a New Project GenomeStudio Project Wizard Loading Sample Intensities Genotyping Project a 222 Please specify the samples you want to load by identifying the U n ci sample sheet and associated data and manifest repositories rao Sample Sheet Wdorkstation 5791 daka GT SampleSheeksjsamplesheet test 1 4 5 Browse Data Repository Wworkstation 579 Data Intensity Data Browse Manifest Repository MwnarksEation 5 79D atataT iManifesEs Browse Cancel lt Back Next gt Finish Figure 22 Loading Sample Intensities Using a Sample Sheet 3 Browse to select the following items e Sample Sheet e Data Repository e Manifest Repository The Sample Sheet is a comma delimited text file csv file Its format is described in Appendix A of this document The Data Repository is the directory that contains your intensity idat files The Manifest
79. io Progress Status Evaluating heritability Cancel Figure 19 Evaluating Heritability GenomeStudio Genotyping Module v1 0 User Guide 18 CHAPTER 2 Creating a New Project SNP data are saved and the Sample Requeue Status Change message appears Figure 20 This message indicates whether any sample statuses have changed between the GenomeStudio project and the LIMS database If sample statuses are updated this is reflected in GenomeStudio If the data from the GenomeStudio project and the LIMS database are the same the Sample Requeue Status Change dialog displays the message No updates were required Sample Re queue Status Change Eg AJ Mo updates were required Figure 20 Sample Requeue Status 14 Click OK The project you selected loads from LIMS and displays in the GenomeStudio Genotyping Module Part 11319113 Rev A Loading Sample Intensities Outside of LIMS 19 Loading Sample Intensities Outside of LIMS Using a Sample Sheet If you are not using a LIMS database for loading intensity data you have two options for loading data outside of LIMS control Loading sample intensities using a sample sheet page 19 Loading samples by selecting directories that contain intensity data files page 23 To load intensities using a sample sheet 1 In the Loading Sample Intensities dialog select Use sample sheet to load sample intensities Figure 21 GenomeStudio Project Wizard Load
80. is mode the Log R Ratio for a sample is the log base 2 ratio of the normalized R value for the SNP from your subject sample divided by the normalized R value from your reference sample In this case the R values from the clusters are not used For example if for a given sample and SNP with e A theta value of 0 2 e an AA cluster at theta 0 1 R 1 5 e an AB cluster at theta 0 4 R 2 5 The estimated R at theta for the sample is 0 2 is 1 5 0 2 0 1 2 5 1 5 0 4 0 1 1 83 If the R value for the SNP is 1 6 the Log R Ratio is log 1 6 1 83 0 196 Figure 85 shows an example of a log R ratio plot GenomeStudio Genotyping Module v1 0 User Guide 106 CHAPTER 7 Performing LOH and Copy Number Analysis Sample 1 1485978235 A O 10 20 30 40 50 60 70 80 90 100110 120130140 150160 170150190 Base Position Mb Decrease in Log R Ratio Smoothing Series Figure 85 Log R Ratio In Figure 85 a region of LOH is shown This LOH event is demonstrated by a decrease in the log R ratio The red line in the log R ratio plot indicates a smoothing series with a 200kb moving average window Part 11319113 Rev A CNV Analysis 107 CNV Analysis GenomeStudio includes a CNV analysis workflow and related visualization tools which provide access to CNV algorithms and allow you to display algorithm results for all samples across the entire genome CNV Analysis algorithms are provided as plug ins by Illumina
81. itions Import cluster positions From a cluster File Guster File n SITES HUNG z Browse Project Settings Options Project Creation Actions Pre Calculate Cluster SMPs Pre Calculate should only be Calculate Sample and SNF Statistics used For memory based projects i Gg calculate Heritability This option will improve speed but requires 4 5x more memory Gen Call Threshold 0 15 Optional Script File Browse Cancel lt Back MH est gt Finish Figure 26 Cluster Positions To import a cluster file e Select Import cluster positions from a cluster file 2 Browse to the cluster file you want to use Li If you do not want to import a cluster file Ww NOTE clear the Import cluster positions from a cluster file checkbox and the Cluster File text field 3 Select Precalculate if you want to optimize your project for speed based on the memory capabilities of your computer 4 Optional In the Project Creation Actions area select the following option for your project e Cluster SNPs If you choose to cluster all SNPs you may also select one or more of the following options Part 11319113 Rev A Importing Cluster Positions 2 e Calculate Sample and SNP Statistics Calculate Heritability Gen Call Threshold Illumina recommends that you use a GenCall ww NOTE Score cutoff of 0 15 for Infinium products and 0 25 for GoldenGate product
82. ject Name and Location 12 Creating a Project 13 Selecting a Project From LIMS 19 Loading Sample Intensities Outside of LIMS 19 Using a Sample Sheet 23 Selecting Directories 25 Importing Cluster Positions GenomeStudio Genotyping Module v1 0 User Guide 8 CHAPTER 2 Creating a New Project Introduction The New Project Wizard offers an easy way to start a new project from within any GenomeStudio module you install The following sections describe how to use the New Project Wizard to begin a new genotyping project Follow the same instructions to create projects that allow you to perform LOH or copy number analyses Starting the New Project Wizard To create a new genotyping project 1 Doone of the following e Select Start Program Files Illumina GenomeStudio hy e Double click the GenomeStudio icon ow on the desktop Genomestudia The GenomeStudio application launches and the Start page appears 2 On the GenomeStudio Start page Figure 7 do one of the following e n the New Project pane click Genotyping Part 11319113 Rev A Starting the New Project Wizard 9 Click Genotyping or 3 Genome5tudio File Edit View Analysis Tools Doi Start Page Recent Projects Genotyping CiTestDatalRepository Projects G7T Genotyping CiTestDatalRepository Projects GT ChIP Sequencing Ci TestDatalRepository ChIPSeg Te RMA Sequencing C TestDatalRepositoryiRN seg Te Genotyping Ci TestDatalRe
83. ks Mark Selected Rows lt Add New gt Select Marked Rows Clear Marks lt All gt GenomeStudio Genotyping Module v1 0 User Guide Description Configures the Samples Table to show only selected rows Edits replicates Edits parental relationships Allows you to configure marks Creates a new mark and marks selected rows Selects marked rows Clears all marks from the table 160 CHAPTER 8 User Interface Reference Part 11319113 Rev A 162 162 163 164 164 Appendix A Sample Sheet Guidelines Topics Introduction Manifests Section Data Section Redos and Replicates Sample Sheet Template GenomeStudio Genotyping Module v1 0 User Guide 162 APPENDIX A Introduction The sample sheet is a comma delimited text file csv It is divided into sections indicated by lines with the section name enclosed by square brackets The required sections are the Manifests and Data sections You can also include a Header section or any other user defined sections Manifests Section The Manifests section contains two columns The first column is populated by A B C etc The second column is populated by the name of the manifest file corresponding to manifest A B C etc For example Manifests A GS0006492 OPA B GS0006493 OPA C GS0006494 OPA D GS0006495 OPA Part 11319113 Rev A Data Section Data Section 163 The first row of the Data section must indicate the column names of the data
84. late Plate 1 Plate Piste 1 Plate 1 Plate 1 Plate T Plate Plato 1 Plate 1 Plate Plato 1 Plate 1 Plate Piste 1 Plate 1 Plate Plato 1 Piste 1 Plate I Plato 1 Plate 1 Plate 1 Plate 1 Plate 1 Piste 1 Plate Plate 1 Plate 1 E A10 All A12 B01 388889228 B10 511 col 88253258 C10 c12 nm ge sae es sean tht Adobe POF TIETIES FOO Br Hi E e Ha remm duke Lr ml sl 31336930 RON COD M 3133593 ROD COU M 31336930 R001_000M 3 1336930 KOO COO M 31332930 FO01_COOM 3 1336930 ROO _COOIM 31396990 ROO1 COO M 31336830 HIN COXM 31336930 ROD COM 3133930 ROD COTIM 3 1335830 R001_C01 M 3133930 KOO COT M 31336930 R002_000 M 31336830 RON C0 M 31336830 ROU2_COOM 31336930 R002_000 M 31336930 ROO COOM 3133832 ROC2 CUIM 31336930 ROO02 C00 M 311336030 ROO COOH F 31336930 ROC2 COO M 31336930 ROO2 COliM 31336030 ROO2 C 1 M 31336830 HUN COT M 3 1336930 ROO3 COO F 31236930 R003_CO0 Mm 313393 R003 COO M 3 1336930 R003_C00 M 31336930 R003 COM 3 1338830 KONG COUIM 3133930 ROO3 COO M 3 1336930 R003 COGM 31336930 ROO3 COM 3133930 KUDI COTM 3 1336930 R003 CO M 31336930 R03 C01 M BARAN EOM OM M KH t i bla GenomeStudio Genotyping Module v1 0 User Guide PCi Parent PPC1 ParPPCt ParE ITestDatalRepository1SampleData1GoldonGatolLinkageDataUngensityData SampleData l oldenGate LinkogeDstalintensityData _ Sample Sheet Template BLIEB S amp B
85. le ID CNW Position eju E8348 punon 1007 Value 40un eag Jon ua F 4OWN E838 Confidence Li The active CNV analysis appears in the m NOTE CNV Analysis Region Display window The legend in the upper right of the CNV Region Display window shows the colors assigned to bins that represent copy number value ranges When you mouse over a region information about that region displays in the status bar at the bottom of the window To view data at a higher resolution use the mouse wheel to zoom in Part 11319113 Rev A CNV Analysis 111 Viewing CNV To view CNV analysis data in the Full Data Table Analysis Data 4 in the Full Data Table select Column Chooser in the Full Data The Column Chooser dialog appears Table 2 Inthe Hidden Subcolumns area select CNV Value and CNV Confidence Click Show 4 Click OK The CNV Value and CNV Confidence Columns appear in the Full Data Table 3 CNV Value and CNV Confidence are NOTE calculated differently by each CNV algorithm CNV Confidence may not be computed by some CNV algorithms Converting To convert CNV analysis data into bookmarks CNV Analysis 1 inthe IGV select View CNV Analysis as Bookmarks Data into The Display CNV Analysis dialog appears Figure 88 Bookmarks HE Display CNY Analysis Of x Select the CNY Analysis to Display as Bookmarks enwPartition 0 3 4 M Create Color Palette Minimum j Color Fill Style Opacit
86. lude GenCall scores in your Final Report select Include GenCall Score c Continue to Step 6 GenomeStudio Genotyping Module v1 0 User Guide 78 CHAPTER 6 Generating Reports Final Report 3rd Party Options Genotyping Report sao How would you like bo Format your Final report U m n a Standard Matrix 3rd Party 3rd Party Options Format Exemplar m General Options Favorite Formats Tab Comma Default Estimated 12 9 MB Create map Files Save Current Size Samples File Estimated File 12 2 MB fe Size Cancel lt Back Next gt Finish Figure 68 Final Report 3rd Party Options Total Rows 5614566 Select a third party format for your Final Report from the 3rd Party Options Format dropdown menu E Currently available 3rd party formats for wW NOTE Final Reports include Exemplar and GeneSpring 6 Inthe General Options area choose from among the following options Select Tab to create the Final Report in tab delimited format or select Comma to create the Final Report in comma delimited format Part 11319113 Rev A Final Report 19 Select Create map files if you want to create map files Use the arrows to the right of Samples File to specify the number of samples per file to include in the Final Report d Select a favorite format Default or Default Small e Click Save Current to save your current selections as the
87. memory varies depending upon many factors including how many other programs are running on your computer simultaneously and the configuration of your virtual memory Use the following guidelines for a computer with the recommended minimum 2 GB of physical memory For HumanHap300 data Approximately 200 samples of HumanHap300 SNP data can be loaded using memory based storage GenomeStudio Genotyping Module v1 0 User Guide 22 CHAPTER 2 Creating a New Project e Ifyou want to load more than 200 samples of HumanHap300 data leave the Precalculate checkbox cleared to optimize memory e If you want to load fewer than 200 samples of HumanHap300 data you may want to select Precalculate to optimize calculation speed For HumanHap550 data Approximately 150 samples of HumanHap550 SNP data can 3 be loaded using memory based storage e If you want to load more than 150 samples of HumanHap 550 data leave the Precalculate checkbox cleared to optimize memory e Ifyou want to load fewer than 150 samples of HumanHap550 data you may want to select Precalculate to optimize calculation speed In the Project Settings area choose one of the following options e Select Precalculate if you expect the number of samples and SNPs to fit within the physical memory of your computer and you want to increase calculation speed e Leave the Precalculate checkbox cleared if you do not expect the number of samples and SNPs you want t
88. moves imported allele calls from the project Displays the Select Column Plug In Form dialog from which you can select an algorithm based column plug in You can use the column plug in to create a new subcolumn GenomeStudio Genotyping Module v1 0 User Guide 150 CHAPTER 8 User Interface Reference Table 23 describes Tools Menu functions Table 23 Tools Menu Functions Toolbar Button Selection Function if used Displays the Project Properties window in Options Project which you can make changes to project settings Opens the GenomeStudio Options window in which you can select Options GenomeStudio options including the GenomeStudio maximum number of project files and display attributes such as font name size and style Allows you to select storage and Options Module memory options Table 24 describes Windows Menu functions Table 24 Windows Menu Functions Selection Function Ber Satton if used The Window menu is populated with a list of available windows to display Windows marked with a check mark are currently displayed Table 25 describes Help Menu functions Table 25 Help Menu Functions Toolbar Button Selection Function if used Brings up the About box for your currently installed GenomeStudio modules which contains version information and the Software Copyright Notice About GenomeStudio Part 11319113 Rev A Graph Window Toolbar 15 Graph Window Toolbar Table
89. n Figure 55 Samples Table E ee diu 2218 capell B ED Y Wo Index Sample ID 2 p 5 Grn p50 Grn p35 Grn p05 Red p50 Red pot 1 4859078108 A Unknown z070 i o BN Shake WAIN 196 257 fa zis ee i 56 8 To BE 5565 His iee i Unknown 27 8 55 Unknown Unknown Unknown Rows a Disp 8 Sel 8 Filter Filter is not active Figure 55 Selected Samples 1 Right click anywhere on the selected samples The context menu appears Figure 56 Part 11319113 Rev A Estimating the Gender of Selected Samples 63 sampes Table Exclude Selected sample Include Selected Samples Recalculate Statistics for Selected Samples Recalculate Statistics for All Samples Estimate Gender For Selected Samples Display Image Set Aux Value Sample Properties Upload Selected Samples to Illumina Controls Database Show Only Selected Rows Configure Marks les BSLOHILohBS Mark Selected Rows les BSL HILOhBS Select Marked Rows SET Der Figure 56 Samples Table conten Menu Select Estimate Gender for Selected Samples The Would you like to populate the Gender column dialog appears Figure 57 Would you like to populate the Gender column as well as the GenderEst column with the result of the calculation Figure 57 Populating the Gender Column Choose one of the following Yes the Gender and Gender Est columns of the Samples Table are populated with the estimated gender for the samples you s
90. n give your Locus x DNA Report a different name by typing the name in the Report Name text field Click Finish Your Locus x DNA Report Figure 80 is saved with the name and parameters you assigned to it in the location you specified Part 11319113 Rev A Locus x DNA Report 23 EJ Microsoft Excel Test5 LocusXDNA csv Bl File Edit View Insert Format Tools Data Window Help Adobe PDF 05423392 TE xus JJ 5 v amp r iilW ew BP ava amp Snagit 5 Window x Bt O Projectld Test5 Loc Project Name GenomeSt GenCall Software Version 6 Number DNAs 551455 Number Loci oligoPoollc recordType data HumanHag Gentrain Scores 0 725991 0 703759 0 703759 0 722009 0 595455 0 716146 0 887882 0 712779 0 735 HumanHag ilmnids MitoA1004 MitoA1055 MitoA1 125 MitoA1 146 MitoA1181 MitoA1230 MitoA1310 MitoA1326 MitoA 14 HumanHar ilmnStrand B T B B T T B T T 45 HumanHar locuslds 1 2 3 4 5 5 Fi 5 16 HumanHar locusNames MitoA1004 MitoA1055 MitoA1 125 MitoA1 146 MitoA1181 MitoA1230 MitoA1310 MitoA1326 MitoA HumanHag olicodeNames 9 05E 08 9 06E 08 9 04E 08 9 02E408 9 05E408 9 07E 08 9 02E4 08 9 01E408 9 06E 18 HumanHag snps T C A G T C T C AIG AIG T C AIG AIG 19 loligoPoollc GTS Locus data HumanHar locus 1 2 3 4 instituteLa plate Well imageDate oligoPoollc bundleld status recordType data 15132710C WGO00010 Apr 07 20C HumanHar 151327100 D calls 15132710C WGO0010 Apr 07 20C HumanHar 151327100 0 Score Call 0 2804 0 2904 15132710C WGO00
91. n single sample mode Name of Bookmark Analysis Comments Figure 92 Autobookmark Analysis The autobookmarking algorithms you have installed appear in the list of available algorithms 5 Click an algorithm name to select an algorithm 6 Enter a name for your bookmark analysis in the Name of Bookmark Analysis text field The bookmark analysis name will be visible in the Data View area under Bookmark Analyses You can display the results of any NOTE bookmark analysis you have previously run by clicking its name in the Bookmark Analyses area 7 Optional Enter comments in the Comments text field 8 Click Next to advance to the next dialog 9 If the algorithm you want to use has editable properties make selections from the available options Part 11319113 Rev A NOTE 10 Click Next Plug ins 117 You may not be able to edit the input pu of some algorithms supplied y Illumina If you cannot edit the input parameters you will see the following message displayed in red in the upper right hand corner of the dialog Algorithm doesn t expose input parameters Continue to Step 8 11 Select the samples you want to include in this autobookmarking analysis You can select all samples or any combination of samples provided that pairs are selected for the paired sample analysis Figure 93 Auto Bookmark Analysis Select Samples for Analysis Rep7 1 15 PC1 Child 17 PC1 Paren
92. nal Samples Import Cluster Positions Export Cluster Positions to LIMS For All SNPs Export Manifest Update Project From LIMS Import Phenotype Information from File 8 Page Setup Cbrl ShiFt U S8 Print Preview Clrl ShifE4 V ey Print Ctrl F Recent Project Exit Alt F4 Figure 51 Export Cluster Positions Selected 2 Choose whether you want to export clusters For Selected SNPs for SNPs you selected or For All SNPs for all SNPs in this project The Save Cluster Positions dialog appears Figure 52 GenomeStudio Genotyping Module v1 0 User Guide 58 CHAPTER 4 Generating Clusters Save in lo Manifest O 7 Er Fe My Recent Documents Desktop o My Documents a Ig My Computer um a My Network File name ler egt Save Places Save as type Cluster Files egt Cancel A Figure 52 Save Cluster Positions 3 Browse to the location where you want to save your cluster position file 4 Click Save The cluster file is assigned a default name based on the name of the project However you can choose to save your file with a different name Your exported cluster positions are saved as an egt cluster file and are available to be imported into a different project Part 11319113 Rev A 60 60 62 64 66 68 69 Chapter 5 Analyzing Your Data Topics Introduction Importing Phenotype Information Estimating the Gender of Selected Samples Editing the Prope
93. ndow ses an nenn DAANG Der ewe P EA ae 123 Data Table TTE 126 Samples Tabl 64025056 TT 136 Project Window zen erden os 143 LOG NINONG Hom AW ANE NATN AMAYA NG KUNAM ASAN AG 144 Main Window Menus 332 21 89 9 19 KIRA ABAKA PLAN wade 145 Graph Window Toolbar gacavrepne pices viu ra que ya s 151 Table Windows Toolbar 0 0 0 eee ee 153 Context MENUS ess oue an euere era eee ees ty 155 GenomeStudio Genotyping Module v1 0 User Guide x Table of Contents Appendix A Appendix B Sample Sheet Guidelines 161 PA ON Tl eenge eck ee eee a cane 162 Manitests CHOU Lass sw Gu eee ren oe ae EIER NES ENS 162 Bea CA 0 ee ee ee ee EEE 163 Redos and Repliedtes s au eu eu nhan Sieh ead PERS 164 Sample Sheet Template 0 cee eee eee 164 Troubleshooting Guide 167 Insgoioiiiedo CPP 168 Frequently Asked Questions 168 Part 11319113 Rev A Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure Figure 8 Figure 9 Figure 10 Figure 11 Figure 12 Figure 13 Figure 14 Figure 15 Figure 16 Figure 17 Figure 18 Figure 19 Figure 20 Figure 21 Figure 22 Figure 23 Figure 24 Figure 25 Figure 26 Figure 27 Figure 28 Figure 29 Figure 30 List ot Figures GenomeStudio Application Suite Unzipping 2 Selecting GenomeStudio Software Modules 3 License AgreemebDt iss esu bis ay ss bs sad gt ew eV EEG an 4 Install
94. ng Sample Intensities by Selecting Directories with Intensity Files 2 Click Next The Loading Sample Intensities dialog appears Figure 25 GenomeStudio Genotyping Module v1 0 User Guide 24 CHAPTER 2 Creating a New Project 9 GenomeStudio Project Wizard Loading Sample Intensities Genotyping Project TT Please specify the samples vou want to load by identifying the U i n ci SNP manifest you want to use and then selecting directories that contain intensity files From your data repositor SNP Manifest ean papo GC agaran nen Browse Data Repository k TestDakatReposikory aT Soldengate SingleManifest IntensityDat Browse Directories in Repository Selected Directories H 1 162 7868028 B 1 1627858037 E 1 1707921014 c 2 1233735 E 2 1627065072 c 1707921005 H 3 1324488 Rena Remove all Remove all E 3 13256555 E 33 1326595 E 3 1326601 H 3 1331231 EIS e aH mtm Cancel lt Back Mest Finteh Figure 25 Loading Sample Intensities by Selecting Directories with Intensity Files Remove Remove Select the following items e SNP Manifest an opa file for GoldenGate assays or a bpm file for Infinium assays The SNP manifest contains the mapping between bead type identifier and SNP e Data Repository the directory that contains subdirectories with intensity files When you change the entry in the data repository field the Directories in Reposi
95. notypes AA_R_Mean Mean of the normalized r values for the AA genotypes Standard deviation of the normalized r values for the AA_R_Std AA genotypes AB_R_Mean Mean of the normalized r values for the AB genotypes Standard deviation of the normalized r values for the AB_R_Std AB genotypes BB_R_Mean Mean of the normalized r values for the BB genotypes BB R Std Standard deviation of the normalized r values for the BB genotypes Part 11319113 Rev A Locus x DNA Report 91 Locus x DNA Report To generate a Locus x DNA Report 1 Run the Report Wizard by selecting Analysis Reports Report Wizard The Report Type dialog appears 2 Select Locus x DNA Report Figure 72 Genotyping Report TEN what type of report would you like to generate U m n a Final Report Locus Summary DNA Report f Locus x DNA Cancel Back Next gt Finish Figure 78 Locus x DNA Selected 3 Click Next The Destination dialog appears Figure 79 GenomeStudio Genotyping Module v1 0 User Guide 92 CHAPTER 6 Generating Reports Genotyping Report a so Where would you like to save your report U m n a Qutput Path c TestDatalRepository Projects GT TestS Browse Report Name Test5_LocusxDNA Cancel lt Back Hests Finish Figure Destination Locus x DNA 4 Browse to select an output path for your Locus x DNA Report 5 A report name is generated by default You ca
96. notyping Module main window select Analysis Create Plug In Column The Select Column Plug In Form dialog appears Figure 97 GenomeStudio Genotyping Module v1 0 User Guide 119 120 CHAPTER 7 Performing LOH and Copy Number Analysis Select Column Plugin x A new column can be created by selecting a CalumnPlugin and a new Column name Genome5 tudio will create the new column by passing the project data to the user designed algorithm and populating the column with the results A ColumnPlugin ix an algorithm written in CH using the I ColummPlugin interface It allows the user to customize calculated columns according to project specific data Details of generating a ColumnPlugin can be found in the documentation New Subcolumn Name Default Column Mame Column Plugin Properties Cancel E Figure 97 Select Column Plug In Form 2 3 Inthe column plug ins table click to select a row from the list of available column plug ins Optional Type a name for the subcolumn in the New Subcolumn Name text field Optional Edit the pre defined properties of a column by clicking in the right hand column of the Column Plug In Properties table and entering new values Click OK The new subcolumn is created and appears in the Full Data Table You can also view the results of applying this algorithm in available visualization tools Part 11319113 Rev A 122 123 145 151 153 155 Chapter 8 User Inte
97. ns and the GenomeStudio Progress Status bar appears Figure 48 ey GenomeStudio Progress Status Cluster 11704 11904 Cancel Figure 48 Clustering Progress When the GenomeStudio Progress Status bar disappears your samples have been reclustered Reviewing Clusters To review clusters gt Cick 1 Normalization to view normalized data reco ended The GenomeStudio Genotyping Module displays the cluster ovals that represent the location of the clusters with two standard deviations For more information about normalization see Normalization on page 35 To shade the calling regions P Click bi Shade Calling Regions The calling regions are shaded in the SNP Graph Figure 49 GenomeStudio Genotyping Module v1 0 User Guide 54 CHAPTER 4 Generating Clusters SNP Graph bei 1 Bl S OO mf rs 23888 40 0 40 0 60 Norm Theta Figure 49 Reviewing Clusters For more information about shading call regions see Shading Call Regions on page 31 Samples are colored according to their genotype call Samples in the lighter shaded regions fall below the user specified Call Score Threshold set in Tools Options Project and are colored black to indicate that they are classified as No Calls Note that you do not have to review all of your SNPs You can sort by GenTrain score in the SNP Table and only review those SNPs that have the poorest clustering Alternatively if you have entered repr
98. o load to fit within the physical memory of your computer You must choose whether to enable we NOTE precalculation in a project at the time the project is created You cannot change this option later in an existing project Optional In the Project Creation Actions area select the following option for your project e Cluster SNPs If you choose to cluster all SNPs you may also select one or more of the following options e Calculate Sample and SNP Statistics Calculate Heritability Gen Call Threshold Part 11319113 Rev A Loading Sample Intensities Outside of LIMS 23 Li Illumina recommends that you use a GenCall Ww NOTE Score cutoff of 0 15 for Infinium products and 0 25 for GoldenGate products After loading intensity data using a sample sheet continue to Importing Cluster Positions on page 25 Selecting To load intensities by selecting directories Directories 4 In the Loading Sample Intensities dialog select Load Sample Intensities by Selecting Directories with Intensity Files Figure 24 GenomeStudio Project Wizard Loading Sample Intensities Genotyping Project 2220 mm Please specify the samples you want to load by identifying the U n ci sample sheet and associated data and manifest repositories T Use sample sheet bo load sample intensities Load sample intensities by selecting directories with intensity Files Cancel lt Back Hert 3 Finish Figure 24 Loadi
99. o determine if a call should be included in the SMP statistics Display a dialog when SNP Statistics are calculated and this option Is enabled Use For All Mew Projects Restore Defaults coed Figure 41 Project Properties 2 Inthe Options area select the Plot excluded samples checkbox 3 Click OK The excluded samples are plotted in the genoplot GenomeStudio Genotyping Module v1 0 User Guide 44 CHAPTER 3 Viewing Your Data Alternatively you can choose to plot excluded samples in the genoplot by right clicking in the genoplot and choosing Include All Samples from the context menu To remove excluded samples from the genoplot 1 Goto Tools Options Project The Project Properties dialog appears Figure 41 2 Inthe Options area clear the Plot excluded samples checkbox 3 Click OK The excluded samples are removed from the genoplot Alternatively you can choose to remove excluded samples from the genoplot by right clicking in the genoplot and choosing Exclude Selected Samples from the context menu Customizing the SNP Table Using the Column Chooser you can select the columns you want to display in the SNP Table and arrange the columns in any order you want to display them See Chapter 8 for descriptions of the columns 1 In the SNP Table click Column Chooser The Column Chooser appears Figure 42 Part 11319113 Rev A Customizing the SNP Table 45 Column Chooser You can drag and dro
100. oducibility or heritability relationships you can sort by heritability or reproducibility errors Rep P C P P C in the SNP Table and review only SNPs that exhibit errors For more information about sorting see Data Table on page 126 Part 11319113 Rev A Editing Clusters 55 Editing Clusters Redefining the Cluster Excluding Samples Shifting the Cluster Location Changing the Cluster Height Width If after reviewing the clustering of a SNP you feel that the loaded cluster file or automated algorithm did not accurately calculate the cluster positions you can manually edit the cluster locations in various ways To redefine the cluster using samples you select 1 Select samples in the graph 2 Right click to display the context menu 3 Select Define AB or AA or BB cluster using selected samples The cluster s location and size are calculated based on the samples you have selected The remaining samples are reclustered To exclude samples in the current graph 1 Select samples in the graph 2 Right click to display the context menu 3 Select Cluster this SNP excluding selected samples Figure 50 To shift the cluster location 1 Press and hold the Shift key 2 Click near the center of the cluster The move cursor appears 3 Drag the cluster to a new location To change the height or width of a cluster 1 Press and hold the Shift key 2 Click near the edge of an oval The or re
101. oncsespeeER com SmEPRROSTIGG C EN vii ISU OF QUE 5452404 ee besa ee oo oe ae ee ee bee howe xi Gst Cr Nab lee i242 bees eee oe eases AA es ene XV Chapter 1 Overview cc cece eee eee eee eens 1 HOCU ON ae ce en pe AA 2 Audience and Purpose m 2 Installing the Genotyping Module 2 Genotyping Module Workflow aa 6 Chapter 2 Creating a New Project 7 IDEO UL On oce Ba een ER PU REP ee RE RE ep ES 8 Starting the New Project Wizard 0 0 0 0 0c eae 8 Choosing a Project Name and Location 11 Creaung a Project sere ew ke s Coad ewe dye ee wer 12 Selecting a Project From LIMS 22 222222 cc 13 Loading Sample Intensities Outside of LIMS 12 Using a Sample Sheet 2 222222 eee eee ee 19 Selecting Directoris wanciacataananenauaeeseheeads 23 Importing Cluster Positions cacti oni ao te dude 25 Chapter 3 Viewing Your Data 29 MTOdUCHON en ne AA 30 GenomeStudio Genotyping Module v1 0 User Guide viii Table of Contents Chapter 4 Chapter 5 AG 30 Shading Gall REGIONS sa vod dex answer annus denne Eu KAY 31 SNP Graph Error Display llle Do Cartesian and Polar Coordinates 22222222 34 Normalization sea een tach EIOS Sd ERU terse tas 35 hYelv em2 aaa a EN a re are ee ee ee ee 35 Selecting SAIMPICS neste sus en sur Foe Ple ses o wasn 36 Markin
102. ons in order to generate the most accurate genotype calls This is because the locations of the heterozygote and homozygotes for each SNP though reproducible can vary trom SNP to SNP Given a population of samples that exhibit the three genotypes for every SNP the GenomeStudio Genotyping Module can automatically determine the cluster positions of the genotypes If certain SNPs have one or two clusters that lack representation the GenomeStudio Genotyping Module can estimate the missing cluster positions One common question is How large does the population of samples need to be This depends on the minor allele frequency of the SNPs The lower the minor allele frequency the more samples are required to achieve representation of all clusters A population of 100 or more samples is typically recommended Running the Clustering Algorithm 1 To run the clustering algorithm do one of the following e Select Analysis Cluster All SNPS e Click Cluster all SNPS Figure 47 ash GenomeStudio Genotyping Test5 File Edit View Analysis Tools Window Help Exclude Samples By Best Run dte Cluster All SNFs Update SNP Statistics Edit Replicates Edit Parental Relationships Update Heritability Reproducibility Errors B Figure 47 Analysis Cluster all SNPs Using this feature clusters all SNPs based NOTE on the samples in your project Part 11319113 Rev A Reviewing Clusters 53 The clustering algorithm ru
103. ook in E Manifest Oo F gt m My Recent Documents Desktop My Documents BL My Computer nga b CES File name Open Places Files of type Phenotype Info Files csv Cancel Figure 53 Importing Phenotype Information 2 Browse to a csv phenotype information file from which you want to import information Figure 54 E3 Micro Exa P1 xl C Phenotypo info file csv Rend Only a B c BP ELF G E K M Y indies Gonder Eihmcity Ago Wigh Height Blood Pressure Systolic Blood Pressen Dashes Blood Type Phenolype Pos 1 Phenotype Pos 3 Phenotype Pos 3 Phoorofypa Meg 1 IM Caucasian 30 120 100 TU AD Pas Paz Fos3 Magi 2M Caucasian KO 1M 100 TD AB Fozi Pos2 Poss Magi 3h Caucasian 2 an 14 LIL DAB Eni Posi Pusa Magi 4 hd Caucasian JA 120 100 TU AD Posi Fasz Pots Magi 5M Caucasian NO 120 100 7D AB Pasil Posi Fos3 Magi Figure 54 Phenotype Information File 3 Select Open Information from the phenotype information file you selected is imported into GenomeStudio and displayed in the Samples Table GenomeStudio Genotyping Module v1 0 User Guide 62 CHAPTER 5 Analyzing Your Data Estimating the Gender of Selected Samples To estimate gender for selected samples 1 In the Samples table select the samples for which you want GenomeStudio to estimate gender The selected samples are highlighted in dark blue Note that the Gender column of each sample contains Unknow
104. orm Theta Figure 99 SNP Graph GenomeStudio Genotyping Module v1 0 User Guide 124 CHAPTER 8 User Interface Reference Sample Graph The Sample Graph Figure 100 displays all SNPs for the currently selected sample in the Samples Table The SNPs are colored according to their genotype calls Use the Sample Graph to evaluate sample quality SNP Graph Sample Graph Errors Table SNP Graph Alt jk 1 BROS a N 1485978258 A 0 40 0 60 Norm Theta Figure 100 Sample Graph Errors Table The Errors Table Figure 101 lists any reproducibility errors or parent child heritability errors found in the data loaded into GenomeStudio Errors Table 5 g Gel Ca f ad A d oo ai d og aoe Parent Paani Eina Ehia Thide 2 D sem sz um one SA BES 4 ween meg Wet Fee Figure 101 Errors Table Part 11319113 Rev A Table 10 Column Error Index Error Type Child Rep Index Child Rep Child Rep GType Parent1 Rep Index Parent1 Rep Parent1 Rep GType Parent2 Index Parent2 Parent2 GType SNP Index SNP Name Detachable Docking Windows The columns in the Errors Table are listed and described in Table 10 Errors Table Columns Description Row index of the error Type of error Rep Reproducibility P C Parent Child heritabilit P P C Parent Parent Child hentabiiiy Sample index of the child sample involved in the error Sample ID of the chil
105. ort the cluster positions from that File Cancel Back Next gt Finish Figure 9 GenomeStudio Project Wizard Welcome 3 Click Next to advance to the Project Location dialog Choosing a Project Name and Location In the GenomeStudio Project Wizard Project Location dialog Figure 10 you must choose a project repository the directory where you will store your projects Each project is saved in a subdirectory that is given the same name as the project All project related files are saved within each project s subdirectory The main project file is given a bsc file extension Additionally you can choose whether you want to create a new project or whether you want to select an existing project from the Laboratory Information Management System LIMS GenomeStudio Genotyping Module v1 0 User Guide 12 CHAPTER 2 Creating a New Project GenomeStudio Project Wizard Project Location Genotyping Project Li e o M Please specify the name and location Far your project U m n ci Projects Repository lentas Browse Project Mame Create Select From LIMS Project will be created in Ci TestDatalRepository Projects aT Cancel lt Back Next gt Finish Figure 10 GenomeStudio Project Wizard Project Location Creating a To create a new project Project 1 Browse to the project repository where you want to store your project 2 Choose one of the following options
106. p columns to re arange their display order Also you can drag them to from the Hidden list to hide show them Display Locked Columns Hidden Calumns ILMM Strand Customer Strand Top Genomic Sequence lllumicode Seq ASO A Displayed Columns lt Show s i Index Name Comment Hw E quil Chr x Concordance Position CNY Begion ChiT est OD g Exp Clusters Het Excess Intensity Onl AA Freg id Displayed Subcolumns Hidden Subcolumns Add scs Manifest GenT rain Score Orig Score Edited Cluster Sep Hide gt lt Showy Cancel Figure 42 Column Chooser 2 In the Column Chooser dialog click to select a column that you want to display 3 Click Show The column you selected is moved to the Displayed Columns list or the Displayed Subcolumns list Alternately you can select and drag a column to the Displayed Columns list 4 To change a column s position in the table click to select a column then drag the column header up or down in the displayed column list 5 Click OK to display columns in their new positions Alternatively click Cancel to retain columns in their current positions GenomeStudio Genotyping Module v1 0 User Guide 46 CHAPTER 3 Viewing Your Data Viewing the Controls Dashboard To view a graphic report displaying system controls information Select Analysis View Controls Dashboard The Controls window appears Figure 43 E Controls File Allele Specific Extension
107. polar coordinates Theta value of the center of the BB cluster in normalized polar coordinates Standard deviation in theta of the BB cluster in normalized polar coordinates R value of the center of the AA cluster in normalized polar coordinates Standard deviation in R of the AA cluster in normalized polar coordinates R value of the center of the AB cluster in normalized polar coordinates Standard deviation in R of the AB cluster in normalized polar coordinates R value of the center of the BB cluster in normalized polar coordinates Standard deviation in R of the BB cluster in normalized polar coordinates Nucleotide substitution for the SNP on the Illumina top strand Design strand designation Type integer float float float float float float float float float float float float string string Visible by Default Part 11319113 Rev A Table 13 SNP Table Columns continued Column Customer Strand Top Genomic Sequence Address 2 Comment Norm ID HW Equil Concordance CNV Region Exp Clusters GenomeStudio Genotyping Module v1 0 User Guide Customer strand designation Sequence on the top strand around the SNP Bead type unidentified for the second allele only used for Infinium User specified comment Right click in the column to view the context menu to set this value Normalization ID for the SNP Hardy Weinberg Equilibri
108. positoryTProjecksVaT G1 Genotyping GX Gene Expression Fl PT Protein Analysis 2 Methylation n ChIP Sequencing nm DAA Sequencing IRS PINA Sequencing Figure Starting a New Project New Project Area e Select File New Project Genotyping Figure 8 GenomeStudio Genotyping Module v1 0 User Guide 10 CHAPTER 2 Creating a New Project select File New Project Genotyping VAIN Analysis Tools Window NN Open Project Ctrl O Save Project Ctrl S Save Project Copy As Ctrl Shift 4 Close Project Ctrl Shift C 5 Page Setup Ctrl Shift U Print Preview Ctrl Shift 3M Print Ctrl P Recent Project Alt F4 o Gene Expression e1 Protein Analysis Methylation ChIP Sequencing DNA Sequencing RNA Sequencing Figure 8 Starting a New Project File Menu The GenomeStudio Project Wizard Welcome dialog appears Figure 9 Part 11319113 Rev A Choosing a Project Name and Location 11 GenomeStudio Project Wizard Welcome Genotyping Project 9 Welcome to Ehe Genotyping Project Wizard U m n a Welcome to Ehe Genotyping Project Wizard This wizard will guide you through the steps needed to create a project For one of Illumina s genotyping assays This analysis module supports the GoldenGate and Infinium assays The assay will be defined by the SNP manifest that you select for your project IF vou have a pre existing cluster File you can choose to imp
109. provided by third parties These plug ins must be downloaded and installed in the correct directory before they are available in GenomeStudio You can view the bookmarks created by an autobookmarking plug in in the IGV the ICB and the Bookmark Viewer To apply autobookmarking algorithms to your data perform the following steps 1 After your data have been loaded into GenomeStudio select Tools Show Genome Viewer to launch the IGV The IGV appears with the Add Favorite Data Plots form prominent Figure 89 Part 11319113 Rev A Plug ins 113 B Illumina Genome Yiewer IGY Microarray File Edit View Data Analysis Help i wa Add Favorite Data Plots Form lo x Table Source Edit GT Samples Data Pl Sample Name Favorite Data Plots 3 Table 1513271004 A at O 1513271004 A at O 1513271004 A id O 1513271005 A at O 1513271005 A at O 1513271005 A id SubColumn N ames SubColumns NENNEN O x Raw O v Raw O Score Ll Theta OR Dx Oly O B Allele Freq Pc ES Ne Cancel Line Style ond Line Width screen pixels Smooth Series Positive GS Red Negative ml Black Y Line Style Line Width Data Properties Display Properties Figure 89 Illumina Genome Viewer 2 Select the data plots you want to view Figure 90 GenomeStudio Genotyping Module v1 0 User Guide 114 CHAPTER 7 Performing LOH and Copy Number Analysis Add Favorit
110. r locus per replicate pair Does not include genotypes with intensities that fall below the no call threshold low GenCall Score Cutoff Equals Correct Errors Reproducibility frequency calculated as sqrt 1 error rate The error rate does not include genotype calls that fall below the no call threshold GenomeStudio Genotyping Module v1 0 User Guide 98 CHAPTER 6 Generating Reports Table 5 is an example of the Duplicate Reproducibility section of a Reproducibility and Heritability Report Table 5 Example Duplicate Reproducibility Rep1 Genotype Rep2 Genotype Correct Errors Repro_Freq AB AB 1 0 1 AA AB O 1 O AA BB 0 1 O AA No call 0 0 NAN Parent Child Heritability Columns Table 6 describes the columns of the Parent Child Heritability section of the Reproducibility and Heritability Report Table 6 Reproducilbility and Heritability Report P C Heritability Column Parent DNA Name Child DNA Name Correct Errors Total PC Heritability Freq Description Name of the sample designated as parent in a P C relationship Name of the sample designated as child in a P C relationship Number of loci with consistent Parent Child genotype comparisons Number of loci with inconsistent Parent Child genotype comparisons Number of total genotype comparisons one genotype comparison per locus per Parent Child pair Does not include genotype comparisons with intensities that fall below the no c
111. r of samples in each cluster are also displayed Figure 27 ile Bl HI TO alt r 508020 0 40 0 60 Morn Theta Figure 27 SNP Graph Part 11319113 Rev A Shading Call Regions 31 Shading Call Regions GenCall Score is a quality metric that indicates the reliability of each genotype call The GenCall Score is a value between 0 and 1 assigned to every called genotype Genotypes with lower GenCall scores are located further from the center of a cluster and have a lower reliability GenCall Scores are calculated using information from the clustering of the samples To get a GenCall Score each SNP is evaluated based on the following characteristics of the clusters angle dispersion overlap intensity There is no global interpretation of a GenCall Score as the score depends on the clustering of your samples at each SNP which is affected by many different variables including the quality of the samples and the loci j A 5096 GenCall Score refers to the 5Oth W NOTE percentile GenCall Score in a particular distribution of GenCall Scores A 50 GenCall Score for a DNA sample represents the 5Oth percentile rank for all GenCall Scores for that sample Similarly a 50 GenCall Score for a particular locus represents the 50th percentile rank for all GenCall scores for that locus In a genotyping project samples are displayed in three distinct shaded areas based on their genotype calls The size of the shaded
112. r the sample across alise A number between 0 and 1 indicating how well the samples clustered for this locus GenCall score at the 50th percentile when scores are ranked for all samples GenCall score at the 10th percentile when scores are ranked for all samples Heterozygote excess frequency calculated as Observed Expected Expected for the heterozygote class If fap is the heterozygote frequency observed at a locus and p and q are the major and minor allele frequencies then het excess is defined as fan 2pq 2pq The value regularizes the estimation of heterozygote excess frequency This reduces the variance of the estimation for cases of extremely low minor allele frequency Hardy Weinberg p value estimate calculated using genotype frequency The value is calculated with 1 degree of freedom and normalized to 100 individuals Cluster separation score Mean of the normalized theta angles for the AA genotype GenomeStudio Genotyping Module v1 0 User Guide 90 CHAPTER 6 Generating Reports Table 2 Locus Summary Report Column Descriptions Column Description Standard deviation of the normalized theta angles for the AA_T_Std AA genotype AB_T_Mean Mean of the normalized theta angles for the AB genotype Standard deviation of the normalized theta angles for the AB_T_Std AB genotype BB_T_Mean Mean of the normalized theta angles for the BB genotypes BB T Std a deviation of the normalized theta angles for the ge
113. rface Reference Topics Introduction Detachable Docking Windows 123 Graph Window 126 Data Table 136 Samples Table 143 Project Window 144 Log Window Main Window Menus Graph Window Toolbar Table Windows Toolbar Context Menus GenomeStudio Genotyping Module v1 0 User Guide 122 CHAPTER 8 User Interface Reference Introduction The GenomeStudio Genotyping Module user interface provides tools for loading intensity files running the clustering algorithm browsing loci and displaying them graphically Figure 98 shows the default window configuration of the GenomeStudio Genotyping Module Graph Window Project Window GenomeStudio Genotyping Test5 File Edit View Analysis Tools Window Help Doa OO m o gg SNP Graph Heat Map hs Full Data Table Paired Sample Table EN S Project k 1 e a Hi MitoA13106G 3 Manifests B Data Score MitoA1004 9048 M 10045 0 7260 0 317 0 203 0 119 0 361 MitoA1055 10551 0 7038 0 307 0 287 0 089 MitoA1125 11252 0 7038 0 119 MitoA1146 11468 0 7220 MitoA1181 11813 0 6955 MitoA1230 12309 Mito41310 MitoA1326 MitoA1378 0 0 20 0 40 0 60080 1 MitoA1423 Norm Theta Mito41456 MitoA1521 MitoA1524 Samples Table MitoA1530 m Pa es MitoA1575 B a ui i 2 MitoA1592 MitoA1616 33333 0 153 0 124 0 114 0 134 0 094 0 069 0 074 0 168 0 153 0 139 0 099 0 114 0 100 222222222 Rows 561466 Disp 561466 Sel 1 Filt
114. romosomes or any combination of chromosomes 14 Click Next to advance to the next dialog Figure 95 Auto Bookmark Analysis Press to Start Analysis Start lt lt Previous Figure 95 Autobookmark Analysis 15 Click Start to run the autobookmarking analysis The algorithm progress bar appears The Algorithm Message Log shows the progress as the algorithm is applied to your data Part 11319113 Rev A Plug ins 16 When the analysis is complete a message appears in the Algorithm Message Log Figure 96 Auto Bookmark Analysis Press to Start Analysis Abort Algorithm Message Log Analyzing sample NA0033 93 Getting sample NA0084 94 data Analyzing sample NA0034 84 Getting sample NADOSS 95 data Analyzing sample NA0095 85 Getting sample NA0096 96 data Analyzing sample NA0096 96 Found 2 bookmarks Elapsed Analysis Time O Hours O Minutes 40 Seconds Analysis is complete lt lt Previous Figure 96 Analysis is Complete 17 Click Close Bookmarks appear in the IGV the ICB the Bookmark Viewer and the Full Data Table Using Column All column plug ins are accessed and run through the Plug Ins GenomeStudio Genotyping Module main window The results of applying the column plug ins appear in the Full Data Table the IGV and the ICB To apply column plug ins to your data perform the following steps 1 In the GenomeStudio Ge
115. rties of Selected Samples Analyzing Paired Samples Using Concordance Features 68 Exporting Allele Calls 68 Importing Allele Calls 69 Concordance Calculations Using Column Plug Ins GenomeStudio Genotyping Module v1 0 User Guide 60 CHAPTER 5 Analyzing Your Data Introduction Use the procedures in the following sections to analyze your data Importing Phenotype Information A phenotype information file is a csv file you can create and import into a project if you want include sample related phenotype information A phenotype information file must contain an Index column that corresponds to the Index column in the Samples Table You can also optionally include the following columns in a phenotype information file Gender Ethnicity Age Weight Blood Pressure Systolic Blood Pressure Diastolic Blood Type Phenotype Pos 1 Phenotype Pos 2 Phenotype Pos 3 Phenotype Neg 1 Phenotype Neg 2 v ow cC YV cvv TY NY YY v ww Fw Phenotype Neg 3 ki The columns listed above are the only columns m NOTE you can import into a GenomeStudio genotyping project using a phenotype information file Additional columns present in a phenotype information file will not be imported into the GenomeStudio project To import phenotype information from a file Part 11319113 Rev A Importing Phenotype Information 61 1 Select File Import Phenotype Information From File The Import Phenotype File window appears Figure 53 L
116. s 5 Click Finish to complete the wizard The Genotyping Module loads your intensity files If you loaded a cluster file go to Chapter 3 If you did not load a cluster file continue to Chapter 4 GenomeStudio Genotyping Module v1 0 User Guide 28 CHAPTER 2 Creating a New Project Part 11319113 Rev A 30 30 34 35 35 36 37 42 43 44 31 46 47 49 Chapter 3 Viewing Your Data Topics Introduction SNP Graph Cartesian and Polar Coordinates Normalization Adjusting Axes Selecting Samples Marking Samples Excluding Samples Plotting Excluded Samples Customizing the SNP Table Shading Call Regions Viewing the Controls Dashboard Exporting Controls Data Viewing the Contamination Dashboard GenomeStudio Genotyping Module v1 0 User Guide 30 CHAPTER 3 Viewing Your Data Introduction SNP Graph This chapter describes how to use graphs and tables to display mark and edit your data in the GenomeStudio Genotyping Module For more information about the various elements of the GenomeStudio user interface such as windows tables and columns see Chapter 8 User Interface Reference The SNP Graph Figure 27 displays all samples for the currently selected SNP in the SNP Table and in the Full Data Table Samples are colored according to their genotype If you view a SNP Graph in polar coordinates with normalization and call region shading turned on the cluster ovals call region shading and numbe
117. s and corresponding toolbar buttons Table 19 describes File Menu functions Table 19 File Menu Functions Selection New Project Open Project Save Project Save Project Copy As Close Project Load Additional Samples Import Cluster Positions Function Opens a new project Opens a previously saved project Saves all current information in this project so you can return to it later Displays the Save Project Copy As dialog in which you can specify a file name and location to save a copy of the current project that does not include currently excluded samples Closes the current project and returns to the start screen of the Genotyping Module Opens the GenomeStudio Project Wizard to the Loading Sample Intensities page which allows you to use a sample sheet to load sample intensities or load sample intensities by selecting directories with intensity files Opens to the last directory used to load clusters so that you can choose a data file from which to import cluster positions GenomeStudio Genotyping Module v1 0 User Guide Toolbar Button if used 146 CHAPTER 8 User Interface Reference Table 19 File Menu Functions continued Selection Export Cluster Positions Export Cluster Position to LIMS Export Manifest Update Project from LIMS Import Phenotype Information from File Page Setup Print Preview Print Recent Project Exit Toolbar Button if used F
118. s equal to the AB cluster s theta mean or 1 if it is equal to or greater than the BB cluster s theta mean B Allele Freq is linearly interpolated between O and 1 or set to NaN for loci categorized as intensity only For loci included in GenomeStudio statistics the base 2 log of the normalized R value over the expected R value for the theta value interpolated from the R values of the clusters For loci categorized as intensity only adjusted so that the expected R value is based upon the weighted mean of the cluster itself Illumina designated top strand genotype Genotype calls for the given sample imported when the Import Allele Calls feature is used Numeric correlation of the top allele call for a SNP in the current project with the imported allele call of a SNP from a different project Genotype call of SNP and sample at the time the project was originally clustered Estimate of copy number at individual locus Level of confidence that the CNV value is correct based on the CNV algorithm used GenomeStudio Genotyping Module v1 0 User Guide Type float float float float string string integer string float float Visible by Default N N 129 130 CHAPTER 8 User Interface Reference SNP Table The SNP Table Figure 104 shows statistics for each SNP Full Data M Paired Sample Table eR aa ela 23 c9 9 AT 58 a BL 03 F ChiTest1 P P
119. shboard Cancel E 2 Browse to the location where you want to save your file 4 Click Save Type a name for your file in the File Name text field The exported controls dashboard file is saved as a csv file in the location you specified Part 11319113 Rev A Viewing the Contamination Dashboard 49 Viewing the Contamination Dashboard To view a graphic report displaying contamination information Select Analysis View Contamination Dashboard The Contamination Controls window appears Figure 46 BR Contamination Controls File 3 1336930 set l 2 02 V and US match expected set 23 3545 U3 and US match expected set 2 2 22 V and US match expected set 44 2864 V and US match expected Figure 46 Contamination Dashboard ri The Contamination Dashboard applies only to W NOTE GoldenGate data There is no Contamination Dashboard for Infinium data GenomeStudio Genotyping Module v1 0 User Guide 50 CHAPTER 3 Viewing Your Data Part 11319113 Rev A 52 52 53 55 56 Chapter 4 Generating Clusters Topics Introduction Running the Clustering Algorithm Reviewing Clusters Editing Clusters 55 Redefining the Cluster 55 Excluding Samples 55 Shifting the Cluster Location 55 Changing the Cluster Height Width Exporting the Cluster File GenomeStudio Genotyping Module v1 0 User Guide 52 CHAPTER 4 Generating Clusters Introduction Illumina s assays require cluster locati
120. sizing cursor appears GenomeStudio Genotyping Module v1 0 User Guide 56 CHAPTER 4 Generating Clusters 3 Drag the edge of the oval to reshape the cluster SNP Graph Sample Graph Errors Table SMP Graph Alt BS ES 1 BR E TS 2 rs1003553 bad Define 44 Cluster Using Selected Samples Define 46 Cluster Using Selected Samples Define BB Cluster Using Selected Samples Cluster this SMP Cluster this SNP Excluding Selected Samples Configure Mark Samples Table Mark Selected Points um Dm Clear Marks a Exclude Selected Samples Include Selected Samples Gender Include all Samples 1485978108 A Unknown Show Legend 1485986027 4 Unknown 1485978034 A Unknown e Show Excluded Samples Unknown 1485978235 A Unknown Auto Scale Axes 1485978266 5 Unknown Properties i 1485978269 A Unknown jiii Rows 8 Disp 8 Sel 2 Filter Filter is not active Figure 50 Editing Clusters The clustering algorithm runs excluding the samples you selected Exporting the Cluster File You can export a cluster file any time after clustering To export the cluster file Part 11319113 Rev A Exporting the Cluster File 57 1 Select File Export Cluster Positions Figure 51 File Edit wiew Analysis Tools Window Help Ni ew Project X Open Project Ctri o ei Save Project Cbrl 5 Save Project Copy As Cbrl Shift 4 Close Project Ckrl 5hift 2 Fal Load Additio
121. sked Questions Table 34 lists frequently asked questions and associated responses Table 34 Frequently Asked Questions 5 Question Response A SNP Manifest is a file containing the SNP to beadtype mapping as well as all SNP annotations For the GoldenGate assay this is an OPA file in l What is a SNP Manifest opa format For the Infinium assay this is a bpm file in binary format You can always export your manifest information to csv format by selecting File Export Manifest The cluster file contains the mean R and standard deviation theta of the cluster positions in 2 What information does a normalized coordinates for every genotype for cluster file contain every SNP The cluster file also includes cluster score information as well as the allele frequencies from the training set used to generate the cluster file Part 11319113 Rev A
122. ss Nie GenCall score at the 50 rank when scores are ranked for all loci GenCall score at the 10 rank when scores are ranked for all loci A formula determines whether a sample is recommended for inclusion or exclusion O Remove 1 Include GenomeStudio Genotyping Module v1 0 User Guide 86 CHAPTER 6 Generating Reports Locus Summary Report The Locus Summary Report is a comma delimited text file csv file that includes the columns described in Table 2 To generate a Locus Summary Report 1 Run the Report Wizard by selecting Analysis Reports Report Wizard The Report Type dialog appears 2 Select Locus Summary Report Figure 72 Genotyping Report TEN What type of report would you like ta generate U m n a Final Report Locus Summary DNA Report Locus x DNA Cancel amp Back Mext gt Finish Figure 75 Locus Summary Report Selected 3 Click Next The Destination dialog appears Figure 76 Part 11319113 Rev A Locus Summary Report 87 Genotyping Report sl a a a Where would you like bo save your report U m n a Output Path c TestDatalRepository Projects GT Test5 Browse Report Name rests Locussummary Cancel lt Back Het gt Finish Figure 6 Destination Locus Summary 4 Browse to select an output path for your Locus Summary Report 5 A report name is generated by default You can give your Locus Summary
123. t 18 PC2 Child 13 PC2 Parent 20 PC3 Child 21 PC4 Child 22 PPC1 Child 23 PPC1 Parent1 24 PPC1 Parent 25 PPC2 Child 26 PPC2 Parentl 27 PPC2 Parent2 28 PPC3 Child 23 PPC3 Parent 30 Rep4 3 3 Rep5 1 10 PPC3 Parent2 31 NA0046 45 NA0032 32 NAO032 33 Redo 34 Redo1 35 NA0036 36 NAD037 37 NA40038 38 NA0039 39 NA0040 40 NA0041 41 NA0042 42 NA0043 43 NA0044 44 NAO0045 45 NA0047 47 NA0048 48 NA0049 43 NAO050 50 NAD051 51 NA0052 52 NA0053 53 NA0054 54 NA0055 55 NAD056 55 NA0057 57 NA0058 58 NA0053 53 NADDEO 60 lt lt Previous Next gt gt Figure 93 Selecting Samples for Analysis NAD061 61 NADOBZ 62 NAD063 63 NA0064 64 NADOES 65 NADD6E 66 NADO6 67 NA0063 58 NA0069 69 NADD O 70 NA0071 71 NA007Z 72 NA0073 73 NA0074 74 NA0075 75 Close ES S EIS ES S EST ST S EST EST ST IST EST ST K umo 7 P FF FF Select All Unselect All EA 12 Click Next to advance to the next dialog Figure 94 GenomeStudio Genotyping Module v1 0 User Guide 118 CHAPTER 7 Performing LOH and Copy Number Analysis Auto Bookmark Analysis Select Chromosome for Analysis Select All Unselect All lt lt Previous Next gt gt Close Figure 94 Selecting Chromosomes for Analysis 13 Select one or more chromosomes for analysis You can select all ch
124. teger string string integer string integer Visible by Default Y Y Y Y Y N The Paired Sample Table also includes per pair subcolumns which are populated from the Reference to Cluster and Reference columns of the Sample Sheet The pairing number for example Paired Sample 1 and sample names appear above the subcolumn list in the Paired Sample Table The subcolumns are described in Table 17 Paired Sample Table Per Pair Subcolumns Description Value of theta for the reference sample Value of theta for the subject sample IdTheta sub ref Absolute value of the difference between subject and reference theta values Allele Freq Ref Allele frequency of the reference sample Allele Freq Sub Allele frequency of the subject sample GenomeStudio Genotyping Module v1 0 User Guide Type float float float float float Visible by Default Y Y 136 CHAPTER 8 User Interface Reference Table 15 Column IdAlleleFreq sub ref R Ref R Sub Log2 Rsub Rref GType Ref GType Sub LOH Score CN Estimate CN Shift Samples Table Paired Sample Table Per Pair Subcolumns continued Visible by Description Type Default Absolute value of the difference between subject and reference allele float Y frequency values Value of R for the reference sample float Y Value of R for the subject sample float Y Log base 2 of the ratio of subject and float Y reference R values
125. to follow The columns can be in arbitrary order and additional user defined columns can be included in the file Table 33 Data Section Required and Optional Columns Column Sample_ID Sample_Name Sample_Plate Sample_Well SentrixBarcode A SentrixPosition A Gender Sample_Group Replicates Parent1 Parent2 Description Sample identifier used only for display in the table Name of the sample used only for display in the table The barcode of the sample plate for this sample used only for display in the table The well within the sample plate for this sample used only for display in the table The barcode of the Universal Array Product that this sample was hybridized to for Manifest A The position within the Universal Array Product this sample was hybridized to for Manifest A and similarly for B C etc depending on how many manifests are used with your project Male Female or Unknown A group if any that this sample belongs to used for exclusion in the Final Report Wizard The Sample ID of a sample that is a replicate to this sample used in reproducibility error calculations The Sample ID of the first parent for this sample The Sample ID of the second parent for this sample GenomeStudio Genotyping Module v1 0 User Guide Optional O or Required R 164 APPENDIX A Table 33 Data Section Required and Optional Columns continued Optional O or Col
126. tory list box is populated with the directories contained in your repository To select the intensity files you want to load 1 2 Browse to the SNP manifest and data repository you want to use Click on one or more directories in the Directories in Repository list box Part 11319113 Rev A Importing Cluster Positions 25 3 Click Add to add the directories to the project The directories appear in the Selected Directories listbox as you choose them All intensity files idat files contained within the selected directories are loaded and added to the project If you are using LIMS if the manifest NOTE name contained in the idat file does l not match the name of the manifest you have loaded that intensity file will be skipped 4 Click Next to advance to the Cluster Positions dialog Importing Cluster Positions The Cluster Positions dialog is the final screen of the GenomeStudio Project Wizard Figure 26 From this screen you can import a cluster file egt file and choose to use these cluster definitions to call genotypes for your samples GenomeStudio Genotyping Module v1 0 User Guide 26 CHAPTER 2 Creating a New Project GenomeStudio Project Wizard Cluster Positions Genotyping Project 9 3 IF vou have an existing cluster File that you want bo import U m n ci cluster positions From enter it here Otherwise vou can cluster the samples you ve selected to determine cluster pos
127. um score for the SNP Measure of agreement between two genotypes from the same SNP locus SNPs and nonpolymorphic probes falling in known CNV regions This column is automatically populated with information from the product manifest and may not be current because the number of known CNV regions is constantly changing This column is for informational purposes only Number of expected clusters for a locus 1 for nonpolymorphic probes 2 for mitochondrial DNA and Y loci 3 for any other loci This column is automatically populated with information from the product manifest This column is for informational purposes only Detachable Docking Windows 133 Type string string string string integer float integer integer integer Visible by Default N 134 CHAPTER 8 User Interface Reference Table 13 SNP Table Columns continued Column Description Visible by Type Default Intensity Only Indicates what type of information is available for a locus 1 Locus with intensity information only that is not included in GenomeStudio statistics such as Call Rate O Locus with intensity and genotyping information that is included in GenomeStudio statistics such as Call Rate This column is automatically populated with information from the product manifest but is also editable This information has been determined based on HapMap samples and therefore m
128. umn Description Required R Path Directory where your data are stored O Used for paired sample analysis Populate Reference this column with the sample ID of the O reference sample Figure 109 is an example sample sheet Your sample sheet header may contain any and as much information as you choose NOTES Your sample sheet may contain any number of columns you choose Your sample sheet must be in a comma delimited csv file format Redos and Replicates Sample entries with the same Sample ID are considered redos in the GenomeStudio Genotyping Module When you generate the Final Report you have the option to keep data for the best run of a redo set If you want to keep data for all redos in the Final Report it is best to make each Sample_ID unique in the Sample Sheet If a Replicate is specified for a Sample ID occurring more than two times in the Sample Sheet considered a redo the GenomeStudio Genotyping Module by default forms one replicate pair with the next occurrence of that Sample ID Sample Sheet Template A template for a sample sheet is provided on your GenomeStudio CD Use this template to create your own user defined sample sheet Part 11319113 Rev A Do a KR Header 3 investigato BeadStudio User G50006482 0OPA NADO34 NA0035 Redo2 OMA Ren Figure 109 Sample Sheet Example Plate Plate 1 Plate 1 Plate Plate 1 Piste Plato 1 Piste 1 P
129. unction Allows you to export cluster position data to an egt file using the following options For selected SNPS allows you to export cluster position data for selected SNPs only For all SNPS allows you to export cluster position data for all SNPS Displays a list from which you can choose to export cluster positions data to LIMS Allows you to export a manifest as a csv file Allows you to update the project from LIMS Allows you to import phenotype information for your samples from a file Opens the Windows Page Setup dialog which you can use to set up the page properties and configure the printer properties Opens the Print Preview window from which you can preview how the selected graph will print Displays the Print dialog Use this dialog to select print options for the currently displayed graph Allows you to select a project you have recently worked on Closes GenomeStudio Part 11319113 Rev A Main Window Menus 147 Table 20 describes Edit Menu functions Table 20 Edit Menu Functions Selection Cut Copy Paste Select All Function Toolbar Button if used Cuts the current selection Copies the current selection to the clipboard Pastes the current selection from the clipboard Selects all rows and visible columns in the current table Table 21 describes View Menu functions Table 21 View Menu Functions Selection Save Current View Restore Default View Sa
130. ve Custom View Load Custom View Log Project Function Toolbar Button if used Allows you to save the window configuration of the open project Restores the default window configuration Allows you to save a custom window configuration Allows you to load a previously saved window configuration Shows or hides the Log window Shows or hides the Project window GenomeStudio Genotyping Module v1 0 User Guide 148 CHAPTER 8 User Interface Reference Table 22 describes Analysis Menu functions Table 22 Selection Auto Exclude Samples Exclude Samples by Best Run Cluster All SNPs Update SNP statistics Edit Replicates Edit Parental Relationships Update Heritability Reproducibility Errors Analysis Menu Functions Function Automatically evaluates each sample and determines its suitability for inclusion based on overall intensity Excludes under performing samples Samples that have been processed more than once appear in the Samples table multiple times These samples can be identified by their matching Sample IDs Using Exclude Samples by Best Run only the sample with the highest GC10 or GC50 score for each particular sample ID will be included The other samples with that sample ID will be excluded Initiates clustering or reclustering based on the samples in a project and determines the dio genotype score for each locus Clustering over rides any cluster files that may have been use
131. y RE Blueviolet Solid CETERI Cancel Figure 88 Display CNV Analysis 2 Select the CNV Analysis to display as bookmarks GenomeStudio Genotyping Module v1 0 User Guide 112 CHAPTER 7 Performing LOH and Copy Number Analysis Plug ins Using Auto bookmarking Plug ins 3 Click OK The CNV analysis is converted into bookmarks and becomes the active bookmark analysis in the IGV and ICB Illumina provides several types of plug ins that you can use for LOH visualization copy number analysis or other types of analysis Plug ins are available from the GenomeStudio Portal You can install one or more plug ins after installing the GenomeStudio Framework and at least one software module Autobookmarking plug ins are external code libraries that create bookmarks in the IGV based on data that appears in GenomeStudio tables and on chromosomal position information You can access autobookmarking plug ins from the IGV Analysis menu CNV Analysis plug ins are external code libraries that create CNV Analyses in GenomeStudio For more information about CNV analysis in GenomeStudio see CNV Analysis on page 107 Column plug ins are external code libraries that create new subcolumns based on data that appears in GenomeStudio tables You can access column plug ins by selecting Analysis Create Plug In Column from the GenomeStudio Genotyping Module main window Report plug ins are customized report formats
132. y integer Y GenomeStudio Genotyping Module v1 0 User Guide 138 CHAPTER 8 User Interface Reference Table 16 Samples Table Columns continued Column p05 Red p50 Red p95 Red p10 GC p50 GC Rep Error Rate PC Error Rate PPC Error Rate Call Rate Aux Description 5th percentile of B allele intensity 50th percentile of B allele intensity 95th percentile of B allele intensity 10th percentile GenCall score over all SNPs for this sample If displayed as 0 000 this column needs to be manually recalculated 50th percentile GenCall score over all SNPs for this sample If displayed as 0 000 this column needs to be manually recalculated Reproducibility error rate for this sample calculated as 1 sqrt 1 errors max possible errors Errors and max possible errors do not include genotype calls that fall below the no call threshold If displayed as 0 000 this column needs to be manually recalculated Parent child heritability error rate for the sample If displayed as 0 000 this column needs to be manually recalculated Parent parent child heritability error rate for the sample If displayed as 0 000 this column needs to be manually recalculated Percentage of SNPs expressed as a decimal whose GenCall score is greater than the specified threshold Arbitrary integer you can use to differentiate and or sort samples Use the context menu to set this value by right clicking anywh

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