TaqMan Genotyper Software v1.0.1 TaqMan Genotyping Data Analysis Software March 2011
Product Overview TaqMan Genotyper Software
TaqMan Genotyper Software Standalone data analysis software for Applied Biosystems TaqMan Genotyping Solutions Showcase Accuracy new genotyping algorithm improves accuracy in automated genotype calling Efficiency provides multi-plate data analysis for high-throughput workflows Flexibility allows for editing or removal of plates or individual data points Versatility allows the use of controls and reference panels for accurate genotype calling Comprehensivene includes quality control tools for troubleshooting your experiments 3
Compatible Real-Time PCR Systems Applied Biosystems Real-Time PCR System ViiA 7 Real-Time PCR System 7900HT Fast Real-Time PCR System Experiment file extension System software *.eds ViiA 7 Software v1.0 *.sds SDS Software v2.1, v2.2.2 (Enterprise), v2.3 (Non-Enterprise), and v2.4 (Enterprise and non- Enterprise) 7500 Fast Real-Time PCR System *.eds 7500 v2.0, v2.01, v2.02, and v2.0.4 *.sds SDS Software v1.4 4 TaqMan OpenArray Real- Time PCR System StepOne and StepOnePlus Real-Time PCR Systems *.spd OpenArray SNP Genotyping Analysis Software, v1.0.2 and v1.0.3 *.eds StepOne Software v2.01 and v2.1
TaqMan Genotyper Software Download this software from www.appliedbiosystems.com/ taqmangenotyper Workflow First Log in + User Accounts Creating a Study + Controls Results + QC Tools Export Data + Transfer Study Study Template Reference Samples Assay Info Sample Info 5
TaqMan Genotyper Software Powerful yet simple to use data analysis features Key Feature Benefits Create Studies and Study Templates Multi-plate data analysis for high-throughput workflow Copy all data analysis criteria for use in future genotyping studies by generating Study templates Import Assay Information File (AIF) and Supplementary Sample Information (SSI) Genotype is displayed as actual nucleotide (A, T, G, C) Assay and sample specific information can be tracked with genotype calls Import Allelic Discrimination (AD) and Absolute Quantification (AQ) files Run multiple plates on real-time instruments without worrying about post-pcr stability issues 6
TaqMan Genotyper Software Powerful yet simple to use data analysis features Key Feature Benefits Two Call Methods to choose from: Autocalling or Classification Scheme User defined quality control settings, plate visualizations, and flags Improved call rate and accuracy in automated genotype calling Classification Scheme is useful for clinical research applications where only few samples are analyzed at a time Easy troubleshooting Edit or remove plates or individual data points Use of controls and reference panels Flexibility of omitting undesired data from analysis Allows manual calling Provides accuracy of genotype calling, help troubleshoot the problems easily 7
TaqMan Genotyper Software Powerful yet simple to use data analysis features Key Feature Benefits New genotyping algorithm Improved accuracy in automated calling Improved capabilities in calling single and two cluster assays Export data in *.cvs, *.xml, *.txt file formats Export scatter plot images as a *.jpg or *.pdf Easy downstream analysis and data management Security and Audit features Software can be used for clinical research applications File based software No need to install Oracle database! Easy installation and removal 8
Literature and Support Tools Literature Getting Started Guide Quick Reference Card TaqMan SNP Genotyping Assays Product Bulletin Release Notes FAQs Support Tools Training Slide Deck Self-paced online Training: TaqMan Genotyper Software 9
Product Training TaqMan Genotyper Software 10
Part 1 First Time Log In Help Menu User Roles User Accounts 11
First Time Log In First time Log in: Default Username: Administrator Default Password: Administrator You will be prompted to change your password. Click ok and change your password Type your new password to log in 12
Where to Find Information Help Menu TaqMan Genotyper Software Getting Started Guide Quick Reference Card About TaqMan Genotyper Software Version and Build Help 13
There are 3 User Roles with different permission levels: Administrator + Scientist + Technician User Roles Partial List: Continued in the Getting Started Guide 14
Go to Tools Security Settings On the Users tab click Create Enter information Select User Role Creating User Accounts 15
Creating User Accounts Security Settings Users and their roles Number of Users per Role Settings Password setup Password expiration 16
System Preferences Default home directory Overwrite study template Display warning when re-analyzing Don t export samples that fail call rate 17
Part 2 Creating a Study Analyzing Data 18
Import experiment files *.eds files *.sds files *.spd files *.sds *.eds *.spd Creating a Study What is a Study? A Study is like a photo album storing a collection of photos A Study is a collection of genotyping experiments that have been created on the same Applied Biosystems Real-Time PCR System platform What to do with a Study? View, analyze, and edit data from multiple plates Obtain the statistical distribution of the alleles Export data 19
Click Create Study In the Study Property Window Name the Study Select the platform Select the experiment type Enter a description (optional) Creating a Study 20
Analysis Settings (1) Creating a Study Tabs in the Analysis Settings Window Call Settings Study Level Settings + Assay-specific Settings Control Identifiers Study Level Settings + Assay-specific Settings QC Settings Well Level QC Flags + Study Level QC Flags 21
Analysis Settings (2) Creating a Study In the Analysis Settings Window Name the Call Method Autocalling or Classification Scheme Select Protect Manual Calls if needed Select Use Reference Panels if applicable 22
Analysis Settings (3) Creating a Study In the Analysis Settings Window Select Hardy-Weinberg for Analysis if you expect a Hardy-Weinberg distribution. Does not apply to X and Y chromosome specific SNPs or mitchondrial SNPs Select Use Positive Controls for Analysis if applicable Select Heterozygote from the drop down menu Allow for autosomal chromosome SNPs Disallow for mitochondrial SNPs Disallow in Males for Y chomosome-specific SNPs 23
Analysis Settings (4) Creating a Study In the Analysis Settings Window Select Baseline for Real-time Data To subtract the baseline fluorescent signal from the final fluorescent signal at default or specified cycle number Specify the cycle number for the final fluorescent signal 24
Analysis Settings (5) Creating a Study Tabs in the Analysis Settings Window Call Settings Control Identifiers QC Settings 25
Analysis Settings (6) Creating a Study Tabs in the Analysis Settings Window Call Settings Control Identifiers QC Settings 26
Importing Data Files (1) Creating a Study Once the Study properties and analysis settings have been specified, import the data files 27
Importing Data Files (2) Creating a Study Select all data files to be imported 28
Call Methods: (1) Autocalling Results Screen display when Autocalling is used 29
Call Methods: (2) Classification Scheme Results Screen display when the Classification Scheme is used. There are several preset Classification Schemes to choose from. Array of Classification Schemes 30
Analysis Features Results Data Analysis Features Select data points Select all data points Zoom in Zoom out Panning Modify Scale of scatter plot Save scatter plot as image Expand or collapse the plot View Legend Bookmarking 31
Flag Summary and Assays Summary Quality Control Flag Summary Assays Summary 32
Experiments Tab Different Plate Layout Displays (1) Quality Control SDS 384-Well Plate Overview screen and drop down menu Display by Assays Display by Samples Display by ROX Ranges Display by Task Display by Genotype Call 33
Experiments Tab Different Plate Layout Displays (2) Quality Control TaqMan OpenArray Plates expand the Plate Layout Display Display by Samples Display by Assays 64 format Display by ROX dye Display by Task Display by Genotype Call 34
Part 3 Export Analysis Data Export an Audit Trail Transfer a Study 35
Exporting Analysis Data The Labels for these Calls can be customized Basic Export Advanced Export 36
Exporting an Audit Trail The audit trail contains: General Study information like date, time, user Headings and recorded information for each time the study is saved For a newly created study, the full set of attributes are listed For subsequent changes, only attributes that were changed are added 37
Transfer out Study Transfer a Study Transfer Study function: Allows you to move a study from one TaqMan Genotyper Software application to another computer if you want to share the Study Transfer out creates an *.las file 38
Transfer in Study Transfer a Study Transfer in the new study in *.las file format If a Study is transferred to another computer and modified, the Study cannot be transferred back to the original computer. Rename the Study and upload 39
Part 4 Study Template Reference Samples Bookmarking Assay Information File (AIF) Supplementary Sample Information (SSI) Optimizing Cluster Resolution for AQ Data 40
Use a Study template if you use the same Study properties the same assays the same traceability information in multiple studies Create or open a study Select File Generate Template Study Template To create a Study from a Study template Create Study from template Choose your template Name your Study All other options are grayed out because they are defined in the Study template 41
Creating a Reference Panel Reference Panel Creating a Reference Panel On the Results tab in the sample table Go to View Check Reference Samples Highlight reference samples in the plot or sample table Go to Tag and select Tag for Ref Panel Go to File Menu Select Generate Reference Panel Save Reference Panel file (*.lap format) to User Data folder 42
Importing a Reference Panel Reference Panel Create a Study Import data files Go to Setup References Import Reference Panel file Reference samples listed in Reference Samples tab 43
Bookmarking Select the sample of interest In the Results table Select View check Bookmarks Select Bookmarks set Bookmarks The bookmarks persist in the Results and Quality Control screens, so you can easily find bookmarked wells 44
Assay Information File (AIF) To populate the information from the AIF, click Replace All 45
Assay Information File (AIF) Updated allele information in the Call column in the results table and along the axes of the plot Updated SNP information The rs number will now be displayed instead of the Celera ID for the assay 46
Before adding information Supplementary Sample Information (SSI) Add a text file with sample information like population and gender information 47
After adding information Supplementary Sample Information (SSI) Under Setup click Samples click Import and upload the SSI 48
AQ Data Only Optimizing Cluster Resolution Improved cluster separation at 38 cycles (left) compared to 50 cycles (right) 49
No NTC / Unassigned NTC A. NTC included and properly assigned. The software identifies it as NTC. B. No NTC included. The algorithm will choose the origin of the plot as a starting point for the angles. This may result in less accurate genotype calling. C. NTC included but not assigned. The algorithm will choose the origin of the plot as a starting point and assign genotype calls. 50
For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use. 2011 Life Technologies Corporation. All rights reserved. The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners. TaqMan is a registered trademark of Roche Molecular Systems, Inc. 51