Release Note. Agilent Genomic Workbench 6.5 Lite

Transcription

1 Release Note Agilent Genomic Workbench 6.5 Lite Associated Products and Part Number # G3794AA G3799AA - DNA Analytics Software Modules New for the Agilent Genomic Workbench SNP genotype and Copy Number detection LOH (Loss/Lack of Heterozygosity) detection. GC Content correction Genotyping of reference samples New visualization panels for SNP + LOH Updated aberration reports with LOH information & SNP Genotype report SNP specific QC Metrics Note: AGW 6.5 supports SNP and LOH analysis of constitutional cytogenetic samples but the algorithms are not designed yet to handle challenging samples. As a result, we will not be in a position to support the following samples: cancer (heterogeneity, polyclonality, ploidy, etc), WGA (whole genome amplification), ULS-labeling, and FFPE. Development is ongoing to be able to support this down the road. Target Enrichment Quality Analyzer Ability to run analysis in workflow mode. Support gzip and zip files (4G uncompressed size limit); support plain.txt formats (no size limit). Support AB output read file. Sample Manager Support SNP reference sample. Workflow Manager Ability to use SNP and LOH algorithms in a workflow.

2 Preloaded Data in DNAAnalytics 6.5 These are the datasets that are preloaded into the DNA Analytics 6.5 application: Type AMADID Genome Build # Probes FE Files (Size) CGH Hg US _ _S01_CGHv4_95_Feb07_1_1 2. US _ _S01_CGHv4_95_Feb07_1_2 3. US _ _S01_CGHv4_95_Feb07_1_1 4. US _ _S01_CGHv4_95_Feb07_1_2 CGH Hg CGH Hg CGH Hg CGH Hg CGH Hg CGH Hg ChIP Hg ChIP Hg CH Hg Expres sion Hg Expres sion mm

3 System Requirements for Agilent Genomic Workbench 6.5 Software Windows and Linux System Requirements: Operating System: Windows XP or Vista with Pentium 4 or later ; Red Hat Linux 5 Processor: 2GHz CPU or greater, Intel Core 2 Duo or better Available memory (RAM): 64-bit: 4GB RAM minimum (need more when working with 244K or higher microarrays) 32- bit: 2GB RAM Hard disk space: Display resolution: Internet connectivity: 40 GB (For analysis of large datasets, more space is required) 1280x768 Display minimum T1 or T3 connection (1.5 Requirements: Mps) for use of earray Mac System Requirements: Operating System: Mac OS X v10.5.x (Leopard or higher) Processor: 3 GHz Intel Core 2 Duo CPU or better Available memory 4 GB (RAM): Hard disk space: 40 GB (For analysis of large datasets, more space is required) Display resolution: 1280 x768 or higher Internet connectivity: 1 Mbps or faster Tips on using Agilent Genomic Workbench 6.5 Software Win 7/Vista: need to change install directory : The software will not install correctly on Win7/Vista machines without the correct install directory. Workaround: User needs to make an install directory, with full permissions. 1. Win 7/Vista: user.home property not set correctly : Sometimes, the user home directory value is wrongly set on Win7/Vista. Due to this, many processes like workflow will not function as they require user settings file which is located at user home directory. Workaround: User needs to get the user home directory corrected by authorized system administrator. 2. Change memory settings if necessary : Sometimes, the user can change the memory settings to speed up the processing. Workaround: If you want to maximize the speed of processing, you can change the memory setting for the heap size of several processes. The heap size is controlled by two flags, Xms<size> and Xmx<size>. JVM starts with -Xms amount of memory and can grow to a maximum of -Xmx amount of memory. The 32-bit machine JVM does not support over 1400MB. To change memory settings for running DNA Analytics 6.5

4 1. In Notepad, open the file.../program Files/Agilent/Agilent Genomic Workbench Standard Edition 6.5/ Agilent Genomic Workbench Standard Edition 6.5.lax. 2. Find the line lax.nl.java.option.additional=-xms1024m -Xmx1400m - Dsun.java2d.noddraw=true. 3. Change the flags to your preferable memory setting. For example, if you have 2 GB RAM, change the line to read lax.nl.java.option.additional=-xms1400m -Xmx1400m - Dsun.java2d.noddraw=true. Note: Make sure the letter m is present at end of size and there is no space between the number and m. To change memory settings for Workflow mode 1. In Notepad, open the file.../program Files/Agilent/ Agilent Genomic Workbench Standard Edition 6.5/config/config_workflow.properties. 2. Find the property, HEAP_SIZE=-Xmx1200m. 3. Change 1200 to your preferable memory setting. For example, if you have 2 GB RAM, change the property to HEAP_SIZE=-Xmx1400m. To change memory settings for the background process for importing FE data files 1. In Notepad, open the file.../program Files/Agilent/ Agilent Genomic Workbench Standard Edition 6.5/config/config_FEImport.properties. 2. Find the property, HEAP_SIZE=-Xmx512m. 3. Change 512 to your preferable memory setting as you did for Workflow mode. 3. User may encounter an error message Could not create Java Virtual Machine Error : There is a known incompatibility between Agilent Genomic Workbench (AGW) versions 6.0 and 6.5 and Microsoft's Application Compatibility Toolkit (ACT) Version 5.5 (MS ACT). Installing MS ACT will result in an error, "Could not create the Java virtual machine", which is displayed when attempting to launch AGW. Workaround: Uninstalling MS ACT 5.5 will return functionality to AGW.. Bug fixes in DNAAnalytics 6.5 Workflow: Console Summary needs Workflow name field. (TT_115735) AGW workflow: Issue with "Use grid file option" on Feature extraction properties dialog. (TT_116475) Workflow extraction save FE has lost folder (TT_118784) Workflow Password UI is incorrect (TT_135150) Common aberration should not run for CHIP or CH3 arrays. (TT_136013) Intervals crossing p/q split (TT_119056) Sample Manager: incorrect view (TT_115825) Create a gene track at the end of differential aberration (TT_085613) View Preferences not stable (TT_135239) UI plot and table user choices are not stable (TT_140416)

5 Aberrations which are not common are also seen in the Text Summary of Common Aberration and also in UI (TT_076245) MAC Machine: Create gene list button is not working in the graphical common aberration report. (TT_130982) White spaces not getting trimmed in Common Aberration node creation. (TT_133157) Common aberration (COCOA) fails for two arrays of 244K design. (TT_154625) pvalue in differential aberration result should not be negative. (TT_155673) Known Issues in DNAAnalytics Combine Track logic In this release operations for combining tracks work by assuming the track to be sets of intervals but do not perform any operations on intervals themselves. For example if a track consists of intervals e1, e2 and another of interval e2, e3 then the logic of intersection would result in a track with just e2. However if a track has interval e1 and another track has interval e2 where e2 is contained in e1 then the intersection would not give common part e2 but rather result would be empty and a message no annotations found would be shown (TT_075144) 2. Cyto Report keeps running for Use Workspace Settings on HMM Steps: 1. Create an Experiment and apply Aberration witth HMM Alogorithm. 2. Create a Cyto Template with option "Use Workspace Settings" selected in Analysis Settings tab. 3, Run the same cyto report. The report keeps running (TT_075661) 3. If any gene list is applied, Aberration in all the views gets updated except in the table Apply gene list functionality is not working on the data table. The gene list only gets applied on the aberrations in the views. Apply gene list only influences the display and not the actual aberration result. (TT_076300) 4. Application becomes very slow after you apply lowess OR variance stabilization with intra array. Chip Context > Application becomes very slow after you apply lowess OR variance stabilization with theintra-array combine algorithm. If you turn off the intra-array algorithm, the application again work properly. Another observation: In case all the normalizations are applied in one step, then it takes a very long time. Instead if you apply all the normalizations one by one,

6 it takes much less time. (TT_115165) 5. Issues with high density ChIP designs: If a million feature ChIP-on-chip design has most of the probes on a few chromosomes only, then analysis may have certain issues. 1. With those designs ChIP workflow also may fail. The probe report may not be generated and application may yield Out of Memory error. 2. Fusing two or more such designs will cause analysis to fail. (TT_118009) 6. Colored filled circle looks like a square. Colored filled circle symbols in gene view looks like squares in the scatter plot views (TT_117963) 7. OutOfMemoryError while restoring auto created experiment from workflow with one hundred 1-million feature arrays OutOfMemoryError while restoring auto created experiment from workflow with 100 million feature data (TT_118045) 8. Aberrations which are not common are also seen in the Text Summary of Common Aberration and also in UI. Aberrations which are not common are also seen in the Text Summary of Common Aberration and also in UI. (TT_076245) 9. Workflow with one hundred 1-Million feature arrays with Z-score and penetrance reports fails. Workflow with 100 Million feature data with Z-score and penetrance reports fails. (TT_118044) 10. Cyto report header has incorrect text. Cyto report header has incorrect text if some special characters are present in the report header section in the cyto report template. (TT_133074)

7 11. ManualQCFlag status not reflected in Sample Manager immediately. If ManualQCFlag is set for any array from QC Metric table, it is not updated in the Sample Manager in same session Quit application and restart it. (TT_133163) 12. If Overwrite if file exists option is not checked in the workflow for reports, workflow will fail if we run more than one workflow continuously. If Overwrite if file exists option is not checked in the workflow for reports, workflow will fail if we run more than one workflow continuously. Cause: when 1 st workflow is running, the 2 nd workflow is in waiting state. When 1 st workflow completes and 2 nd one starts, the report file is already present. (TT_132376) 13. Sometimes workflow keeps in waiting state. After user starts the run of a workflow, it keeps in waiting state even though no workflow is already running. Switch to home tab and come back to Workflow tab. The workflow will show as running. (TT_138074) 14. Sometimes the table view is missing. When application is launched 1 st time after fresh installation, sometimes the table view is missing and only 3 plot views are displayed. This may also happen after the application has been installed and used. Switching to Open Application, or any other tab, and then back to Genomic Viewer brings back the Table View. (TT_132357, TT_144158) 15. Workflow Console screen blank at Completion. Sometimes at the conclusion of a workflow run, the console log screen is blank. Switching to Summary Console, then back to the workflow console will show the log correctly. (TT_130489) 16. SNP plots not showing; have to change tabs. Sometimes SNP plots do not show data. Change tabs & come back, now the data are visible. (TT_145136) 17. When doing an extraction in the workflow mode, you may get a security alert concerning Java binary files. When doing an extraction in the workflow mode, you may get a security alert concerning Java binary files. When prompted, choose "Unblock" to allow the workflow to continue. You may

8 resolve this by changing your firewall security options (TT_115733) Important : DNAAnalytics CGH aberration boundaries will be different between AGW6.0 and AGW6.5. a) In the previous releases of AGW and DNAAnalytics, the start and stop of the aberration intervals are extended on either side by 200bp. With the increased density of our SurePrint G3 microarrays, this interval margin is no longer applicable and it is set to 0 bp in AGW 6.5. b) The stop position of the last probe is considered as the end of the interval. In the previous releases of AGW and DNAAnalytics, the start position of the last probe is considered and 200 bp is added to that to define the end of the interval. In AGW 6.5, the stop position of the last probe is considered as the end of the aberration interval. 2. In contrast to regular CGH QC metrics, the SNP QC metrics of a CGH+SNP microarray aren t calculated until after the SNP copy Number calculation is done. When an array is imported in the data node or added to an experiment, the SNP QC metrics for that array will not be available. SNP QC metrics are available only after the SNP Copy Number (CN) has been calculated. Just selecting the array will not make the SNP QC metrics available, but once the SNP CN has been calculated once, the metrics are available for that array even if it is not selected. 3. For CGH+SNP microarrays, it is mandatory to associate a reference sample with a microarray. In AGW6.5, it is now possible for the user to associate the red and green sample information for a workflow from the workflow panel. Associating a reference sample can be done in three ways: 1. In the sample manager. 2. From the interactive mode. 3. From the workflow mode. The 3 rd option was added to the software after the manual was finalized; hence this option is not described in the manual. For the third method, the software assumes the array polarity is+1; thus, it is mandatory to add the reference to the Green sample in the workflow mode, if the workflow has SNP analyses. 4. Aberration results in AGW 6.5 may differ slightly from AGW 6.0 The method on how the chromosomes are split between the p and q arm has changed so the aberrations around the centromeres can differ slightly. 5. Aberration filter now has an option to split the nested aberrant intervals. This option is set TRUE in the software by default. This split happens when the child interval gets filtered out on height criteria (e.g. a small amplified interval within a bigger deleted interval) but the parent interval (bigger deletion) passes the criteria. In this case, the parent interval is split into two separate intervals and these two splits are reported as separate intervals. In such cases the results of aberration filter would be different from previous version of the software. Also one may see aberrations with fewer probes than the aberration filter criteria.