Release Notes. Agilent CytoGenomics v For Research Use Only. Not for use in diagnostic procedures. Product Number

Transcription

1 Release Notes Agilent CytoGenomics v4.0.3 Product Number G1662AA CytoGenomics Client 1 year named license (including Feature Extraction). This license supports installation of one client and server (to host the CytoGenomics database) on one machine. For additional client only installations, which connect to the same database on the central server, additional copies of this license are needed. Overview CytoGenomics is a cytogenetics research software tool designed to streamline your workflow for processing, analyzing and reporting of cytogenetic measurements. This includes copy number changes and copy neutral Loss of Heterozygosity and Uniparental Disomy data, generated with human samples on Agilent SurePrint G3 CGH-only and CGH+SNP microarray platforms. With CytoGenomics 4.0 we now offer an even more streamlined workflow with a highly sophisticated user interface. CytoGenomics is designed to: (1) import raw TIFF images generated from the Agilent microarray scanner as well as some non-agilent scanners and (2) run Feature Extraction and perform analysis using customizable workflows. Utilizing the built-in database, CytoGenomics allows the user to store and query samples and aberrations by classification information or location information. In addition, users can connect from aberration annotations to OMIM, DGV and Entrez public databases to analyze sample aberrations. During sample review, multiple users can annotate, edit and classify aberrations with full record traceability and generate signed-off reports on processed samples. CytoGenomics supports an enterprise server/client model for concurrent usage and collaboration. With strong analysis algorithms, data visualization, data management and reporting functionality, CytoGenomics software extends the Agilent microarray based product offerings into a complete cytogenetic research solution. Key new features (added in v4.0) Improved performance in multiple processes of the application, especially when a large number of analyzed samples are present in the CytoGenomics database, including opening and operating Triage Viewing, signing off samples, auto-processing, loading supporting files, etc. Updated ISCN strings that use the ISCN nomenclature 2016 guidelines A brand new Triage View with a completely redesigned interface that allows you to triage results from multiple samples in the same window, compare common and uncommon aberrations among samples, and generate differential aberration summaries and graphical penetrance summaries Tools for analyzing the results of spike-in control probes added to the sample to help ensure fidelity of sample tracking. Agilent CytoGenomics Release Notes 1

2 The ability to compare sample results to a dynamic aberration track that contains all aberrations from all signed off samples of the same genome build, greatly facilitating the quick identification of commonly occurring variants. New track viewing features that allow you to view tracks as individual intervals, as heatmaps, or as frequency plots. Expanded features for the analysis of single cell samples, including the ability to compare samples to a reference from another slide and use feature extracted microarray text output as the sample files. An improved SNP algorithm to support the new GenetiSure Postnatal Research and Cancer Research CGH + SNP designs, with enhanced LOH detection down to 2.5 Mb resolution, helping to ensure that important aberrations are not missed. An optional new parameter for the SNP algorithm that optimizes detection of whole genome triploidy in prenatal research samples. New advanced filtering options that allow you to include or exclude aberration results based on user-defined genomic regions of interest. New and updated pre-loaded tracks. The ability to disable and re-enable standard notes, classifications, and custom analysis methods, maximizing your control over the use of these features. Installation Instructions New Installation Refer to the installation guide available at Points to note regarding results generated in v4.0.3 (read before upgrading to v4.0.3) Upgrade is only supported from CytoGenomics 2.9 or CytoGenomics 3.0 released version or CytoGenomics (v , , or or V ) to CytoGenomics CytoGenomics version prior to 2.9 (i.e., 1.0, 1.5, 2.0,2.5 and 2.7) will not be upgraded to 4.0. User needs to upgrade to version 2.9 using CytoGenomics 2.9 installer. Agilent Informatics Support team can provide an older CytoGenomics installer upon request. In case of upgrade from v2.9 or v3.0, same PostgreSQL server will be upgraded to 4.0. There will not be a new server installation. Hence server and client installation will be in different folders on disk and need to be uninstalled separately. Earlier versions of CytoGenomics (v3.0.6 and earlier) supported JAVA 1.7, while CytoGenomics 4.0 supports JAVA 1.8. Some improvements/changes were implemented in JAVA 1.8 which might lead to different results between CytoGenomics 4.0 and an earlier version of the software with the same analysis settings. In the samples that Agilent has tested, the observed results in v4.0 are better than earlier versions with respect to SNP fit and LOH calling. There are two new parameters available in the analysis methods in v4.0.3: Call LOH across P-Q arm and Detect whole genome triploidy. Because these options were not available in previous versions of CytoGenomics, after upgrading to CytoGenomics to 4.0.3, these options are set to False in the previous analysis methods. In CytoGenomics 4.0, changes were made to the SNP algorithm that improve detection of triploidy samples that would have been called as diploid in previous versions of CytoGenomics. As a result of these algorithm changes, there could be a difference in the results for CGH calls between CytoGenomics 4.0 and an earlier version of the software. Agilent CytoGenomics Release Notes 2

3 Due to the bug fix in the Allele Specific Copy Number (ASCN) detection algorithm where the reported LOH boundaries in the centromere region might be incorrect, changes in the CGH and LOH results will be impacted as follows: o CGH calls near the centromere boundary might have different start or end positions. o Since a different number of probes are being used as a consequence of the fix, the diploid centralization values will change and as a result affect the CGH probe log ratios that get adjusted by the normalization. This in turn can change median interval log ratios across the design. Intervals with median log ratios just above or below the aberration filter thresholds before the bug fix will likely be affected by this change. o LOH boundaries are going to change because of the exclusion of SNPs that are within the centromere. The number of SNPs being used as part of the SNP distribution plot will also be different resulting in corresponding changes to the SNP QC metrics. Note: The degree to which CGH and LOH intervals reported earlier will change will depend on the array design and on the number of CGH or SNP probes present inside the centromere region. Upgrading from the previous version of CytoGenomics You need to manually remove the client of the previously installed version and then run the installer for CytoGenomics x. Please follow the steps described below. Upgrading from v2.9.x or v3.0.x or v4.0.2.x On Windows machine, launch the 'Uninstall Agilent CytoGenomics' application in the 'Uninstall_Agilent CytoGenomics' subfolder of the installation folder. On a Macintosh machine, launch the 'Uninstaller' application in the 'Uninstall_Agilent CytoGenomics' subfolder of the installation folder. Click Next to proceed and select 'Uninstall Specific Features'. In the next window, select the 'Client' option and proceed. On machines with only a client installation, the 'Uninstall Specific Features' option may not be displayed. In such cases, continue with the uninstall procedure as prompted. Note: Do not uninstall Server as you will lose all your previously analyzed data. After client uninstallation of 4.0.2, 3.0, or 2.9 is complete, launch CytoGenomics installer to start the installation wizard. At the Choose Install Set screen, select 'Both Client and Server' and click Next. A message notifies you that CytoGenomics Server already exists and it will be upgraded to the latest version. Click OK to proceed with the installation. The installer installs CytoGenomics client application and upgrades existing CytoGenomics 4.0.2, 3.0, or 2.9 server to Upgrading from versions prior to v2.9 First upgrade the previous version (v1.0, 1.5, 2.0, 2.5, or 2.7) to version 2.9 using CytoGenomics 2.9 installer. Agilent Informatics Support team can provide that CytoGenomics installer upon request. Then follow steps specified in above section Upgrading from v2.9.x or v3.0.x or v4.0.2.x. Agilent CytoGenomics Release Notes 3

4 Upgrading from v4.0.2 via the Agilent cloud (Internet connection is required) Note: If CytoGenomics is installed on a machine that is behind a proxy server, make sure required proxy credentials are provided on the Configure Settings > Partners > Set Proxy Settings screen. Restart CytoGenomics. The following dialog box automatically displays after opening. To automatically download these software updates: 1. Mark the Software update check box in the Updates Available dialog box. This will enable the Download button. 2. Click Download.The Confirm message box opens asking you to confirm that you want to start downloading software update files. 3. Click OK to start the download process. A Progress Status message displays. The application is unavailable for use during the software update download. 4. Once the download is complete, a Download Successful message displays, and counts down from 5 seconds to close the application. Skip the countdown by clicking OK. 5. A dialog box indicates that the application has been updated. Click OK to launch CytoGenomics. 6. Upon logging in, a dialog box indicates that the Agilent CytoGenomics application was upgraded successfully. Click OK to continue. Default and Preloaded Content The hg19 version of the design file for the SurePrint G3 Human CGH Microarray 4X180K (022060) design is provided as part of CytoGenomics 4.0 installation. Hg18 and hg19 version design files for the below listed commonly used designs can be downloaded from the CytoGenomics download page ( SurePrint G3 Human CGH+SNP Microarray 2X400K (028081) SurePrint G3 Human CGH+SNP ISCA Microarray 4X180K (029830) SurePrint G3 Cancer CGH+SNP Microarray 4x180K (030587), hg19 only SurePrint G3 Human CGH Microarray 4X180K (031748) SurePrint G3 Human CGH Microarray 2X105 (031750) SurePrint G3 Human CGH Microarray 8X60K (031746) SurePrint G3 Human CGH Microarray 4X180K (022060) Agilent CytoGenomics Release Notes 4

5 SurePrint G3 Human CGH Microarray 8X60K (021924) SurePrint HD Human CGH Microarray 4X44K (014950) SurePrint HD Human CGH ISCA Microarray 4X44K (031747) The following frequently used tracks are provided upon installation: Agilent Female CNV Reference Agilent Male CNV Reference CNV-DGV_hg18_v4_July2015 CNV-DGV_hg19_v4_July2015 CNV-DGVsupp_hg18_v4 CNV-DGVsupp_hg19_v4 CpG-Islands_hg18_v2_Nov2011 CpG-Islands_hg19_v2_Nov2011 Cytoband_hg18_v2_Nov2011 Cytoband_hg19_v2_Nov2011 Genes_hg17_Feb2016 Genes_hg18_v3_Feb2016 Genes_hg19_v3_Feb2016 mirnas_hg18_v2 mirnas_hg19_v2 Multi Transcripts for Genes hg18_feb2016 Multi Transcripts for Genes hg19_feb2016 OMIM-hg18_Feb2016 OMIM_hg19_Feb2016 Pseudo Autosomal Regions_hg18_v2_Nov2011 Pseudo Autosomal Regions_hg19_v2_Nov2011 Agilent recommended Feature Extraction protocols for CGH microarrays (CytoCGH_0209_1x_Mar14, CytoCGH_0209_2x_Mar14, CytoCGH_0209_4x_Mar14 and CytoCGH_0209_8x_Mar14, CytoCGH_0300_SingleCell_Nov14) and QC metric sets for CGH microarrays ( CytoCGH_QCMT_1x_Mar14, CytoCGH_QCMT_2x_Mar14, CytoCGH_QCMT_4x_Mar14 and CytoCGH_QCMT_8x_Mar14,CytoCGH_QCMT_SingleCell_Nov14) are provided as default. Agilent recommended CGH analysis settings (Default Analysis Method - CGH v2); CGH+SNP analysis settings (Default Analysis Method CGH + SNP v2); Mosaic analysis settings (Mosaic Analysis Method) and Single cell analysis settings (Single Cell Small Aberration Analysis Method, Single Cell Long Low Aberration Analysis Method, and Single Cell Recommended Analysis method) are provided as default. Agilent Feature Extraction for CytoGenomics Overview Agilent Feature Extraction (FE) for CytoGenomics is a component within CytoGenomics. FE performs TIFF image processing, background subtraction and normalization of microarray data. The user has the option of using this component as part of a CytoGenomics workflow or as a standalone tool. Agilent CytoGenomics Release Notes 5

6 System Requirements for Agilent CytoGenomics Minimum Requirements for Windows For Research Use Only. Not for use in diagnostic procedures. Operating system 64-bit Windows 7 Enterprise Any program that enables you to open PDF files (for example, Adobe Reader) Processor > 2 GHz Working memory (RAM) 4 GB Available hard disk space from 40 GB to 500 GB (large datasets require more space) Display Resolution 1280 x 768 or higher Recommended Requirements for Windows Operating system 64-bit Windows 7 Enterprise or 64-bit Windows 10 Enterprise Any program that enables you to open PDF files (for example, Adobe Reader) Processor > 3 GHz Working memory (RAM) 8 GB Available hard disk space from 40 GB to 500 GB (large datasets require more space) Display Resolution 1280 x 768 or higher Minimum Requirements for Macintosh Operating System OS X Yosemite or Mavericks Any program that enables you to open PDF files (for example, Adobe Reader) Processor 3 GHz Intel Core 2 Duo CPU or better Working memory (RAM) 4 GB Available hard disk space 40 GB (For analysis of large datasets, more space is required) Display resolution 1280 x 768 or higher Recommended Requirements for Macintosh Operating System OS X Yosemite or Mavericks. Any program that enables you to open PDF files (for example, Adobe Reader) Processor 3 GHz Intel Core 2 Duo CPU or better Working memory (RAM) 8 GB Available hard disk space 500 GB (For analysis of large datasets, more space is required) Display resolution 1440 x 900 In an effort to improve the performance and overall user experience with CytoGenomics, as of version 4.0.3, CytoGenomics is no longer supported on 32-bit machines Issues Fixed in CytoGenomics Issues fixed since v4.0.2 For certain workflows, the Restriction Control QC metrics erroneously reports a value of -1.0 in the CGH&SNP Fit dialog box. (TT# ) Agilent CytoGenomics Release Notes 6

7 In specific instances, the Favorites tool in Triage View uses the wrong gene list in the database to mark genes as favorites. (TT# ) In Triage View, the Common-Uncommon interval table reports the array name instead of the global display name when the sample has a global display name that is not the default. (TT# ) When the Scan Date is displayed as a sample attribute, the value for this attribute does not match that in the FE file. (TT# ) In Triage View, when the Browse to DGV command is used, CytoGenomics sends the detailed symbol name (i.e., with author, loss gain info) rather than the required symbol name (TT# ) The database backup feature fails when the CommonStorage is on a different machine than the server. (TT# ) In Triage View, the log ratio scale values do not always adhere to the settings in the View Preferences. (TT# ) Sometimes application does not launch and gets stuck at the splash screen (TT # ) During analysis of multipack CGH+SNP arrays, the SNP QC metrics are not properly measured for array 1_1. (TT# ) When configuring a workflow in the Single Cell Configuration dialog box, the software does not allow the reference to be assigned using an SAF file. (TT# ) During sign-off of a sample workflow, if the settings on the Configure Settings > Reports screen specify that the other PDF reports are to be saved to two folder locations, the software fails to save the reports to the second folder location and instead saves copies of the jpg files. (TT# ) The software does not allow users to resubmit a workflow if any of the required sample attributes exceed 50 characters, even when those attributes are not used in the output folder name. (TT# ) In workflows that specify a spike-in identifier, the Spike-In summary is not reported for some samples. (TT# ) The ISCN column of the Interval table of the Triage View contains extraneous syntax when the samples were analyzed with a design that contains fewer than 24 chromosomes. (TT# ) The tooltips that appear when the cursor is hovered over the ISCN column of the Triage View Interval table includes extraneous spaces within the start position values and stop position values. (TT# ) Sample records which were successfully analyzed by Auto-Processing sometimes have their workflow status changed to Failed after additional Auto-Processing workflows are completed. (TT# ) When the Triage View is opened and closed multiple times for the same sample, the copy number assignment in the ISCN string sometimes changes from 2 to 3 for LOH calls. (TT # ) For certain samples, the software may assign the breakpoint of an LOH interval to a centromere region. (TT# ) The Model System Metrics option from QC Metrics dialog is removed in this version. (TT# ) Software should not report ISCN for Hemizyous LOH. (TT# ) Known Issues for CytoGenomics When the Gene View panel of the Triage View is displaying horizontally, large white spaces appear at the top of the tracks and tracks width are not remembered when the Triage View is closed and re-opened. (TT# ) Agilent CytoGenomics Release Notes 7

8 For Research Use Only. Not for use in diagnostic procedures. In the Single Cell Triage View, when comparing two samples, if the rendering style is changed from Overlaid to Stacked, then samples [Male/Female] are not displayed in order. (TT# ) Application becomes unresponsive when more than two clients connected to a server try to open the QC metrics dialog at the same time. (TT# ) In analyses in which genomic region filtering is set to exclude calls, the software does not always filter all calls that it should. (TT# ) Nested aberrations are displaying on same line as the parent aberration in the Gene View panel of the Triage View. (TT# ) In the Cyto report template, the software re-orders the sample attributes from what the user has selected. (TT# ) Separability metric range value is displayed incorrectly in some places in the software. (TT# ) - Workaround :- Re-analyze the records for which the metric range value is not displayed. Classification is not assigned to an aberration if user creates that classification while record is open in Triage View. (TT# ) - Workaround :- Close the Triage View and open it again. The classification can be seen in the interval table. Sometimes application is unable to connect to database on MAC machine. (TT# ) - Workaround :- Relaunch the application Sometimes database restore fails. (TT# ) Duplicate intervals are displayed in the Interval table in the new Triage View. (TT# ) - Workaround :- Relaunching the Triage View corrects the issue. Application gets stuck when user clicks on the Sorting button for a column on the Sample Review screen. (TT# ) In the Legacy Triage View, the Gene View scale does not always display correctly. (TT# ) In the new Triage View, the message No aberration for selected chromosome is not displayed when the user tries to open the Interval table for a chromosome which is not the chromosome for the presently displayed aberration. (TT# ) In analyses in which the custom analysis method uses a Genomic Region Filter, the filter does not work properly for certain designs. (TT# ) In the Create/Edit Cyto Report Template dialog boxes, some of the options for displaying the Audit Trail are not available. (TT# ) In certain instances of Auto-Processing, the Global Display Name displayed on the Sample Review screen is incorrect. (TT# ) In Windows 10, sometimes the application cannot open Triage View. (TT# ) Known issues for Feature Extraction for CytoGenomics Changing the color scale does not work while in grid mode. If user attempts to change color scale from All Channels to Red Channel or Green Channel, it does not change. (Legacy TT 2309) In rare instances, the switch to configure mode button will not be enabled after the extraction is complete. The extraction will have to be closed and re-opened to enable to configure/run mode toggle. (Legacy TT 2069) When viewing shape files, feature outliers are not visible until the image is zoomed or cropped (which effectively zooms the image). (Legacy TT 1955) Protocol, DyeNormList, or GridTemplate cannot have special characters in the name or description. The character that is sure to break is "'". (Legacy TT 652 & 657) In rare instances, the QC report can fail to generate. This is true when 30 micron feature size 2-pack arrays are used in FE, using a CGH protocol that generates an old style CGH QC Agilent CytoGenomics Release Notes 8

9 report. For the 2-pack 30-micron feature size arrays, the new streamlined CGH QC report must be used. (Legacy TT 2019) While creating a grid file of Agilent arrays during manual gridding process, some annotation columns may be lost. Currently only the primary annotation columns are certain to make it into the grid file {Probe Name, Systematic Name, and Gene Name}. Other annotation fields are not certain to be in the output. There is no workaround to this issue. (Legacy TT 1917) For large grid templates, using the dye normalization list editor can take a very long time. This is a function of the number of probes that have to read from the database and loaded into the editor. It is possible to create the lists outside of FE and load them into the software without using the list editor. Please consult the FE manual for details. (Legacy TT 1913) Calculating spot size and centroids in manual grid mode, using a high resolution scan of a third party array, will cause FE to crash. (Legacy TT 2032) It is not recommended to run projects, containing multiple extractions, directly through FeNoWindows; that is, projects containing multiple 30-micron feature size 1 million feature arrays. FE will run out of memory if run directly using FeNoWindows. The work around is to either use the FE GUI to run these projects or to break up the project into multiple projects each containing 1 extraction. (Legacy TT 2016) Scans of 2, 3 and even 5 micron resolution using full sized scan regions are quite large, creating memory issues for the software. In order to address memory and performance issues, the following restrictions are true about the imaging. The new view window feature (with Ctrl-N as the shortcut) that allows users to open one channel of the scan will not work for new format scans. When cropping a new format scan to view the image close up, what FE refers to as high fidelity mode, zoom out is disabled below 200%. Agilent CytoGenomics Release Notes PR