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

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1 Release Notes Agilent CytoGenomics v4.0.2 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) 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. 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. Agilent CytoGenomics Release Notes 1

2 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. Support for Windows 7, Windows 10, Windows Server 2008 R2, Macintosh OS X Mavericks, and Macintosh OS X Yosemite. Installation Instructions New Installation Refer to the installation guide available at Points to note for upgrade from older version of CytoGenomics to CytoGenomics 4.0: Upgrade is only supported from CytoGenomics 2.9 or CytoGenomics 3.0 released version (v , , or ) 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. There are two new parameters available in the analysis methods in v4.0.2: 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 4.0.2, 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. 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 result changes 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. Agilent CytoGenomics Release Notes 2

3 Upgrading from the previous version of CytoGenomics For Research Use Only. Not for use in diagnostic procedures. 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 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 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 4.0 client application and upgrades existing CytoGenomics 3.0 or 2.9 server to 4.0. 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. 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) SurePrint G3 Human CGH Microarray 8X60K (021924) SurePrint HD Human CGH Microarray 4X44K (014950) SurePrint HD Human CGH ISCA Microarray 4X44K (031747) Agilent CytoGenomics Release Notes 3

4 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 4

5 System Requirements for Agilent CytoGenomics Minimum Requirements for Windows For Research Use Only. Not for use in diagnostic procedures. Operating system 32-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 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 Issues Fixed in CytoGenomics Issues fixed since v3.0.6 In Single Cell Triage View, the progress bar that is displayed while generating the Cyto report is blank. (TT# ) [Cyto Patch] When sending reports to Cartagenia BENCH and the transfer fails, the status tooltip displays incomplete text. (TT # ) In the Track dialog box, when viewing a dynamic track that contains aberrations, the colors used to display amplification/gain and loss/deletion are the same. (TT # ) Agilent CytoGenomics Release Notes 5

6 [Cyto ] [Ticket ID :- PR # 19698] In specific scenarios, the CytoGenomics installer is unable to find/locate the server while upgrading from a previous version. (TT # ) One of the functions exported by ActiveX object that can also be accessed from a web page, if used with abnormal parameters, could allow a web page to execute code downloaded from the web. (TT # ) Licensing website link in CytoGenomics application needs to be updated. (TT # ) The Single Cell Cyto report incorrectly displays the same QC metrics for multiple arrays. (TT # ) QC metric values should be limited to 6 decimal places in Cyto reports. (TT # ) In the Chromosome View of Triage View, expanding the selected region by dragging and dropping does not work for some of the chromosomes. (TT # ) In Triage View Interval Table, values of the tracks are reported in the Classification column incorrectly and the selected track column appears blank. (TT # ) Values of 'NA' are observed in the Loss column of Interval based report when the analysis method uses the flat intervals option. (TT # ) In Multisample window, performing a 'find in column' search on a gene name fails to return search results. (TT # ) Changes to Local Settings and View Preferences sometimes get reset after restarting the application. (TT # ) During export of a dynamic track, the Interval Type column shows 255,175,175 values for some intervals. (TT # ) In Triage View, progress bar does not refresh during sign off of a sample. (TT # ) When sending data to partners, the CGH log ratio in the zip file for GGX shows the CGH data for one extra record. (TT # ) Aberration filter does not work correctly when nesting is set to non-legacy mode. (TT # ) Using spaces in the global display name in the Single Cell Configuration dialog box impacts analysis results when compared to the results generated without any space in the global display name. (TT #245289) In Triage View, cannot search aberrations using the Aberration Search dialog box. (TT #244242) In the Aberration Filter, the Nesting filter does not work when the Fuzzy Zero option is selected. (TT # ) When a Genomic Boundary parameter is applied to an analysis method, and the selected track contains duplicate intervals, one of the regions to be included or excluded gets swapped (from included to excluded or from excluded to included) and aberrations are incorrectly called. (TT # ) In Triage View, the scatter plot tooltip is not displayed in Gene View when orientation is horizontal. (TT # ) In zip files created for export to GGX, dye flip value shows NA in QC Metrics table. (TT # ) If record peaks are manually reassigned and the diploid peak is also changed, then the manually reassigned record reports aberrations that should be assigned as gains as amplifications and aberrations that should be assigned as losses as deletions. (TT # ) Dynamic tracks are getting corrupted after using them for multiple updates. Once corrupted, the application freezes when displaying track details. (TT # ) In rare instances, the application assigns duplicate aberration result IDs to multiple workflows while saving the results. Consequently, the samples with duplicate IDs have incorrect results in Triage View. (TT # ) Agilent CytoGenomics Release Notes 6

7 PR # :- Application reports nested interval in incorrect order. The larger interval is reported earlier than the smaller interval. Also, opening Triage View multiple times duplicates calls in the interval table. (TT # ) PR # Application becomes unresponsive when two clients connected to a server try to open the QC metrics dialog at the same time. (TT # ) Known Issues for CytoGenomics For some custom report templates, the application encounters a heap space error while generating a Cyto report with that template. The workaround is to restart application and try again. (TT # ) For some actions that take longer to complete, sometime the busy/wait cursor does not display (TT # ) In Triage View, clicking on an aberration in Genome View can cause a cursor position in Chromosome View that does not match the aberration. (TT # ) In the OS X Mavericks operating system, the Multisample window is blank when more than one sample is displayed. (TT # ) In the Multisample window, the right-click menu for the Multi Transcript track is missing options on gene info. (TT # ) The applications sometimes freezes when opening Single Cell Triage View. (TT # ) When genome build hg18 is selected as the default, and both hg19 and hg18 design files are imported, application still shows hg19 as a default. (TT # ) [Ticket# ] In horizontal view of track, large white space at the top of the track start appearing and tracks width are not remembered (TT # ) On the Single Cell Triage, while comparing two samples, if the rendering style is changed from Overlaid to stacked, the 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 # ) On Windows 10, takes time to add workflows on Analysis workflow tab from single cell dialog and for normal image files as well (TT # ) No interval label (annotation symbol) is displayed for some intervals in a dynamic track (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 aberration is displaying on same line as the parent aberration in the Gene View. (TT # ) In Cyto report template, the sample attribute order is changed from what user has selected. (TT # ) Set annotation symbol name is not able to save if track has lots of data (TT # ) Sometimes when a report is created in the new Triage View and then the Legacy Triage for the same sample is opened, the software may freeze. (TT # ) Workaround :- Close the Legacy triage and open it again. Sometimes application does not launch and gets stuck at the splash screen. (TT # ) Workaround :- Terminate the application process (Javaw.exe) from the task manager and relaunch the application again. When CytoGenomics is updated from v to v via the cloud, Auto-Processing does not start. (TT # ) Workaround :- Uninstall the client for Cyto and upgrade directly to v Agilent CytoGenomics Release Notes 7

8 Separability metric range value is displayed incorrectly in some places in the software. (TT # ) Classification is not assigned to an interval 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. In rare instances, Genome View does not render the scatter plot for some of the chromosomes. (TT # ) Workaround :- Close the Triage View and open it again or restart the application. 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 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