N E X U S C O P Y N U M B E R H O W T O G U I D E S

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1 HOW TO ACCESS THE ISCA DATA STORED IN BIODISCOVERY NEXUS DB GENOMIC DATA REPOSITORY: The ISCA (International Standard for Cytogenomic Arrays) consortium database contains whole genome array data from a subset of the ISCA Consortium clinical diagnostic laboratories. CNV calls and their clinical interpretations are available to the public and this great resource can be viewed and queried easily in the BioDiscovery Nexus genome browser. There are two ways to make use of this data. One is by loading the data (BED files) as custom annotation tracks within BioDiscovery Nexus. This process is explained in another guide found here. The second way is to access this data in Nexus DB. BioDiscovery has loaded the ISCA data into the Nexus DB genomic repository so that this data can be queried and downloaded by users. This second access method is described below. 1. If you already have a Nexus DB account, skip to Step 5. If not, go to Step 2. You must have a valid license to BioDiscovery Nexus Copy Number, BioDiscovery Nexus Solo, or BioDiscovery Nexus Solo Reader in order to obtain a Nexus DB account. 2. Click on Log in to Nexus DB either from the main BioDiscovery Nexus workspace or from the Nexus DB menu and click the blue Register Account link on the bottom left of the resulting pop up. 3. Enter your information and click the Submit button. Please double check to make sure you have entered your address correctly. 4. Once your account is created, an will be sent to you containing your username and password to log into Nexus DB. 5. Login into Nexus DB and click on My Groups. This lists all the Nexus DB groups to which you belong. If you already belong to the ISCA group, skip to Step 9.

2 6. Access to data in Nexus DB is determined by the Nexus DB groups you belong to and the access level set by the project owner. To be able to access the ISCA data in Nexus DB, you need to belong to the ISCA group within Nexus DB. This is not the same as registering or becoming a member at the ISCA consortium s site. 7. To request access to the Nexus DB ISCA data, click on the Join Group button. Highlight the ISCA group and click Join. A request with your Name and Institution will be ed to the Group Leader asking him to approve your request. 8. Once the Group Leader approves the request, the ISCA group will show up under My Groups. 9. In order to query the ISCA data, you need to make sure you have it selected for querying. Click on Visible Projects and check off the boxes next to the ISCA groups. If you don t see the ISCA projects, make sure you don t have the ISCA group filtered out. Click on the Filter button to select any projects you want to filter out and remove from querying. In the figure below, since the ISCA group is marked off, any project belonging to this group will not be displayed when you look at your visible projects and also will not be queried.

3 10. In the figure below, the ISCA projects in the Visible Projects page are marked off and will be available for querying. 11. Querying a region in the database can be done in two ways. a. You can select the Query Database icon and then click on an aberration in the frequency plot. Or, you can right click on a region in the drill down and select Query database :

4 Both methods give the same results. b. In the figure above, querying for the loss on chr 5 shows the loss was found in an ISCA project data and out of the 11,970 samples in the project, 23 had this loss. c. Clicking on the blue name will bring up another window listing the submitted cases with the loss and their classification. Here, you can see that most of the cases were classified as pathogenic. d. Now if you want, you can download one or more of these samples and add them to your project. Just mark off the checkboxes for the samples you want to download and click either Download or Download and View. e. In this case, we are only going to download the first sample and after clicking Download a prompt appears asking for a tag for the sample. This value will be added to the Data Set tab in an additional column called Nexus DB tag.

5 f. Once the sample is downloaded, it shows up in the Data Set tab: g. Now this sample can viewed alongside all your other samples in the project. h. The ISCA_CNV_details column may have a link (hyperlinked text: External Link) that when clicked upon opens up the page for the aberration on the ISCA site. Please review the User s Manual (accessible from Help->User Manual from within the BioDiscovery Nexus application) for more information on using data in Nexus DB. For further assistance, please contact BioDiscovery Support here.