CNVinspector

Tutorial
 

best viewed with Mozilla Firefox

This tutorial is as brief as possible, if you are interested in more detailed information or in the implementation, please consult the documentation. Unless mentioned here, there is no need to change any settings on the interfaces.

If you are only interested in the output of CNVinspector, you don't have to upload CNVs first. Simply open the display / find CNVs page and select one of the existing public projects and move to section 2 of this tutorial. The sample file used in this tutorial is also there, under the intuitive name 'Sample CNVs'.

1. Create a personal account

Go to the create profile page and enter your name, an e-mail address, your organisation and select your login name and a password. You will be logged in automatically (your browser must accept cookies for this function). If you return to CNVinspector (we hope you will), go to the login page to create and access your private data. More about the publication and the exchange of your data can be found in the documentation.

2. Upload CNVs

First, you must upload CNVs. For this tutorial, sample CNVs exist. To actually upload the CNVs to the database, open the upload page.

  1. Describe your study under description (e.g. 'a test').
  2. Under method (brief), select the method that best suits the method you used (we recommend 'other').
  3. Enter a more detailed description of your method under method (e.g. 'just a test').
  4. Enter the number of samples contained in your study under sample size. If you use the sample file, the number should be 150.
  5. Choose the correct genome build (does not matter for the sample file).
  6. Select the file you want to upload (e.g. the sample file).
  7. Click on submit and wait for 15 seconds (that's presumably not enough for a cup of tea or a pint).
  8. When the upload finished, click on the link 'Study your CNVs'.

3. Display CNVs within a genomic region.

Open the display / find CNVs page (unless it's already open - it should be if you followed the "Study your CNVs" - link).

  1. Select your project as cases (if you followed the link after the upload it should already be selected)
    or click here to use the sample CNVs already in the database.
  2. Choose some other studies as controls (by checking display as controls)
  3. Enter '4:178209702-178853622' in Region.
  4. Click on display region.

4. Study the region

This page shows the genes and the CNVs (from the projects you selected) contained within your region. In the plot, genes are indicated as green bars, duplications in blue, and deletions in red. Control CNVs are displayed in light colours. Example.

  1. Click on a gene (green bar) to read gene information in GeneDistiller (after the analysis it should already be selected).
  2. Scroll to the bottom to read the actual positions of the genes and CNVs in the genome build you selected (36 by default).

5. Find / filter CNVs

Open the display / find CNVs page (unless it's already open).

  1. Check the button show filtering options in order to change to filtering mode with advanced filtering options.
  2. Select your project as cases (if you followed the link after the upload it should already be selected)
    or click here to use the sample CNVs already in the database.
  3. Choose some other studies as controls by checking display as controls) and those used to filter (check filter) the CNVs. You might like to try another test sample, 'Sample CNVs (Controls)'.
  4. Enter filtering criteria for the samples: Use '15' as frequency in cases [%].
  5. Enter filtering criteria for the controls to exclude common CNVs: Use '15' as frequency in controls [%].
    Note: If you leave this field blank, you should see more CNVs, e.g 13:78719222-80693770 for the sample cases/controls).
  6. Click on find CNVs

6. Study the CNV list

This page shows a list of the CNVs found in your cases and matching your criteria. CNVs that are found in any of the control samples and fulfil the exclusion criteria are now shown. Example.

  1. Scroll to chromosome 4, 178209702 Mbp.
  2. You'll see that there are also CNVs in the controls but their frequency is 14%, i.e. below our threshold.
  3. Click on the display link right of the samples CNVs to see the region.
  4. Click on a gene symbol to read gene information.

7. Remove projects or analysis

Go to the delete your data page. All projects and analyses owned by you will be displayed.

  1. Select an analysis or project you want to delete.
  2. Click on the Delete selected projects button.
  3. On the page that now opens, click on the Confirm button.

Congratulations!

You have now completed the tutorial.

This tutorial is meant only as a brief introduction to CNVinspector. Please read the documentation if you are interested in the elements not mentioned here. And if any questions remain unanswered, don't hesitate to ask us (e-mail to dominik.seelow (at) charite.de). We would also appreciate hearing of your experiences, bugs you discovered, and suggestions to improve this application.