iFuse structural variants from NGS data

ErasmusMC Bioinformatics Department

Go to iFUSE application

iFUSE is a web-based fusion gene explorer. Upload your Complete Genomics junctions files, or your FusionMap FusionReport.txt file, and iFUSE will analyze and visualize your fusion gene candidates, and report the resulting sequences on the DNA, RNA and protein levels.

screenshot of the iFUSE application

Here is a list of frequently asked questions with answers. If your question is not among the list, please consult our manual or contact us.

  1. How can I upload an additional file?
    The file upload menu can be found under the Home tab at the top of the screen.

  2. How do I switch between files?
    If you have uploaded multiple file. You can switch between these files by going to the Files tab at the top of the screen, right-click on the file you want to visualize and select Set as active from the menu.

  3. How can I jump to a specific page?
    You can jump to a particular page by clicking on the page number at the bottom of the screen. A dialog will pop up, asking you for the desired page number.

  4. How can I download the iFUSE raw-file?
    To download the processed input file, go to Files tab at top of the screen, right click on the file in question, and select Download iFUSE raw data file.

  5. How can I remove a file?
    To remove a file from iFUSE, go to the Files tab at the top of the screen, right-click on the file you wish to delete, and select Delete from the menu.

  6. How do I remove a filter setting?
    To remove the current filter and/or sort settings, click on the Home tab. Clicking it a second time will take you to the iFUSE home screen
iFUSE Tutorial

This page will give you a brief tutorial on how to use iFUSE. For more information, please consult our manual.

Currently, iFUSE accepts 3 types of input files:

  1. Complete Genomics Junctions files (example)
  2. For more information about Complete Genomics, visit their website.
  3. FusionMap output report files (example)
    Details on the FusionMap program can be found here.
  4. iFUSE raw files (example)
    Raw files are files already processed by iFUSE previously.

Step-by-Step Guide

  • Step 1: Login or Register

    Go to the main page. Here you can either login with your username and password, or register for an account.
    All that is required for registration is a valid e-mail address.

  • Step 2: Uploading a file

    Once logged in, you will see a screen like this:

    Here you must provide a file to be analyzed and displayed by iFUSE. The following settings must be provided:

    • NGS input file: Download one of the example files at the top of this page and use this as the input the file.
    • Select input format: Select the appropriate option here, depending on the type of file.
    • Input has a first line header. If the first row in the file contains the column headers, select yes. Otherwise, select no.
      All of the example files contain a header, so select yes here.
    • Reference Genome: Select the appropriate reference genome here.
      For the example files, select reference genome hg18.

  • Step 3: Exploring results

    If all went well, you will have arrived at a page looking like this:

    All junctions listed in the input file will be visualized here, starting with the fusion gene candidates. Each box represents a single event. Let's zoom in on such a box:

    The leftmost cell contains, from top to bottom, the event ID, the shared gene ID, the associated junctions ID, and the related junctions ID. Associated Junctions ID is an ID shared by all junctions falling within a particular gene. Shared gene ID is an ID for junctions that have the same gene on either the left or the right side. And Related Junctions ID is an identifier shared by all junctions that fall within 100bp of each other. (see also the file format description page or the manual)

    The next cell contains an image. The top bar visualizes the original left side of the junction. The middle bar visualized the original form of the right side of the junction, and at the bottom is the constructed (fusion) event. To the left of the image the gene names and starting positions of the visualisations can be found, and to the right of the images, the length and end position of the visualistion are displayed. The image itself shows introns and exons, the promotor is represented by a triangle on either the left or the right side. The junction itself is represented by a red box, with either an arrow above it if two sides are on the same strand, or a cross if they are not.

    So in this example we have a fusion event with gene RRFB1 on the left, and VTA1 on the right side, both coming from chromosome 6, and both on the positive strand, with a length of 138417 basepairs.

    The box can be expanded to display more information by right-clicking on it and selecting Show/Hide -> Details. The result is a screen such as this:

    The first section, just below the image, contains details of the left and right part of the event. Details include gene name, accession number, coordinates of the coding sequence, transcript, and junction site. The next section contains ensemble sequences, derived from the reference genome. The DNA section contains the sequence constructed from the left-hand side sequence (uppercase)and right-hand sequence (lowercase). The RNA sequence is derived from the DNA sequence and the coordinates of the promotor-donor-gene. If there is no promotor donating gene, no RNA can be given. Also, when there is no start codon in the donating gene, no sequence can be given. For both the DNA and RNA sections, the right-hand side gives a shortened sequence (500bp upstream and downstream of the junction). The protein sequence is derived from the RNA and the transcript coordinates of the donor region. Only the sequence between the start and stop codons is shown. And finally, the last section contains the coordinates of the exons within the gene. Exons in the event (fusion gene) are displayed in black, those that are not are displayed in gray.

    Sorting and Filtering
    By default, the events are sorted to prioritize for (potential) fusion genes. But you can also define your own filters or sorting criteria. By right clicking on an event and selecting the filter option, you can select filters based on this event (for example filter on events involving the same genes), or you can filter on general properties such as whether the two sides are on different genes, whether they are on the same strand, the type of event etc.

    As an example we will describe how to set your filter to only display events having a different gene on either side, and both on the same strand. (so likely fusion events). If you have any filters set, click on the Home tab to clear them. Now right click on any event in the list, and go to Filter -> Using General Properties -> Gene Mismatch -> Yes. The list of events displayed should now be limited to events having a gene on either side of the junction, and these genes differ. Next, right click on any event again, and select Filter -> Using General Properties -> Gene Orientation -> Same orientation. This will display only those events where the two sides are in the same orientation. For the time being, it is not possible to combine filters.

    In a similar fashion you can sort the events by certain attributes. This can be done either through the right-click menu or through the sort tab at the top of the screen. If you want to do more complex sorting such as sort by property X, then by property Y use the sort menu at the top. Here you can specify which columns to sort on, and in which order.

  • Step 4: Downloading iFUSE raw-file for later use

    The input file from Complete Genomics or FusionMap is annotated by iFUSE. The resulting file can be downloaded by going to the Files tab at the top of the screen, and right clicking on the file and selecting Download iFUSE raw data file. This file can then be inspected in excel (or similar) or later be re-uploaded to iFUSE to visualise the junctions. This is especially useful for large files, as they will not need to be analyzed again, but can be displayed immediately.

For further questions about iFUSE please refer to our manual and FAQ section, or contact us.

Here we provide a brief description of the file formats which can be used as input to iFUSE.

  1. Complete Genomics junction file (example file)

  2. For more information about Complete Genomics, please visit their website. The example file is from one of their public (cancer) datasets (HCC1187). This and other publicly available datasets can be downloaded from Complete Genomics via ftp here.

    Either the allJunctionsBeta-[ASM-ID].tsv file or the highConfidenceJunctionsBeta-[ASM-ID].tsv file (or the somaticAllJunctionsBeta-[ASM-ID].tsv file) can be used as input to iFUSE. These files can be found in the ASM/SV/ directory from Complete Genomics. Below is description of the columns in these files:

    FusionReport.txt file format

  3. FusionMap Report file (example file)
  4. The FusionReport.txt file output by the FusionMap program can also be input to iFUSE. Below is a description of the file format.

  5. iFUSE raw file (example file)
  6. The input files are processed by iFUSE. The resulting file can be downloaded and can also be used as input to iFUSE. A description of this raw file format can be found below:

User manual and installation guide: iFUSE Manual

Installation files
If you would like to install iFUSE on your own system, please download the following installation files and follow the instructions in the manual.
iFUSE application (zip file)

User manual and installation guide:
iFUSE Manual

Example Input Files
Here we provide some sample input files for use with the iFUSE application. These files come from 2 publicly available breast cancer samples (primary ductal carcinoma, TNM stage IIA, grade 3) Full samples are publicly available from Complete Genomics: ftp2.completegenomics.com/Cancer_pairs

Sample HCC1187 Tumour highConfidenceJunctions
Sample HCC1187 Normal highConfidenceJunctions
Sample HCC2218 Tumour highConfidenceJunctions
Sample HCC2218 Normal highConfidenceJunctions

Sample HCC1187 Tumour highConfidenceJunctions
Sample HCC1187 Normal highConfidenceJunctions
Sample HCC2218 Tumour highConfidenceJunctions
Sample HCC2218 Normal highConfidenceJunctions