Translocations Overview Page

• Welcome to the translocation overview page. This page is used to display details of translocations/gene fusion mutations for a selected gene pair .

Explanation of Inferred Breakpoints and Observed mRNA Transcripts

Many papers determine fusions between genes using expression technologies, such as RT-PCR. A number of these studies have identified more than one transcript per sample, some finding over four different products between the same gene pair in one tumour. This implies significant alternative splicing of the mRNAs expressed from the fused gene pair. In order to simplify this data for display and navigation, we have inferred the position of the genomic breakpoint from the experimental data whilst maintaining the original results.

To do this, it has been assumed that each sample's breakpoint lies between the most 3' expressed exon of the 5' gene and the most 5' exon of the 3' gene, from the mRNAs reported in that sample. For instance, in sample 1038776 , four mRNAs were reported:

TMPRSS2{NM_005656.2}:r.1_71_ERG{NM_004449.3}:r.38_3097

TMPRSS2{NM_005656.2}:r.1_71_ERG{NM_004449.3}:r.226_3097

TMPRSS2{NM_005656.2}:r.1_142_ERG{NM_004449.3}:r.226_3097

TMPRSS2{NM_005656.2}:r.1_365_ERG{NM_004449.3}:r.226_3097

This was reduced to one inferred breakpoint, between TMPRSS2 r.365 and ERG r.36;

TMPRSS2{NM_005656.2}:r.1_365_ERG{NM_004449.3}:r.38_3097

In the display, the 'Inferred breakpoint' section is the breakpoint position we have determined using the rule above, and the 'Observed mRNAs' are the expressed products actually reported as the results of experimental procedures. A single inferred breakpoint can allow the expression of a number of gene fusion mRNA variants, as above. However, additionally, a single observed mRNA can, between samples, be derived from a number of different breakpoints.

Fusion mutation 25 has been observed in samples with 9 different breakpoints as inferred by the spectrum of their expressed fusion mRNAs

Inferred Breakpoints Table

The table below displays a list of all the Inferred Breakpoint mutations defined for this gene pair, with explanations of the data:

Observed mRNA Transcripts

The diagram below represents all the observed mRNA transcripts for eack of the inferred breakpoints. The images in the website are clickable, linking to the mutation details page for that fusion mutation (more details):
 

Details

The details section provides information of the number of samples that were analysed in all the curated papers, and the number and percentage of those that contained mutations in this gene pair, for the tissue tested. The 'More Details' links display further information, and allow export of the data:
 

References

Shows the total number of references that have been curated for this fusion gene pair. Clicking 'Publications' will display a list of all the references, with their current status, and links to pubmed.
 

Any More Questions?

• If you can not find the help you need in these pages please contact cosmic@sanger.ac.uk