Every Man’s Nightmare

The mere mention of prostate cancer is enough to send a chill down every adult male’s spine. This malignant ‘killer’ strikes deep in the male reproductive system, and is prevalent among males above the age of fifty. It is more than capable of spreading to nearby bones and lymph nodes, which often leads to death.

The genetics behind prostate cancer has been studied extensively over the years. Research has shown that no single gene is responsible; instead the blame is assigned to a combination of genes, or fusion genes. Fusion genes are part of a larger form of mutation called ‘structural variations’.

Fusion genes can occur due to translocations, resulting in ‘structural variations’. In a recently-published study, researchers studying gene expression discovered marked over-expression of the ETV4 gene in the TMPRSS2:ETV4 gene fusion, a prime suspect in the initiation of prostate cancer development.

SynaSV is an MGRC online tool specifically designed to visualise structural variations. This powerful application can use both single and paired-end reads as the query input.

SynaSV is an MGRC online tool specifically designed to detect and display structural variations in human chromosomes. This powerful application can be used to analyse both single and paired-end reads. Highly accurate and sensitive, SynaSV is optimised to pinpoint and highlight a wide array of structural variations such as fusion genes and Indels.

Here we showcase SynaSV’s functional capabilities for viewing and identifying structural variations in the TMPRSS2:ETV4 gene fusion

Full paper : Cancer Research

Click here, then click on .

Once you have obtained the alignment results, note that the two highest scoring matches are two different targets. Select these targets by clicking on the check box. A structural variation graph will appear.

From the graph, observe that the query (middle) is split across a breakpoint where the first part matches to chromosome 21 (top) and the second part to chromosome 17 (bottom).

Below the structural variation graph, observe the statistics table which indicates that the structural variation is an inter-chromosomal translocation.