how to get exact break point in COSMIC fusion gene?

Question

[imlituan]

there's one item in COSMIC fusion

Mutation Id COSF463 Type This fusion structure is derived from the range of fusion mRNAs reported. Translocation Name EML4{ENST00000318522}:r.1_1751_ALK{ENST00000389048}:r.4080_6220

How to infer the exact breakpoint from the this item, like 'chr:xxxxxxxx'

[Titus]

I think you have to translate it ... I had the same problems in my lab because some people use only amino acid mutation ... I don t know software whitch reverse that , may be with some "home made solution" using annovar , snpEFF or VEP ?

[Max Ivon]

The problem is that COSMIC arrange data from different sources and exact breakpoints are not always known just becaase the source experiment employed rna-seq - genome break point just can be grasped in this case. If you want to determine the spectrum of breakpoints of ALK fusions I would recommend you to have a look at MSK-impact study results (all detected fusion breakpoints genome positions are listed in supplementary information of the article http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.4333.html). Of course this is not a mutation database and may be used as rough approximation but the sample size is large enough (the largest done so far for pan-cancer study) to suppose that all major fusion variants were detected (though questions on possible population biases remains open).

[cpad0112]

Back calculation of gSyntax from cSyntax is some times tricky, esp for SV. Probably this is the reason, why gSyntax is not calculated by default, by COSMIC.

Answer 1

[chen]

COSMIC doesn't give the exact break point.

But it you want to detect gene fusion with break point, you can try GeneFuse ( https://github.com/OpenGene/GeneFuse ), this tool gives you the break point and the inferred protein. It reports in HTML format and shows interactive information.

See an example of report (http://opengene.org/GeneFuse/report.html):