Question: how to get exact break point in COSMIC fusion gene?
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gravatar for imlituan
9 weeks ago by
imlituan20
imlituan20 wrote:

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'

ADD COMMENTlink modified 9 weeks ago by chen1.1k • written 9 weeks ago by imlituan20

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 ?

ADD REPLYlink written 9 weeks ago by Titus430

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).

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Max Ivon110

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.

ADD REPLYlink written 9 weeks ago by cpad01123.0k
0
gravatar for chen
9 weeks ago by
chen1.1k
github.com/OpenGene
chen1.1k wrote:

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):
enter image description here

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by chen1.1k
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