Question: How to Interpret COSMIC/HGVS Gene Fusion Format
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gravatar for krc3004
2.9 years ago by
krc300410
krc300410 wrote:

Hi all,

I'm trying to analyze gene fusion data from COSMIC and am having difficulty interpreting the HGVS format/documentation.

Here is documentation from COSMIC: http://cancer.sanger.ac.uk/cosmic/help/fusion/summary

and here is documentation from HGVS: http://www.hgvs.org/mutnomen/recs-RNA.html

But there are still cases in the COSMIC data that I don't understand. For example, this case is easy enough:

BRAF{ENST00000288602}:r.1_1201_AKAP9{ENST00000356239}:r.3552_12471

I'm pretty sure this means nucleotides 1-1201 (RNA) are fused to 3552-12471 of AKAP9.

But what about something like this:

AKAP9{ENST00000356239}:r.1_3551+364_BRAF{ENST00000288602}:r.1202-1794_2480

I think +364 means 364bp downstream of intron/exon in BRAF (the format doesn't specify intron or exon), but what does 2480 mean? Since I'm planning on using ensembl to extract the actual sequence, does the 2480 even matter (since I could just use 1-3551 of AKAP9, and 1202-1794)?

Thanks very much for your help.

p.s. someone asked a similar question a while ago but I'm not sure it was ever resolved.

translocation fusion cosmic hgvs • 1.6k views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 2.9 years ago by krc300410
AKAP9{ENST00000356239}:r.1_3551+364_BRAF{ENST00000288602}:r.1202-1794_2480

Fusion event involves:

  1. AKAP9 transcript. Exon 1 (1-3551) + intron (364bp downstream of exon 1)
  2. BRAF transcript : transcript bases starting from intron (1202bp) upstream of exon (spanning1202-1794) till the end of BRAF transcript

http://cancer-legacy.sanger.ac.uk/cosmic/fusion/summary?id=1014.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by cpad011213k
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