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9.2 years ago
j.d.helix
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Dear all,
I'm a cell biologist, so please forgive me if I'm asking a stupid question...
I'm interested in a fusion gene found in a gastric cancer study published by TCGA in 2014 (Comprehensive molecular characterization of gastric adenocarcinoma). However, I could not find the full sequence of that fusion transcript in the paper (and supplementary data).
I wonder if such information is available somewhere online? If so, where can I find it?
Or, I have to download the data from TCGA and do analysis by myself...?
Thanks you very much for your time!
Dan
did you ask the author of the paper ? Otherwise if the fusion coordinates are in the paper, it should be easy to pick up the sequences from ENSEMBL
Dear NicoBxl,
First of all, thank you very much for your reply!!
Forgive me, I'm not quite familiar with the term "coordinates" in your reply. Does it means "breakpoints"? In the supplementary data, they included a table listing all CLDN18-ARHGAP26/6 gene fusion events they found. There's a column called "Breakpoints (RNA-Seq)" containing something like "3:137749947|5:142393645". I wonder if it is the one you're referring to?
However, my case is probably more complicated. The 5' gene, CLDN18, has two transcript variants in human, with different 5' exons. These two transcripts have the same number of nucleotides but different 5' sequences. I need to know exactly which transcript variant is fused to the 3' gene ARHGAP26. That's why I'm looking for the full sequence. I guess I wouldn't be able to find out this information from ENSEMBL, am I right?
Probably I should just contact the author for information.
Again, I really appreciate your help!
Best,
Dan
For the coordinates, yes that's what I mean (the breakpoints). 3:137749947|5:142393645 means fusion between chr3;137749947 and chr5:142393645.
And Yes you should contact the author. He should be able to tell you that based on RNA-Seq alignment
Dear NicoBxl,
Thanks a lot for replying me again!
May I ask one more question about the breakpoints? According to ENSEMBL, CLDN18 locates in Chromosome 3: 137,998,735-138,033,655, and the paper said the fusion point is in its last exon (exon 5). But the breakpoint (3:137,749,947) listed in the table is even not within CLDN18 gene... Where am I wrong?
Thanks!
Dan
Dear j.d.helix,
definitively, one should contact here the author of that study/paper!
That kind of information which you require usually is not given by the fusion finders which use RNA-seq data because most of the fusion finders are focusing on the (i) fusion junction, and (ii) the region of +/- 300 bp around it (this depends on the fragment size). Therefore I would say that if those 5' exons, which you are looking for, are more than 300 bp (i.e. fragment size) far from the fusion point then it would be really tricky to figure that out because assembly of transcripts using RNA-seq data has on average an error rate of ~30-40%. If one gets really lucky then those two transcripts between which you need to discriminate would be differentially expressed very strongly (one is almost not expressed and the other is highly expressed) and in this case one could see which is the interesting transcript just looking to the coverage plots.
Best,
En
Dear En,
Thank you so much for your detailed explanation!! I've learnt a lot.
You make a very good point! Yes, the 5' exon is more than 300 bp far from the fusion point. I should ask the authors which isoform is predominantly expressed in the sample.
Again, thanks a lot for helping me!
Best,
Dan
if you want to find IF there are fusion genes between f.e. the 6th and 16th chr, how can someone find that out ? Is there any software?