Identifying transcripts from exome sequencing?!!

Question

[nilakshafreezon]

Is there any possibility to predict the specific transcript (obtained by alternative splicing) of a gene present in a particular individual just by exome sequencing and calling variants?

Because we got an analysis report from a recognized institute for an exome sequence we sent which says that they have identified a nucleotide substitution of xxxxx gene, A>G and they have given the transcript ID [ENST00000xxx] as well.

And when I explored further I found this from 1000genomes where they only did exome sequencing but have annotated SNPs with transcript IDs.

http://pilotbrowser.1000genomes.org/...0000323668#ALL

Please could somebody explain this to me? I'm a novice bioinformatician

Answer 1

[Devon Ryan]

On the example from 1000 genomes, if you click on one of the "Show" links, e.g. for "Frameshift coding variants", you'll see exactly how this works. Basically, a single variant can end up getting associated with all of the transcripts that overlap it. So if you have a variant at 5:149720925, then it'll have 4 associated transcripts. These sorts of annotations are mostly for convenience, so you can quickly assess how causative a variant is (if none of the associated transcripts are expressed in your tissue of interest, then the variant is unlikely to be causative).

[nilakshafreezon]

Thanks for the information. So It's all about the transcripts that overlap with the SNP. :) Thanks again.