How to validate translocation detected in RNA-seq data?

Question

[alisaber814]

Hi everyone,

Recently, we performed paired end RNA-seq. and last week I got detected translocation list from our bioinformatician. In the file that I have there are both genes involved in the fusion transcript and also number of split and span reads and sequence of the fusion (almost 150 bp from each side). Now, I am trying to BLAT this sequences, make pictures for each fusion gene, design the primer and sequence them for validation. But, I have some problems with some of the fusions. In some of the cases I have complementary sequence of gene A fused with correct sequence of gene B (both genes in the same direction in the chromosome). How can this happen? Is it because of inversion (in the report, indicated that there is no inversion)? How should I design the primers; should I used reference genome for primer design or the sequence that I have from RNA-seq? Thank you very much.

Ali

Answer 1

[emissrto]

could it be two isoforms or variants unspecified Refseq RNA# artifact with specific DNAs results. (The fusion molecules could supress or inhibit DNA assay or reassembly) refer to: Similar posts if you have (at least >100 bp ..Ngs Data V.S Microarray Data) somebody might have tried this before.

[emissrto]

Also I would think it would be an allel Api Variation Tools And 1000Genomes Dbsnp132 (comment) with undefined exon or intron which has a (tag) efetch not in the currently usage in use in the human reference assembly