Gene Fusion and chimeric transcripts

[harshinamdar]

Does gene fusion happen at genomic level or transcript level ? what is the difference between fusion genes and chimeric transcripts, are they the same?

[krobison]

In answer to your first question, both. Most fusions of biological interest appear to be driven by genomic rearrangements. However, there are definitely examples in which mutations in splicing or polyadenylation signals lead to the formation of fusion transcripts from unrearranged (but adjacent) genes.

[bernardo_bello]

We have recently sequenced a bacterial transcriptome with 316 chip from IonTorrent (1.5 million sequences). After filtering low quality data and trimming adapters we noticed that only 51.33% sequences were mapped on reference genome. Looking for the unmapped sequences we can see that most of them are chimeric transcripts, so impossible mapping for them an also causing bias on results. Also many of the unmapped are sequences lacking homology in 20% of the starting sequence.

I would like to know your opinion about it.
Should I have to move to 454 or Illumina? Our Sequencing Department have no idea of why we have so many chimeras.

Thank you, Bernardo

[bharati]

I would recommend illumina as it has more advanced and standardized protocol with high accuracy. Or u can refer
"Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample" at

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030087