Entering edit mode
6.7 years ago
hiekeen
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0
What softwares can detect fusion genes from SNP-array data? For Human660W-quad array. Thank you very much in advance.
I'd be a bit surprised if that were even possible.
So was I, but googling
snp array gene fusionbrings up a few papers. I don't see how that would work though.Hmm, the methods all seem to be CNV based, assuming that the fusions are all associated with them. I wonder how valid that is compared to things like gene read through.
Yes mostly CNV based finding chromosomal break points. I found this for SNP array.
It sounds like a far from optimal approach.
Most likely the field has moved ahead of making something with SNP array with advent and now more revolutionary detection of fusion transcripts from RNA-Seq and WGS and having said that RNA-Seq also allows understanding if it's based on alternative splicing or not. These are important pre-requisites for finding fusion genes. My first encounter was when I started learning RNA-Seq and tophat was able to find fusion transcripts and this was amazing for me then but not pursued in our lab. With time mostly RNASeq improved and more fusion transcript identification tools came up. With SNP array am not sure if one will find it or not to that effect.
what about this article here
that paper precisely tries to look into famous fusion genes with visualizing them on IGV and using SNP array data but that's not a software for detection of fusion genes from the SNP array per se.
Yup, that's one of the ones I read through. It seems like a really problematic way to find fusions. I would think that low coverage mate-pairs or low-coverage long reads would be more useful (or just using RNAseq and looking at fusion transcripts or notably DE genes).