Hi all,
I was wondering if anyone has attempted using RNA-Seq for applications like prognostic or diagnostic classifier model generation? There are numerous examples of this being done with microarrays (e.g. Mammaprint) however I am not aware of any NGS work in the field.
Any help appreciated.
It depends:
RNA-Seq signatures in publications: Lots. Here are some off the top of my head:
http://genomebiology.com/content/14/10/R110
http://www.jci.org/articles/view/65833
https://peerj.com/articles/159/ (algorithm applied to microarray and RNA-Seq data)
RNA-Seq diagnostics in clinic: Probably none. It takes several years to get FDA approval for a diagnostic. Plus, identification of a signature via RNA-Seq doesn't mean final application to use RNA-Seq. For example, I believe most microarray-based signatures in papers that actually made it to the clinic were implemented via qPCR for only the genes in the signature.
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didn't we cover this?A: Next Gen Sequencing Vs Microarray Advanced Applications
What would be the conceptual difference between doing it for RNA-seq-derived as opposed to microarray-derived expression data?
Jeremy - no I don't think so. My previous question referred to both classifiers and association and I don't believe I got any answer on the classification.
Mikael - I don't know myself! I believe the concept must be pretty much the same but I'm guessing there have to be some technology-specific factors that would complicate matters. I'm trying to determine if anyone has actually attempted it.