Question: Rna-Seq And Multivariate Classifiers
0
gravatar for Travis
8.1 years ago by
Travis2.8k
USA
Travis2.8k wrote:

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.

ADD COMMENTlink modified 5.4 years ago by Biostar ♦♦ 20 • written 8.1 years ago by Travis2.8k

didn't we cover this? http://biostar.stackexchange.com/questions/7668/next-gen-sequencing-vs-microarray-advanced-applications/7675#7675

ADD REPLYlink written 8.1 years ago by Jeremy Leipzig18k

What would be the conceptual difference between doing it for RNA-seq-derived as opposed to microarray-derived expression data?

ADD REPLYlink written 8.0 years ago by Mikael Huss4.7k

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.

ADD REPLYlink written 8.0 years ago by Travis2.8k
0
gravatar for Charles Warden
5.8 years ago by
Charles Warden7.2k
Duarte, CA
Charles Warden7.2k wrote:

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.

ADD COMMENTlink written 5.8 years ago by Charles Warden7.2k
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