Rna-Seq And Multivariate Classifiers
1
0
Entering edit mode
13.1 years ago
Travis ★ 2.8k

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.

next-gen sequencing classification rna • 3.9k views
ADD COMMENT
0
Entering edit mode
ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode
10.9 years ago

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 COMMENT

Login before adding your answer.

Traffic: 833 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6