Question: Combined Association Of Expression, Genetic, Clinical Phenotypes
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gravatar for User 7754
7.7 years ago by
User 7754230
United Kingdom
User 7754230 wrote:

Hi all,

Can we do an expression-genotype-biomarker/disease association using RNA samples, genotypes, and biomarker/disease outcome from one sample combined with genotypes and biomarker/disease outcome (but no expression data) with another sample? I imagine we can just combine the data for the genotype-expression and also biomarker information, but I am not sure about the disease outcome… Any thoughts? Thank you, -f

genetics association eqtl • 1.9k views
ADD COMMENTlink modified 7.6 years ago by Larry_Parnell16k • written 7.7 years ago by User 7754230
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gravatar for Burlappsack
7.7 years ago by
Burlappsack660
Burlappsack660 wrote:

Have you thought about using Connectivity Mapping? A quote from the website describes it as such: "This research effort aims to generate a detailed map that links gene patterns associated with disease to corresponding patterns produced by drug candidates and a variety of genetic manipulations"

ADD COMMENTlink written 7.7 years ago by Burlappsack660
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gravatar for Francy
7.7 years ago by
Francy20
Francy20 wrote:

Hi burlappsack,

thanak you for the link, it seems like an interesting resources. However my question was more a methodological one: would it be possible to merge all of the genetic and phenotype data and do an eQTL association even though we have eQTL, genotype and phenotype data only for a subset of these?

ADD COMMENTlink written 7.7 years ago by Francy20

@francy: Welcome to the site. This is a question and answer forum, so the correct thing to do if you're responding to someone's question is to use the "add comment" link under their question rather than creating a new answer.

ADD REPLYlink written 7.4 years ago by David Quigley11k
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gravatar for Larry_Parnell
7.6 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

You can only perform the association tests using those samples for which you have the appropriate data - that is, the subset you mention. Basically, you are talking about closing a triangle formed by genetic variant, mRNA and biomarker, with the mRNA-biomarker link being the one that adds a lot to the understanding of disease risk/onset/progression.

ADD COMMENTlink written 7.6 years ago by Larry_Parnell16k
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