Combined Association Of Expression, Genetic, Clinical Phenotypes

Question: Combined Association Of Expression, Genetic, Clinical Phenotypes

9.4 years ago by

User 7754 • 250

United Kingdom

User 7754 • 250 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 • 2.2k views

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modified 9.3 years ago by Larry_Parnell ♦ 16k • written 9.4 years ago by User 7754 • 250

9.4 years ago by

Burlappsack • 660

Burlappsack • 660 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 COMMENT • link written 9.4 years ago by Burlappsack • 660

9.4 years ago by

Francy • 20

Francy • 20 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 COMMENT • link written 9.4 years ago by Francy • 20

@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 REPLY • link written 9.1 years ago by David Quigley ♦ 11k

9.4 years ago by

Larry_Parnell ♦ 16k

Boston, MA USA

Larry_Parnell ♦ 16k 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 COMMENT • link written 9.4 years ago by Larry_Parnell ♦ 16k

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