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JonJala / mtag

Python command line tool for Multi-Trait Analysis of GWAS (MTAG)
GNU General Public License v3.0
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genetic correlation #152

Open ooozcl opened 2 years ago

ooozcl commented 2 years ago

Hi paturley, I have another question. I see a literature that calculates the genetic correlation of diseases and traits associated with AD. Only family history has a high correlation. Is it appropriate to use MTAG analysis in this case?

paturley commented 2 years ago

I don't understand your question. What do you mean family history having a high correlation?

On Thu, Dec 9, 2021 at 7:59 AM ooozcl @.***> wrote:

Hi paturley, I have another question. I see a literature that calculates the genetic correlation of diseases and traits associated with AD. Only family history has a high correlation. Is it appropriate to use MTAG analysis in this case?

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ooozcl commented 2 years ago

sorry，maybe I didn't make myself clear. Here is the description in the literature: The common variant genetic architecture of LOAD was positively correlated with a maternal family history of Alzheimer’s disease/dementia (rg for the genetic correlation of two traits =0.81; FDR P=2.79 ×10−7), similar to the Marioni et al. family proxy analyses, which found maternal genetic correlation with Alzheimer’s disease to be higher than that for paternal Alzheimer’s disease (rg=0.91 and 0.66, respectively) rg.xlsx

paturley commented 2 years ago

Sorry for the delayed response here. In the MTAG paper, we advise people to use phenotypes where the rg is high because there is less room for assumptions to be violated if rg is high. For example, if rg = 1, then MTAG's assumptions necessarily hold. That isn't to say that they don't hold at lower rg--it's possible for MTAG's assumptions to hold for any value of rg--but it's possible find yourself in different situations where things break as rg gets low.

So as long as you are willing to explicitly assume that MtAG's assumptions hold, I think you are fine.

On Fri, Dec 10, 2021 at 2:34 AM ooozcl @.***> wrote:

sorry，maybe I didn't make myself clear. Here is the description in the literature: The common variant genetic architecture of LOAD was positively correlated with a maternal family history of Alzheimer’s disease/dementia (rg for the genetic correlation of two traits =0.81; FDR P=2.79 ×10−7), similar to the Marioni et al. family proxy analyses, which found maternal genetic correlation with Alzheimer’s disease to be higher than that for paternal Alzheimer’s disease (rg=0.91 and 0.66, respectively) rg.xlsx https://github.com/JonJala/mtag/files/7690868/rg.xlsx

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ooozcl commented 2 years ago

Thank you very much!