NONMEM Users Network Archive

Hosted by Cognigen

Re: question about incorporting genotyping data in disease progression model

From: Ahmed N Mohamed <ammohame>
Date: Wed, 29 Aug 2012 13:07:03 -0400 (EDT)

Kehua,

Have you tried looking into correlations between the different genotypes? May be you can collapse them into 2-3 haplotypes if some of those 60 occur together. I assume these are not all within the same gene.

----- Original Message -----
From: kehua wu <kehuawumail
To: nmusers
Sent: Wednesday, August 29, 2012 12:20:39 PM
Subject: [NMusers] question about incorporting genotyping data in disease progression model

Dear NONMEM users,



I am working on a model in asthma patients and trying to build a model of FEV1, which is the evaluation of lung function.



I have 500,000 genotyping data. First, I screened the genotyping data by running GWAS to find out the potential genotyping data, which gave me about 60 genotypes. Then, I tried to add these 60 genotyping data into model to find out if the progress of FEV1 is related with gene expression.



But the problem is that too many genotypes were related with a significant change in OFV, which does not sound reasonable to me. I was hoping to find few (2-3) genotypes are associated with the progress in lung function.




I have tried to include the genotyping data as discrete covariate (if genotyping =1 then parameter=theta(1); if genotyping =2 then parameter=theta(2); if genotyping=3 then parameter =theta(3)), and power function (genotype**(theta)).



Did I do something wrong when including the genotyping data in the model as covariate?





Thanks a lot in advance!



Kehua
Received on Wed Aug 29 2012 - 13:07:03 EDT

The NONMEM Users Network is maintained by ICON plc. Requests to subscribe to the network should be sent to: nmusers-request@iconplc.com.

Once subscribed, you may contribute to the discussion by emailing: nmusers@globomaxnm.com.