Question: Understanding Conditional analysis
gravatar for OborneE
3.9 years ago by
OborneE20 wrote:


I'm new to data analysis and I'm having some trouble understanding the process and need help with a few questions.

I am running a conditional analysis on chromosome 19 in relation to Alzheimer's disease, I understand that conditional analysis tests whether SNPs have association independent of the SNP/SNPs you're conditioning for. I want to test if the SNPs in chr 19 are independent of my top SNP rs2075650.

I have run the conditional analysis on ~9500 SNPs from chr 19. I have read that you continue to add SNPs from the results to the list of SNPs you are conditioning for and re-running the analysis until the results are no longer genome wide significant.

Are the SNPs you add to the list secondary signals?

So far I have done the above 33 times and still the large majority of results from the results file are genome wide significant, do I just carry on? as it seems like there will be many hundreds more to add.

I have also read elsewhere that once you condition for your top SNP that SNPs remaining significant are assumed to have an independent effect on the phenotype with respect to the conditioned SNP. Is this true, otherwise why do the above?

About 200 of the 9500 SNPs are no longer significant after conditioning for my top SNP, does this mean those 200 are not independent of my top SNP?

Thanks, Emma

gcta snp conditional analysis • 5.1k views
ADD COMMENTlink modified 3.1 years ago by Veera 90 • written 3.9 years ago by OborneE20

Hi Emma, I am also doing a conditional analysis in order to see how many independent significant SNPs are in my locus of interest. Would you advise to condition all the SNPs in the locus on the lead SNP (SNP with lowest p-value) recursively, till there is no more significant SNP left? Do you remember where you have read this? Please let me know. Thanks, Alessandro.

ADD REPLYlink written 2.4 years ago by alessandrotestori7390
gravatar for Veera
3.1 years ago by
Veera 90
Veera 90 wrote:

Conditional analysis to identify the independently associated SNPs, can be done just with the summary statistics using GCTA software. (link:

ADD COMMENTlink written 3.1 years ago by Veera 90

Hi Veera, the link/page is not found. Can you share the recent/up to date link please?

ADD REPLYlink written 13 months ago by alhamidi.reem10

ADD REPLYlink written 13 months ago by genomax80k
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