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Why should the LD plot (LD heatmap) be created in control samples, not cases?

I would like to create the LD plot (LD heatmap) based on GWAS result.

On the other hand, I read that the LD plot should be made in control samples, not cases.

Is there any specific reason why the LD plot only comes from control samples?

Thanks advanced.

snp
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written by sjunlee89 • sjunlee89

On the other hand, I read that the LD plot should be made in control samples, not cases.

Please quote the source(s).

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written by Kevin Blighe Kevin Blighe

Thank you so much for your comment. Is there any specific reason why LD plot should be created in control samples?

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written by sjunlee89 • sjunlee89

I read that the LD plot should be made in control samples, not cases.

Where did you read this?

Is there any specific reason why LD plot should be created in control samples?

It depends on the analysis that you are doing.

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written by Kevin Blighe Kevin Blighe

I'm sorry to say that I am not familiar with GWAS analsys.

I read that the figures' descriptive in some of papers says "~~LD plots in ~~ controls".

I would like to know what you said that "it depends on the analysis that you are doing."

Thanks advanced.

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written by sjunlee89 • sjunlee89

Well, looking at LD in control samples and then comparing this to LD in samples with an inherited disorder/disease can reveal potentially useful information about the disease.

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written by Kevin Blighe Kevin Blighe

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