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

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5.9 years ago

sjunlee89 ▴ 10

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 • 1.4k views

ADD COMMENT • link 5.9 years ago by sjunlee89 ▴ 10

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

Please quote the source(s).

ADD REPLY • link 5.9 years ago by Kevin Blighe 88k

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

ADD REPLY • link 5.9 years ago by sjunlee89 ▴ 10

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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.

ADD REPLY • link 5.9 years ago by Kevin Blighe 88k

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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.

ADD REPLY • link 5.9 years ago by sjunlee89 ▴ 10

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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.