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2.8 years ago
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Hi everyone,
I have a question. Is there a relationship between heterozygosity and GWAS manhattan plot?
For example, we have two populations that have low heterozygosity and vis versa. I saw significant signals in the population that had high heterozygosity. Does it mean that the population has experienced high genetic variation? I cannot find a relationship between them and why that population with high heterozygosity had significant signals? Can you guide me in this regard?
Did you adjust for population stratification in your analysis? e.g. adjust for PCs
I simulated my populations. They are separate from each other.
When you did the GWAS regression, did you add PCs as a covariate? If not, then your GWAS are capturing the population differences. Or maybe you can clarify what GWAS equation did you do? Pheno ~ Genotype or Population ~ Genotype? How did you simulated your data?
Sam, No, I don't put PCs as covariate in my model. I used MLM by GCTA software. Generally, what's your opinion on the relationship between heterozygosity and GWAS manhattan plot?