This is a test version of Biostars. For the public version, visit https://www.biostars.org.
GWAS and Hetrozygosity

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?

snpchip gwas heterozygosity
• 1,895 views • link
updated by seidel seidel • written by Star:) • Star:)

Did you adjust for population stratification in your analysis? e.g. adjust for PCs

• 0 views • link
written by Sam Sam

I simulated my populations. They are separate from each other.

• 0 views • link
written by Star:) • Star:)

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?

• 0 views • link
written by Sam Sam

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?

• 0 views • link
written by Star:) • Star:)

0 answers

No answers yet.

Log in to answer this question.

More posts like this