genomic inflation factor (lambda)=1
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2.5 years ago
putty ▴ 40

Dear Community members, Does genomic inflation (lambda)= 1 indicate that there is no obvious population stratification in GWAS? I did GWAS (binary phenotype) and while running --glm in plink2, the output gives lambda=1. Even when i don't include my principal components the lambda value is = 1; so does that mean i need not include my principal components (PCs) as covariates in my regression analysis? OR do we need to include the PCs irrespective of lambda=1. My understanding was that PCs are included as covariates only if we suspect ethnic outlier. ( Also I have removed all ethnic outliers after plotting my PCA while doing QC).

Thank you all.

GWAS stratification inflation factor population genomic • 770 views

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