Question: Whether to include reference genome in PCA for association analysis?
gravatar for Phoenix Mu
3 months ago by
Phoenix Mu0
Phoenix Mu0 wrote:

When doing QC for GWAS, genotype from a reference panel like 1000 Genomes is typically used to calculate PCA together with our own data to find individuals with unmatched population ancestry.

My question is if I want to calculate PCs used for adjusting population admixture in my GWAS, do I also need to include a reference panel in my PCA?


pca gwas • 155 views
ADD COMMENTlink modified 3 months ago by zx87546.7k • written 3 months ago by Phoenix Mu0
gravatar for zx8754
3 months ago by
zx87546.7k wrote:

Use reference panel to get PCs, this step is useful to filter out outlier samples. Then exclude outlier samples and reference samples, and re-run PCA. These are the PCs we want to use for analysis.

See this paper for more info:

ADD COMMENTlink written 3 months ago by zx87546.7k
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