Whether to include reference genome in PCA for association analysis?

Question

[Phoenix Mu]

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?

Thanks

Answer 1

[zx8754]

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:

• Data quality control in genetic case-control association studies