Question: Whether to include reference genome in PCA for association analysis?
0
gravatar for Phoenix Mu
9 months ago by
Phoenix Mu10
Phoenix Mu10 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?

Thanks

pca gwas • 283 views
ADD COMMENTlink modified 9 months ago by zx87548.2k • written 9 months ago by Phoenix Mu10
1
gravatar for zx8754
9 months ago by
zx87548.2k
London
zx87548.2k 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 9 months ago by zx87548.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2753 users visited in the last hour