Ancestry-specific PCs
I need to compute the principal components of the cohort I’m working with and merge them with a reference dataset (1000 genomes for example) to get ancestry-specific genetic principal components.
The UK biobank provides the first 40 genetic PCs but these are not ancestry specific PCs. Does the Biobank/RAP provide these PCs? If not, can I get help with how to do this analysis?
Comments
3 comments
Field 26201 provide the first 4 PRS genetic principal components that are ancestry specific ( https://www.nature.com/articles/ng1847). Let us know if this is not what you are looking for.
Thanks for the response.
From my understanding, these aren't the UKB participant's ancestry-specific genetic PCs? They are the PCs from the 1000g dataset.
What I was looking for was the genetic PCs of the UKBs participants after matching UKB genotypes and reference data and merging to compute “ancestry-specific” PCs
The gnomAD data includes the genetic ancestry PCA https://gnomad.broadinstitute.org/downloads#v4-genetic-ancestry-group-classification. Version 4 includes data from UK Biobank participants https://gnomad.broadinstitute.org/news/2023-11-gnomad-v4-0/ . I hope this helps.
Please sign in to leave a comment.