AMP-PD codes to get genetic overviews (Ancestry, population PCs and PRS)

Analyzing and Reusing Data
, , ,
1

I would like to share some scripts for AMP-PD v3 whole genome sequencing data to calculate the genetic PCs with the 1000 genome project reference panel, infer ancestry and calculate polygenic risk scores for PD.

The followings are the summary of N per ancestry

As @vdardov announced the release version 4 of AMP-PD, this may be out-of-date but basically you should be able to use the scripts by changing the path to the new data. Your comments and suggestions are welcome!

4 Likes
2

Thank you for sharing this code! Iā€™m sure this will be useful for me in the future!

1 Like
3

Thank you for sharing!

1 Like
4

Just FYI, PRS and PCs for the PPMI participants are now available @ PPMI LONI > Study Data > Subject Characteristics > Project 9001.

  1. Please note that if you are going to use PRSs, it is recommended to limit your analysis on ones with European ancestry as PRS is primarily calculated from European GWAS.
  2. PPMI Genetics groups are highly enriched to some specific populations. It is worth adjusting for genetic PCs when comparing people in the LRRK2-PD, GBA-PD vs idiopathic PD to adjust for population factors.
3 Likes