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

**URL:** <https://rcop.michaeljfox.org/t/amp-pd-codes-to-get-genetic-overviews-ancestry-population-pcs-and-prs/242>\
**Category:** Analyzing and Reusing Data\
**Tags:** code, ancestry, amp-pd, genetic-data\
**Created:** [November 20, 2023, 7:38pm UTC](https://rcop.michaeljfox.org/t/amp-pd-codes-to-get-genetic-overviews-ancestry-population-pcs-and-prs/242 "2023-11-20T19:38:14Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![hirotaka](https://sea1.discourse-cdn.com/michaeljfox/user_avatar/rcop.michaeljfox.org/hirotaka/32/58_2.png) [@hirotaka](https://rcop.michaeljfox.org/u/hirotaka)\
**Post date:** [November 20, 2023, 7:38pm UTC](https://rcop.michaeljfox.org/t/amp-pd-codes-to-get-genetic-overviews-ancestry-population-pcs-and-prs/242/1 "2023-11-20T19:38:15Z")

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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

- EUR 10119
- EAS 32
- AFR 111
- OTHER 156  
 ![image](https://us1.discourse-cdn.com/michaeljfox/original/1X/a064edae66d27bec984bfae16ad32ad3956eb818.png)

As @vdardov announced [the release version 4 of AMP-PD](https://rcop.michaeljfox.org/t/amp-pd-release-4-is-available/240), this may be out-of-date but basically you should be able to use the scripts by changing the path to the new data.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!

> **[GitHub - GP2code/amp-pd-v3-pc-prs: PC and PRS calculation for the AMP-PD release v3...](https://github.com/GP2code/amp-pd-v3-pc-prs)**
>
> PC and PRS calculation for the AMP-PD release v3 WGS data

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**Author:** ![danieltds](https://sea1.discourse-cdn.com/michaeljfox/user_avatar/rcop.michaeljfox.org/danieltds/32/62_2.png) [@danieltds](https://rcop.michaeljfox.org/u/danieltds)\
**Post date:** [November 22, 2023, 5:46pm UTC](https://rcop.michaeljfox.org/t/amp-pd-codes-to-get-genetic-overviews-ancestry-population-pcs-and-prs/242/2 "2023-11-22T17:46:57Z")

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Thank you for sharing this code! I’m sure this will be useful for me in the future!

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**Author:** ![paularp](https://sea1.discourse-cdn.com/michaeljfox/user_avatar/rcop.michaeljfox.org/paularp/32/52_2.png) [@paularp](https://rcop.michaeljfox.org/u/paularp)\
**Post date:** [November 24, 2023, 5:15pm UTC](https://rcop.michaeljfox.org/t/amp-pd-codes-to-get-genetic-overviews-ancestry-population-pcs-and-prs/242/3 "2023-11-24T17:15:07Z")

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Thank you for sharing!

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**Author:** ![hirotaka](https://sea1.discourse-cdn.com/michaeljfox/user_avatar/rcop.michaeljfox.org/hirotaka/32/58_2.png) [@hirotaka](https://rcop.michaeljfox.org/u/hirotaka)\
**Post date:** [April 30, 2024, 5:15pm UTC](https://rcop.michaeljfox.org/t/amp-pd-codes-to-get-genetic-overviews-ancestry-population-pcs-and-prs/242/4 "2024-04-30T17:15:17Z")

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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.