Post-GWAS analysis

One of the projects from the 2021 GP2/IPDGC Hackathon. The related manuscript can be found on bioRxiv: https://www.biorxiv.org/content/10.1101/2022.05.04.490670v1
Contributers: Julie Lake, Raquel Real, Bernabe Bustos, Bharati Jadhav, Lesley Wu

Table of Contents

1. About The Project
   • Quick Description
   • Background/motivation
   • Workflow Summary
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. Acknowledgments

About The Project

Quick Description

The goal for this project was to develop a pipeline for some common post-GWAS follow up analyses.

Background/motivation

Genome-wide association studies (GWAS) are popular and useful tools for investigating genetic risk associated with a trait. Successful GWAS should be accompanied with various follow-up analyses such as heritability estimates and polygenic risk scores (PRS). It can be confusing and time-consuming when it comes to choosing and coding GWAS follow-up analyses. This workflow serves as an example for how to perform some common GWAS follow-up analyses using AMP-PD data to help give guidance to other researchers performing GWAS.

Workflow Summary

PD_LRRK2_hackathon.ipynb

1. Setting up
2. Preparing clinical files
3. Genetic QC
4. Heritability
5. Genetic risk score

runs_of_homozygosity.ipynb

1. Setting up
2. Quality control
3. Runs of homozygosity

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Getting Started

Prerequisites

• Plink
• GCTA

Installation

1. Clone the repo

   git clone https://github.com/ipdgc/GP2-post-GWAS-analysis.git

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Usage

These notebooks can be directly uploaded to your workspace on Terra. They are designed to be used on Terra with AMP-PD data, but by changing the file paths you can use these notebooks anywhere other than Terra and for any data.

For more examples, please refer to Plink documentation and GCTA documentation

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Acknowledgments

• AMP-PD

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