Alzheimer's Disease GWAS & Polygenic Risk Score (PRS) Pipeline

This repository contains a bioinformatics pipeline for performing a Genome-Wide Association Study (GWAS) and developing a Polygenic Risk Score (PRS) using data from the Alzheimer's Disease Neuroimaging Initiative (ADNI).

Project Overview

The goal of this project is to identify genetic variants (SNPs) associated with Alzheimer's Disease (AD) and evaluate the predictive power of these variants using a risk modeling approach.

Pipeline Structure

• Quality Control: QC of PLINK genomic data for SNPs and individuals (Cell rate, MAF, HWE, heterozigosity, sex discrepancies and relatedness).

• SNP Discovery: Identification and functional annotation of AD-associated SNPs.

• Risk Modeling: Calculation of Polygenic Risk Scores (PRS) and construction of predictive models.

• Evaluation: Assessment of predictive performance using Receiver Operating Characteristic (ROC) curves and AUC metrics.

Main Report

The full methodology, visualizations, and biological interpretations are documented in the final report:

📄 View the Full Report (GWAS_PRS.pdf)