Applying Genome-Wide Association Study to Analyze Novel Variants That Potentially Relate to Alzheimer’s Disease Open Access

Zhang, Lidan (Spring 2020)

Permanent URL:


Alzheimer’s disease is a progressive and irreversible brain disease that is a common cause of dementia. Alzheimer’s patients will gradually lose their ability to think independently, remember, make decisions, and function independently. Alzheimer's disease is the sixth leading cause of death in the United States and there is no cure. In this study, we used datasets from ROSMAP, a project related to aging and dementia, to conduct Genome-Wide Association Study (GWAS). GWAS is an approach to relate gene data with specific diseases or traits. We used the gene expression data of 640 individuals with Alzheimer’s disease and matched with 1608 GWAS SNPs. A differential expression analysis was conducted over the expression data for the GWAS SNPs. A gene set enrichment analysis (GSEA) was followed to determine which pathways show significance and are related to the cause of Alzheimer’s disease.

Keyword: Alzheimer’s disease, genome-wide association study, gene set enrichment analysis, SNP, differential expression analysis, pathway

Table of Contents

Table of Contents


Methods and Materials


Data Processing

Differential Expression (DE) Analysis

Gene Set Enrichment Analysis (GSEA)

Pathway Visualization




About this Master's Thesis

Rights statement
  • Permission granted by the author to include this thesis or dissertation in this repository. All rights reserved by the author. Please contact the author for information regarding the reproduction and use of this thesis or dissertation.
Subfield / Discipline
  • English
Research Field
Committee Chair / Thesis Advisor
Committee Members
Last modified

Primary PDF

Supplemental Files