Year: 2015
Type: dissertation
Abstract: Analysis and interpretation of DNA variations is very crucial for research trying to solve genetic background of heritability, diseases and other traits.Because of the massive amounts of data produced by modern genetics research technologies, computational methods are required to solve these challenges.This thesis briefly introduces the field of molecular biology and basic principles of genetics, discusses genetic variation annotation methods, genome-wide association studies (GWAS) and enrichment analysis methods with their implementation algorithms.As a part of this thesis, we introduce a novel web tool called Varanto that can be used to annotate, visualize and analyse genetic variations.The thesis describes the preparation of Varanto's background database, including descriptions of extracting and importing data from public genome databases.Varanto can be used to perform hypergeometric test based annotation enrichment analysis for a set of genetic variations, and to visualize the annotation results by heatmaps and hierarchical clustering.Varanto includes a web based user interface developed using Shiny web application framework for R. Varanto's performance and functionality is tested and showcased by performance benchmarks and by analysing and interpreting data from previously published genome-wide association studies, including examples from GWAS on body mass index (BMI) and GWAS on Chrohn's disease.
Author: Tibor Fülöp
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W3095840421