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Module 12: Variant effect analysis

2024-01-27

Overview

Module 12 focuses on variant effect analysis, a crucial step in genomics that interprets the functional consequences of genetic variants. This module will guide students through the process of analyzing the effects of variants on genes and pathways, using tools and databases for gene ontology and KEGG pathway analysis. Additionally, students will learn how to identify orthologs and homologs, which is essential for understanding the evolutionary relationships and functional conservation of genes across different species. Through theoretical discussions and practical labs, students will gain insights into how variants can affect biological processes and how this knowledge can be applied in research and clinical practice.

Introduction

  • The importance of understanding the effects of genetic variants on gene function and biological pathways
  • An overview of the tools and methods used in variant effect analysis
  • The role of gene ontology and pathway analysis in interpreting variant data

Topics

Gene Ontology Analysis

  • Introduction to gene ontology (GO) terms and their classification into biological processes, molecular functions, and cellular components
  • Using GO annotations to understand the potential impact of variants on gene function
  • Tools and resources for gene ontology analysis, such as the Gene Ontology Consortium database and software like DAVID

KEGG Pathway Analysis

  • Overview of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and its use in linking genetic variants to biological pathways
  • Techniques for mapping variants to KEGG pathways to predict their effects on metabolic and signaling networks
  • Utilizing KEGG analysis tools like KEGG Mapper and pathway enrichment analysis software

Identification of Orthologs and Homologs

  • The concepts of orthology and homology and their significance in variant effect analysis
  • Methods for identifying orthologous and homologous genes across different species
  • Tools for ortholog and homolog identification, such as BLAST, OrthoMCL, and Ensembl Compara

Integrating Variant Effect Analysis

  • Combining gene ontology, pathway analysis, and ortholog/homolog identification to provide a comprehensive view of variant effects
  • Case studies demonstrating the application of variant effect analysis in research and clinical diagnostics

Labs

  • Lab 1: Gene Ontology Enrichment Analysis for Variants
  • Lab 2: KEGG Pathway Mapping and Analysis of Variant-Impacted Pathways
  • Lab 3: Identification and Analysis of Orthologs and Homologs Affected by Variants

Learning Outcomes

By the end of this module, students will be able to:

  • Explain the significance of variant effect analysis in the context of genomic research and medicine.
  • Perform gene ontology analysis to predict the functional impact of genetic variants.
  • Map variants to biological pathways using KEGG and interpret the potential effects on cellular processes.
  • Identify orthologs and homologs of genes affected by variants to understand evolutionary relationships and functional conservation.
  • Integrate various analytical approaches to provide a comprehensive assessment of variant effects.
  • Communicate the findings from variant effect analysis clearly and effectively in both scientific and clinical contexts.