Candidate gene association studies: a comprehensive guide to useful in silico tools

Area of Science:

• Genetic Epidemiology
• Bioinformatics
• Genomics

Background:

• The candidate gene approach has historically been crucial in genetic epidemiology for identifying disease-associated alleles.
• Technological advancements have led to a surge in in silico tools for genetic research.
• These tools offer efficient strategies for discovering causal gene variants in genetic studies.

Purpose of the Study:

• To review candidate gene prioritization methods.
• To summarize approaches for single nucleotide polymorphism (SNP) prioritization.
• To discuss tools for assessing the functional relevance of risk variants, considering their genomic location.

Main Methods:

• Review of existing literature and in silico tools.
• Description of candidate gene prioritization strategies.
• Summary of SNP prioritization techniques and functional assessment tools.

Main Results:

• Identification of various in silico tools for genetic variant analysis.
• Discussion of strategies applicable to candidate gene and genome-wide association studies (GWAS).
• Highlighting tools relevant for functional validation in the context of GWAS and next-generation sequencing (NGS).

Conclusions:

• The discussed strategies and tools are broadly applicable to studies of genetic risk factors for diseases.
• These resources are valuable for both traditional candidate gene studies and modern GWAS.
• The tools aid in the functional validation of variants, crucial for the era of large-scale sequencing.