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Open Access Highly Accessed Review

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

Radhika Patnala, Judith Clements and Jyotsna Batra*

Author Affiliations

Australian Prostate Cancer Research Centre – Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia

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BMC Genetics 2013, 14:39  doi:10.1186/1471-2156-14-39

Published: 9 May 2013


The candidate gene approach has been a pioneer in the field of genetic epidemiology, identifying risk alleles and their association with clinical traits. With the advent of rapidly changing technology, there has been an explosion of in silico tools available to researchers, giving them fast, efficient resources and reliable strategies important to find casual gene variants for candidate or genome wide association studies (GWAS). In this review, following a description of candidate gene prioritisation, we summarise the approaches to single nucleotide polymorphism (SNP) prioritisation and discuss the tools available to assess functional relevance of the risk variant with consideration to its genomic location. The strategy and the tools discussed are applicable to any study investigating genetic risk factors associated with a particular disease. Some of the tools are also applicable for the functional validation of variants relevant to the era of GWAS and next generation sequencing (NGS).

Candidate gene; SNP; LD; In-silico; Association studies; Cancer