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

Patnala, Rhadhika, Clements, Judith, & Batra, Jyotsna (2013) Candidate gene association studies : a comprehensive guide to useful in silico tools. BMC Genetics, 14, p. 39.

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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).

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ID Code: 63899
Item Type: Journal Article
Refereed: Yes
Keywords: candidate gene, SNP, LD, in-silico, association studies, cancer
DOI: 10.1186/1471-2156-14-39
ISSN: 1471-2156
Divisions: Current > Schools > School of Biomedical Sciences
Current > QUT Faculties and Divisions > Faculty of Health
Current > Institutes > Institute of Health and Biomedical Innovation
Copyright Owner: Copyright 2013 the authors.
Copyright Statement: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Deposited On: 01 Nov 2013 04:37
Last Modified: 15 Apr 2014 13:37

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