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Bioinformatics Advance Access originally published online on July 23, 2008
Bioinformatics 2008 24(18):2105-2107; doi:10.1093/bioinformatics/btn359
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework

Ryan Abo 1,*, Stacey Knight 1, Jathine Wong 1, Angela Cox 2 and Nicola J. Camp 1

1Department of Biomedical Informatics, University of Utah, UT, USA and 2Institute for Cancer Studies, University of Sheffield Medical School, Sheffield, UK

*To whom correspondence should be addressed.


  Abstract

Summary: Haplotypes carry important information that can direct investigators towards underlying susceptibility variants, and hence multiple tagging single nucleotide polymorphisms (tSNPs) are usually studied in candidate gene association studies. However, it is often unknown which SNPs should be included in haplotype analyses, or which tests should be performed for maximum power. We have developed a program, hapConstructor, which automatically builds multi-locus SNP sets to test for association in a case-control framework. The multi-SNP sets considered need not be contiguous; they are built based on significance. An important feature is that the missing data imputation is carried out based on the full data, for maximal information and consistency. HapConstructor is implemented in a Monte Carlo framework and naturally extends to allow for significance testing and false discovery rates that account for the construction process and to related individuals. HapConstructor is a useful tool for exploring multi-locus associations in candidate genes and regions.

Availability: http://www-genepi.med.utah.edu/Genie

Contact: ryan.abo{at}hsc.utah.edu

Associate Editor: Alex Bateman

Received on February 20, 2008; revised on May 22, 2008; accepted on July 14, 2008

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