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Bioinformatics Advance Access published online on June 22, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm316
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© 2007 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.

HaploBuild: An algorithm to construct noncontiguous associated haplotypes in family-based genetic studies

Jason M. Laramie 1,2,*, Jemma B. Wilk 1,3, Anita L. DeStefano 1,4 and Richard H. Myers 1,2,3

1Department of Neurology, Boston University School of Medicine, Boston, MA, 2Program in Bioinformatics, Boston University, Boston, MA, 3Department of Medicine, Boston University School of Medicine, Boston, MA, 4 Department of Biostatistics, Boston University School of Public Health, Boston, MA

*To whom correspondence should be addressed. Mr. Jason Laramie, E-mail: laramiej{at}bu.edu


  Abstract

Summary: We have created a program that searches densely genotyped regions for associated noncontiguous haplotypes using a standard family-based haplotype association test. This program was designed to expand upon the "sliding window" methodologies commonly used for haplotype construction by allowing the association of subsets of single nucleotide polymorphisms (SNPs) to drive the construction of the haplotype. This strategy permits HaploBuild to construct more biologically relevant haplotypes that are not constrained by arbitrary length and contiguous orientation.

Availability: http://snp.bumc.bu.edu

Associate Editor: Prof. Keith Crandall

Received on March 20, 2007; revised on May 9, 2007; accepted on June 6, 2007

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