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Bioinformatics Advance Access originally published online on November 21, 2006
Bioinformatics 2007 23(2):255-256; doi:10.1093/bioinformatics/btl580
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

WHAP: haplotype-based association analysis

Shaun Purcell 1,2,*, Mark J. Daly 1,2 and Pak C. Sham 3

1 Center for Human Genetic Research, MGH Boston, MA, USA
2 Broad Institute of Harvard and MIT Cambridge, MA, USA
3 Genome Research Center, University of Hong Kong Pokfulam, Hong Kong

*To whom correspondence should be addressed.


  Abstract

Summary: We describe a software tool to perform haplotype-based association analysis, for quantitative and qualitative traits, in population and family samples, using single nucleotide polymorphism or multiallelic marker data. A range of tests is offered: omnibus and haplotype-specific tests; prospective and retrospective likelihoods; covariates and moderators; sliding window analyses; permutation P-values. We focus on the ability to flexibly impose constraints on haplotype effects, which allows for a range of conditional haplotype-based likelihood ratio tests: for example, whether an allele has an effect independent of its haplotypic background, or whether a single variant can explain the overall association at a locus. We illustrate using these tests to dissect a multi-locus association.

Availability: WHAP is a C/C++ program, freely available from the author's website: http://pngu.mgh.harvard.edu/purcell/whap/

Contact: shaun{at}pngu.mgh.harvard.edu

Associate Editor: Keith A Crandal

Received on August 2, 2006; revised on October 26, 2006; accepted on November 13, 2006

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