Bioinformatics Advance Access published online on November 21, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl580
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1 Center for Human Genetic Research, MGH, Boston, USA; Broad Institute of Harvard and MIT, Cambridge, USA
* To whom correspondence should be addressed.
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/.
Received August 2, 2006
Revised October 26, 2006
Accepted November 13, 2006
Applications note
WHAP: haplotype-based association analysis
Shaun Purcell 1 *, Mark J. Daly 1, and Pak C. Sham 2
2 Genome Research Center, University of Hong Kong, Pokfulam, Hong Kong
Shaun Purcell, E-mail: shaun{at}pngu.mgh.harvard.edu
Abstract
Associate Editor: Keith A Crandall
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. P. Reiner, C. S. Carlson, B. Thyagarajan, M. J. Rieder, J. F. Polak, D. S. Siscovick, D. A. Nickerson, D. R. Jacobs Jr, and M. D. Gross Soluble P-Selectin, SELP Polymorphisms, and Atherosclerotic Risk in European-American and African-African Young Adults: The Coronary Artery Risk Development in Young Adults (CARDIA) Study Arterioscler. Thromb. Vasc. Biol., August 1, 2008; 28(8): 1549 - 1555. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Duesing, G. Fatemifar, G. Charpentier, M. Marre, J. Tichet, S. Hercberg, B. Balkau, P. Froguel, and F. Gibson Evaluation of the Association of IGF2BP2 Variants With Type 2 Diabetes in French Caucasians Diabetes, July 1, 2008; 57(7): 1992 - 1996. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Sookoian, C. Gemma, T. F. Gianotti, A. Burgueno, G. Castano, and C. J. Pirola Genetic variants of Clock transcription factor are associated with individual susceptibility to obesity Am. J. Clinical Nutrition, June 1, 2008; 87(6): 1606 - 1615. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Y. Lee, E. N. Vithana, R. Mathur, V. H. Yong, I. Y. Yeo, A. Thalamuthu, M.-W. Lee, A. H. Koh, M. C. Lim, A. C. How, et al. Association Analysis of CFH, C2, BF, and HTRA1 Gene Polymorphisms in Chinese Patients with Polypoidal Choroidal Vasculopathy Invest. Ophthalmol. Vis. Sci., June 1, 2008; 49(6): 2613 - 2619. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. R. Wendland, P. R. Moya, M. R. Kruse, R. F. Ren-Patterson, C. L. Jensen, K. R. Timpano, and D. L. Murphy A novel, putative gain-of-function haplotype at SLC6A4 associates with obsessive-compulsive disorder Hum. Mol. Genet., March 1, 2008; 17(5): 717 - 723. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. S. Zeiger, B. C. Haberstick, I. Schlaepfer, A. C. Collins, R. P. Corley, T. J. Crowley, J. K. Hewitt, C. J. Hopfer, J. Lessem, M. B. McQueen, et al. The neuronal nicotinic receptor subunit genes (CHRNA6 and CHRNB3) are associated with subjective responses to tobacco Hum. Mol. Genet., March 1, 2008; 17(5): 724 - 734. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Benn, M. C. A. Stene, B. G. Nordestgaard, G. B. Jensen, R. Steffensen, and A. Tybjaerg-Hansen Common and Rare Alleles in Apolipoprotein B Contribute to Plasma Levels of Low-Density Lipoprotein Cholesterol in the General Population J. Clin. Endocrinol. Metab., March 1, 2008; 93(3): 1038 - 1045. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. H. Perlis, S. Purcell, J. Fagerness, A. Kirby, T. L. Petryshen, J. Fan, and P. Sklar Family-Based Association Study of Lithium-Related and Other Candidate Genes in Bipolar Disorder Arch Gen Psychiatry, January 1, 2008; 65(1): 53 - 61. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Ramirez-Lorca, A. Grilo, M. T. Martinez-Larrad, L. Manzano, F. J. Serrano-Hernando, F. J. Moron, V. Perez-Gonzalez, J. L. Gonzalez-Sanchez, J. Fresneda, R. Fernandez-Parrilla, et al. Sex and Body Mass Index Specific Regulation of Blood Pressure by CYP19A1 Gene Variants Hypertension, November 1, 2007; 50(5): 884 - 890. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. L. Simpson, P. Hysi, S. S. Bhattacharya, C. J. Hammond, A. Webster, C. S. Peckham, P. C. Sham, and J. S. Rahi The Roles of PAX6 and SOX2 in Myopia: Lessons from the 1958 British Birth Cohort Invest. Ophthalmol. Vis. Sci., October 1, 2007; 48(10): 4421 - 4425. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. M. Plenge, M. Seielstad, L. Padyukov, A. T. Lee, E. F. Remmers, B. Ding, A. Liew, H. Khalili, A. Chandrasekaran, L. R.L. Davies, et al. TRAF1-C5 as a Risk Locus for Rheumatoid Arthritis -- A Genomewide Study N. Engl. J. Med., September 20, 2007; 357(12): 1199 - 1209. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Thys, I. Schrauwen, K. Vanderstraeten, K. Janssens, N. Dieltjens, K. Van Den Bogaert, E. Fransen, W. Chen, M. Ealy, M. Claustres, et al. The coding polymorphism T263I in TGF-{beta}1 is associated with otosclerosis in two independent populations Hum. Mol. Genet., September 1, 2007; 16(17): 2021 - 2030. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. L. Stone, B. Merriman, R. M. Cantor, D. H. Geschwind, and S. F. Nelson High density SNP association study of a major autism linkage region on chromosome 17 Hum. Mol. Genet., March 15, 2007; 16(6): 704 - 715. [Abstract] [Full Text] [PDF]
|
|