WHAP: haplotype-based association analysis

• Published in: Bioinformatics 2007-01, Vol.23 (2), p.255-256
• Main Authors: Purcell, Shaun, Daly, Mark J., Sham, Pak C.
• Format: Article
• Language: English
• Subjects: Algorithms; Base Sequence; Biological and medical sciences; Chromosome Mapping - methods; Fundamental and applied biological sciences. Psychology; General aspects; Genetic Markers - genetics; Genetic Variation - genetics; Genetics, Population; Haplotypes - genetics; Linkage Disequilibrium - genetics; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Molecular Sequence Data; Polymorphism, Single Nucleotide - genetics; Quantitative Trait Loci - genetics; Sequence Alignment - methods; Sequence Analysis, DNA - methods; Software; Statistics as Topic
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btl580

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: Contact:[e-mail]