WHAP: haplotype-based association analysis.
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.


BACKGROUND
WHAP is a C/C++ program, freely available from the author's website: http://pngu.mgh.harvard.edu/purcell/whap/
Purcell
Shaun
S
Center for Human Genetic Research, MGH, Boston, MA, USA. shaun@pngu.mgh.harvard.edu
Daly
Mark J
MJ
Sham
Pak C
PC
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D005819:Genetic Markers / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D005828:Genetics, Population; D006239:Haplotypes / Q000235:genetics*; D015810:Linkage Disequilibrium / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013223:Statistics as Topic
D005819:Genetic Markers