Biostatistics 666: Haplotype Association Tests
This lecture introduces the idea of haplotype association tests. It includes a discussion of when haplotype association tests might be preferable to single marker association tests (and when they might be less powerful) and of commonly encountered problems in the implementation of haplotype association tests (particularly commonly encountered problems that result when frequencies are estimated separately in cases and controls). Likelihood ratio tests and regression based tests for haplotype association are discussed, together with a flavour of newer methods that use genealogical information.
Lin S, Chakravarti A, Cutler DJ (2004) Exhaustive allelic disequilibrium tests are a new approach to genome-wide association studies. Nature Genetics 36:1181-1188.
Zaykin DV, Westfall PH, Young SS, Karnoub MC, Wagner MJ, Ehm MG (2002) Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Human Heredity 53:79-91.