Permutation Test for Marker Phenotype Association

This program tests for associations between molecular markers and a quantitative character. This is a non-parametric permutation based test initially described by Doerge and Churchill (1996) in the context of QTL mapping. It turned out to also be quite useful in the context of association mapping (e.g., Long et al. 1998, 2000). It takes marker haplotypic structure into account, so it is generally more powerful than Bonferroni type approaches.

Doerge, R.W., and G.A. Churchill. 1996. Permutation tests for multiple loci affecting a quantitative character. Genetics 142: 285-294. PubMed

Long, A.D., R.F. Lyman, C.H. Langley, and T.F.C. Mackay. 1998. Two sites in the Delta gene region contribute to naturally occuring variation in bristle number in Drosophila melanogaster. Genetics 149: 999-1017. PubMed | PDF (236 KB)

Long, A.D., R.F. Lyman, A.H. Morgan, C.H. Langley, and T.F.C. Mackay. 2000. Both naturally occurring insertions of transposable elements and intermediate frequency polymorphisms at the achaete-scute complex are associated with variation in bristle number in Drosophila melanogaster. Genetics 154: 1255-69. PubMed | PDF (240 KB)