Naive application of permutation testing leads to inflated type I error rates.
Genetics 2008 Jan; 178(1):609-10.
Failure to account for family structure within populations or in complex mating designs via uninformed applications of permutation testing will lead to inflated type I error rates. Careful consideration of the design factors is essential since some situations allow several valid permutation strategies, and the choice that maximizes statistical power will not always be intuitive.
Churchill, G A. and Doerge, R W., "Naive application of permutation testing leads to inflated type I error rates." (2008). Faculty Research 2000 - 2009. 1716.