Artikel,
An incomplete enumeration algorithm for an exact test of Hardy-Weinberg proportions with multiple alleles
THEORETICAL AND APPLIED GENETICS, 115 (3): 393-398 (2007)
Zusammenfassung
Testing of Hardy-Weinberg proportions (HWP) with asymptotic
goodness-of-fit tests is problematic when the contingency table of
observed genotype counts has sparse cells or the sample size is low,
and exact procedures are to be preferred. Exact p-values can be (1)
calculated via computational demanding enumeration methods or (2)
approximated via simulation methods. Our objective was to develop a new
algorithm for exact tests of HWP with multiple alleles on the basis of
conditional probabilities of genotype arrays, which is faster than
existing algorithms. We derived an algorithm for calculating the exact
permutation significance value without enumerating all genotype arrays
having the same allele counts as the observed one. The algorithm can be
used for testing HWP by (1) summation of the conditional probabilities
of occurrence of genotype arrays with smaller probability than the
observed one, and (2) comparison of the sum with a nominal Type I error
rate alpha. Application to published experimental data from seven maize
populations showed that the exact test is computationally feasible and
reduces the number of enumerated genotype count matrices about 30%
compared with previously published algorithms.
