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are linked, multiple comparisons at the same locus are correlated, and not all DNA markers are equally
 

Summary: are linked, multiple comparisons at the same locus
are correlated, and not all DNA markers are equally
informative. Instead of a Bonferroni correction, we
used an empirical permutation test. We created rep-
licates of the observed sample, in which genotype
and phenotype distributions were preserved, but any
linkage between genotype and phenotype was re-
moved by randomly reassigning the observed pheno-
typic values. We then asked how often any replicates
that conformed to the null hypothesis (the indepen-
dence of genotype and phenotype) produced P values
in excess of the P value observed for the real data.
This test preserved both the observed marker infor-
mativeness and the overall phenotype distribution.
23. E. Lander, L. Kruglyak, Nature Genet. 11, 241 (1995).
24. Linkage of the resistance allele to two distinct marker
alleles, 2 and 4, could be explained by recombination
between resistance and marker alleles or by multiple
entry of the resistance allele into the family. An
attempt to distinguish by reconstructing flanking

  

Source: Abagyan, Ruben - School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego
Hartl, Daniel L. - Department of Organismic and Evolutionary Biology, Harvard University

 

Collections: Biology and Medicine; Environmental Sciences and Ecology