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When C is large, linkage disequilibrium has the same sign as that of epistasis [51].
Linkage disequilibrium has both positive and negative impacts on association testing.
A method that simultaneously accounts for HIV phylogeny and codon covariation, in addition to HLA linkage disequilibrium, has recently been developed by Carlson et al [27], and we have applied it in this study.
Strong linkage disequilibrium has been found between 3161G P1054RR) and the variant allele at 2572C (F858L).
Linkage disequilibrium has been reported to exist between certain variants (Palmer et al, 2000).
Admixture mapping, also known as mapping by admixture linkage disequilibrium, has become an important tool for localizing disease genes.
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First, Carlson et al.[32] had resequenced the CRP gene in 23 unrelated European-descent individuals (EA) in the Utah/Centre d'Etude du Polymorphisme Humain (CEPH) panel (Coriell Institute for Medical Research, Camden, NJ), and using linkage disequilibrium had selected tagSNPs that summarized the common variation in the CRP gene.
This cyto-nuclear disequilibrium had already been noticed earlier by Avise et al.[ 12].
Moreover, high levels of linkage disequilibrium have been detected for genetic variation within the bovine PRNP promoter and intron 1 [ 31].
It is of note that HLA-DR4 subtypes, some of which are linked with DQ8 due to linkage disequilibrium, have been associated with RP [ 2, 26].
Stemming from the establishment of a comprehensive genotyping/haplotyping methodology, the results suggested that a number of different recombination events intertwined with strong linkage disequilibrium have been directly involved in the expansion and contraction of the KIR locus.
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