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. 2005 Dec 30;6 Suppl 1(Suppl 1):S83.
doi: 10.1186/1471-2156-6-S1-S83.

Examining the effect of linkage disequilibrium on multipoint linkage analysis

Qiqing Huang  1 , Sanjay Shete, Michael Swartz, Christopher I Amos
Affiliations

Examining the effect of linkage disequilibrium on multipoint linkage analysis

Qiqing Huang et al. BMC Genet. .

Abstract

Most linkage programs assume linkage equilibrium among multiple linked markers. This assumption may lead to bias for tightly linked markers where strong linkage disequilibrium (LD) exists. We used simulated data from Genetic Analysis Workshop 14 to examine the possible effect of LD on multipoint linkage analysis. Single-nucleotide polymorphism packets from a non-disease-related region that was generated with LD were used for both model-free and parametric linkage analyses. Results showed that high LD among markers can induce false-positive evidence of linkage for affected sib-pair analysis when parental data are missing. Bias can be eliminated with parental data and can be reduced when additional markers not in LD are included in the analyses.

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Figures

Figure 1
Figure 1
Linkage analysis results for the 20 SNPs and the three SNPs with strong LD. The left panel indicates results using a nonparametric NPL approach, while the right panel indicates results from a parametric linkage analysis allowing for locus heterogeneity.
See this image and copyright information in PMC

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