Examining the effect of linkage disequilibrium between markers on the Type I error rate and power of nonparametric multipoint linkage analysis of two-generation and multigenerational pedigrees in the presence of missing genotype data.

ABSTRACT: Because most multipoint linkage analysis programs currently assume linkage equilibrium between markers when inferring parental haplotypes, ignoring linkage disequilibrium (LD) may inflate the Type I error rate. We investigated the effect of LD on the Type I error rate and power of nonparametric multipoint linkage analysis of two-generation and multigenerational multiplex families. Using genome-wide single nucleotide polymorphism (SNP) data from the Collaborative Study of the Genetics of Alcoholism, we modified the original data set into 30 total data sets in order to consider six different patterns of missing data for five different levels of SNP density. To assess power, we designed simulated traits based on existing marker genotypes. For the Type I error rate, we simulated 1,000 qualitat

SUBMITTER: Kim Y 

PROVIDER: S-EPMC2216429 | biostudies-literature | 2008 Jan

REPOSITORIES: biostudies-literature