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1.  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 
Genetic epidemiology  2008;32(1):41-51.
Since most multipoint linkage analysis programs currently assume linkage equilibrium (LE) 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 (COGA), we modified the original dataset into 30 total data sets in order to consider 6 different patterns of missing data for 5 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 qualitative traits from random distributions, unlinked to any of the marker data. Overall, the different levels of SNP density examined here had only small effects on power (except sibpair data). Missing data had a substantial effect on power, with more completely genotyped pedigrees yielding the highest power (except sibpair data). Most of the missing data patterns did not cause large increases in the Type I error rate if the SNP markers were more than 0.3 cM apart. However, in a dense 0.25 cM map, removing genotypes on founders and/or founders and parents in the middle generation caused substantial inflation of the Type I error rate, which corresponded to the increasing proportion of persons with missing data. Results also showed that long high-LD blocks have severe effects on Type I error rates.
doi:10.1002/gepi.20260
PMCID: PMC2216429  PMID: 17685456
SNPs; Type I error rate; False Positives; Linkage Disequilibrium; Pedigree Structure

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