Abstract
The central issue for Genetic Analysis Workshop 14 (GAW14) is the question, which is the better strategy for linkage analysis, the use of single-nucleotide polymorphisms (SNPs) or microsatellite markers? To answer this question we analyzed the simulated data using Duffy's SIB-PAIR program, which can incorporate parental genotypes, and our identity-by-state – identity-by-descent (IBS-IBD) transformation method of affected sib-pair linkage analysis which uses the matrix transformation between IBS and IBD. The advantages of our method are as follows: the assumption of Hardy-Weinberg equilibrium is not necessary; the parental genotype information maybe all unknown; both IBS and its related IBD transformation can be used in the linkage analysis; the determinant of the IBS-IBD transformation matrix provides a quantitative measure of the quality of the marker in linkage analysis. With the originally distributed simulated data, we found that 1) for microsatellite markers there are virtually no differences in types I and II error rates when parental genotypes were or were not used; 2) on average, a microsatellite marker has more power than a SNP marker does in linkage detection; 3) if parental genotype information is used, SNP markers show lower type I error rates than microsatellite markers; and 4) if parental genotypes are not available, SNP markers show considerable variation in type I error rates for different methods.
Highlights
A key issue in nonparametric linkage analysis is the accuracy in the estimation of the relative pair identity-bydescent (IBD) distributions
The central issue for Genetic Analysis Workshop 14 (GAW14) is the question, which is the better strategy for linkage analysis, the use of single-nucleotide polymorphisms (SNPs) or microsatellite markers? To answer this question we analyzed the simulated data using Duffy's SIB-PAIR program, which can incorporate parental genotypes, and our identity-by-state – identity-by-descent (IBSIBD) transformation method of affected sib-pair linkage analysis which uses the matrix transformation between IBS and IBD
With the originally distributed simulated data, we found that 1) for microsatellite markers there are virtually no differences in types I and II error rates when parental genotypes were or were not used; 2) on average, a microsatellite marker has more power than a SNP marker does in linkage detection; 3) if parental genotype information is used, SNP markers show lower type I error rates than microsatellite markers; and 4) if parental genotypes are not available, SNP markers show considerable variation in type I error rates for different methods
Summary
A key issue in nonparametric linkage analysis is the accuracy in the estimation of the relative pair identity-bydescent (IBD) distributions. The Genetic Analysis Workshop 14 (GAW14) simulated data provide an opportunity to evaluate new or existing methods for linkage analysis since the "answers" were known to the designers of the simulated data. The first method is the affected pedigree member (APM) method implemented in Duffy's. SIB-PAIR program [1], which uses all the pedigree information including the parental genotypes and parentalsibling relationships and based on Weeks and Lange's method [2]. IBS-IBD (identity-by-state – identity-by-descent) transformation method, which generalizes Lange's affected sibpair method [3] and uses the affected sib-pair genotypes (page number not for citation purposes). Number of replicates with p
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