Caroline Durrant, Krina T. Zondervan, Lon R

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Presentation transcript:

Linkage Disequilibrium Mapping via Cladistic Analysis of Single-Nucleotide Polymorphism Haplotypes Caroline Durrant, Krina T. Zondervan, Lon R. Cardon, Sarah Hunt, Panos Deloukas, Andrew P. Morris The American Journal of Human Genetics Volume 75, Issue 1, Pages 35-43 (July 2004) DOI: 10.1086/422174 Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 1 Example of a genealogical tree representing the shared ancestry of chromosomes at the disease gene. Disease chromosomes (D) carrying the same mutation (1 or 2), share more recent common ancestry than normal chromosomes (N) carrying no mutation (0). The American Journal of Human Genetics 2004 75, 35-43DOI: (10.1086/422174) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 2 Example of a cladogram representing haplotype diversity within a window of SNPs. The cladogram is constructed using hierarchical group average clustering on pairwise haplotype differences, expressed in terms of the proportion of marker mismatches within the window of SNPs. The American Journal of Human Genetics 2004 75, 35-43DOI: (10.1086/422174) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 3 Generating the SNP haplotype carried by a chromosome carrying allele 1 at the disease SNP, x. The American Journal of Human Genetics 2004 75, 35-43DOI: (10.1086/422174) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 4 Power to detect disease-marker association in windows of 8 markers overlapping the region flanking a disease gene, under the assumption of a 5% experimentwise significance level, with Bonferroni correction for multiple testing. Power is presented as a function of the disease model, for a disease allele frequency of 0.05. The three analysis methods are the best partition of haplotypes, T[MAX]; the first partition of haplotypes, T[h]; and a single-locus test. The American Journal of Human Genetics 2004 75, 35-43DOI: (10.1086/422174) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 5 Power of the best partition of haplotypes, T[MAX], to detect disease-marker association in windows of varying size (numbers of markers) overlapping the disease gene, under the assumption of a 5% experimentwise significance level, with Bonferroni correction for multiple testing. Power is presented as a function of the disease model, for a disease allele frequency of 0.05. The American Journal of Human Genetics 2004 75, 35-43DOI: (10.1086/422174) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 6 Distribution of single-marker association with CF across a 1.8-Mb candidate region flanking the CFTR gene (Kerem et al. 1989). The solid vertical line indicates the true location of ΔF508 at 0.88 Mb, the most common disease mutation identified in the CFTR gene. The dashed line indicates the distribution of association with CF of the best partition of haplotypes, T[MAX], using a sliding window of 6 markers across the candidate region. The American Journal of Human Genetics 2004 75, 35-43DOI: (10.1086/422174) Copyright © 2004 The American Society of Human Genetics Terms and Conditions