Methodology article
On the use of haplotype phylogeny to detect disease susceptibility loci
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* Corresponding author: Claire Bardel bardel@vjf.inserm.fr
1 Unité de recherche en Génétique Épidémiologique et structure des populations humaines, INSERM U535, Villejuif, France
2 Laboratoire Bordelais de Recherche en Informatique, UMR 5800, Bordeaux, France
3 Programme Avenir, INSERM U458, hôpital Robert Debré, AP-HP, Paris, France
4 Fondation Jean Dausset, Paris, France
BMC Genetics 2005, 6:24 doi:10.1186/1471-2156-6-24
Published: 18 May 2005Additional files
Additional File 1:
Average pairwise linkage disequilibrium for the 10 simulated date sets. The average pairwise LD (over 1000 replicated) is calculated using the r2 measure for each of the 10 tree topologies (T1 to T10). The matrices are plotted with GOLD[44].
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Additional File 2:
Tree topologies of the 10 simulated date sets
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Additional File 3:
Pairwise linkage disequilibrium for the Crohn data. (A) shows the pairwise linkage disequilibrium (LD) calculated with the D' measure. (B) shows the LD calculated with the r2 measures. The matrices are plotted with GOLD [44]. A high degree of LD can be observed. The differences between the r2 and the D' values are explained by the difference in the allelic frequency for the different SNPs.
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