Computational protocol: Identification of Loci Modulating the Cardiovascular and Skeletal Phenotypes of Marfan Syndrome in Mice

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Protocol publication

[…] The synteny analysis was carried out using the Mouse Map Converter application, to convert the QTL regions (cM) to physical distance intervals (bp), and the SyntenyTracker to identify the homology blocks between the mouse and human genomes. The existence of human homologues associated with diseases affecting MFS-related organ systems was verified with the Human-Mouse: Disease Connection tool available in the Mouse Genome Database. [...] All statistical analysis were conducted in R version 2.12, with significance set at p = 0.05. The R/QTL package was used to identify genomic regions in linkage disequilibrium with each phenotype; markers that did not conform to Hardy-Weinberg equilibrium were removed from the analysis. Missing genotypes and pseudo-markers created every 1 cM were estimated using 1024 imputations. The suggestiveness (p < 0.63) and significance threshold (p < 0.05) were defined by 1024 stratified permutations due to the selective genotyping used to generate the data. The confidence intervals for each QTL were estimated using a Bayesian method as implemented in the R/QTL package. […]

Pipeline specifications

Software tools SyntenyTracker, R/qtl
Applications Genome annotation, WGS analysis
Organisms Mus musculus, Homo sapiens
Diseases Marfan Syndrome