Computational protocol: Genetic variants in PARP1 (rs3219090) and IRF4 (rs12203592) genes associated with melanoma susceptibility in a Spanish population

Similar protocols

Protocol publication

[…] We used the Haploview v4.2 tool from the HapMap webpage, in order to analyze linkage disequilibrium blocks for SNPs in the PARP1 gene in order to know the frequencies of each haplotype in our population and HapMap populations from Northern Europe (CEU) and Tuscany Italians (TSI). We try to asses possible functional implications of all the polymorphisms in the genes of interest by using both the online software Pupasuitev3.1 (http://pupasuite.bioinfo.cipf.es) and the web tool “ECR Browser “(http://ecrbrowser.dcode.org/) to establish a comparison between the human genome and those of other animal species in order to analyze whether gene variations studied in this work are located in sequences important to the function of the protein and to search for the phylogenetically conserved regions of such genes as PARP1, ATM and IRF4 genes. […]

Pipeline specifications

Software tools Haploview, PupaSuite, ECR Browser
Applications GWAS, Genome data visualization
Diseases Eye Abnormalities, Melanoma