Computational protocol: Genetic Association and Altered Gene Expression of Mir-155 in Multiple Sclerosis Patients

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Protocol publication

[…] SNP case-control analyses on allele and genotype frequency data were performed with χ2 statistics (Fisher exact test) by using the PLINK software v.1.07 []. All analyzed SNPs had a minimal overall call rate of 95% and were tested for HWE in controls before inclusion in the analyses (PHWE > 0.05).The LD structure of the genomic region was determined from our SNP data using the Haploview v4.0 program []. Haplotype analysis (sliding-window option) and haplotype phasing were performed using the PLINK software. Only phased haplotypes with posterior probability of 1 were included for determining OR and 95% CI (risk haplotype vs all of the other alleles). All reported p values were not corrected for the number of comparisons.Power estimates indicated that, if each analyzed polymorphism (disease allele frequency of 15%) were to directly confer a 1.5-fold increase in the relative risk of MS, the case/control cohort used in this research would be of sufficient size to have 92% power to detect a significant association at the 0.05 level. [...] The URLs for data presented in this work are as follows:OMIM, Online Mendelian Inheritance in Man, http://www.ncbi.nlm.nih.gov/omim/The dChip software, http://www.dchip.org/The PLINK software, http://pngu.mgh.harvard.edu/~purcell/plink/The Haploview software, http://www.broad.mit.edu/mpg/haploview/The University of California Santa Cruz Genome Browser (UCSC), http://genome.ucsc.edu/The smiRNAdb repository, http://www.mirz.unibas.ch/cloningprofiles/The miRNA MAP website, http://mirnamap.mbc.nctu.edu.tw/The GeneCards website, http://www.genecards.org/The dbGaP database, http://www.ncbi.nlm.nih.gov/gap […]

Pipeline specifications

Software tools PLINK, Haploview, MirZ
Databases dbGaP GeneCards miRNAMap smiRNAdb
Applications GWAS, Genome data visualization
Organisms Homo sapiens
Diseases Basal Ganglia Diseases, Brain Diseases, Demyelinating Diseases, Multiple Sclerosis, Demyelinating Autoimmune Diseases, CNS